From 8b2f77eb499a4e3405f7b49eda295186393536f5 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 2 Nov 2026 20:26:09 +0000 Subject: [PATCH 1/6] Phase 1: renaming R files --- NAMESPACE | 44 +- R/{asFactorDS1.R => asFactor1DS.R} | 4 +- R/{asFactorDS2.R => asFactor2DS.R} | 4 +- R/{BooleDS.R => booleDS.R} | 0 ...aFrameSubsetDS1.R => dataFrameSubset1DS.R} | 24 +- ...aFrameSubsetDS2.R => dataFrameSubset2DS.R} | 25 +- R/{glmDS1.R => glm1DS.R} | 14 +- R/{glmDS2.R => glm2DS.R} | 14 +- R/{glmSLMADS1.R => glmSLMA1DS.R} | 12 +- R/{glmSLMADS2.R => glmSLMA2DS.R} | 6 +- R/glmSLMADS.assign.R | 2 +- R/{glmerSLMADS2.R => glmerSLMA2DS.R} | 8 +- R/glmerSLMADS.assign.R | 2 +- R/{histogramDS1.R => histogram1DS.R} | 6 +- R/{histogramDS2.R => histogram2DS.R} | 4 +- R/{kurtosisDS1.R => kurtosis1DS.R} | 4 +- R/{kurtosisDS2.R => kurtosis2DS.R} | 4 +- R/{lexisDS1.R => lexis1DS.R} | 6 +- R/{lexisDS2.R => lexis2DS.R} | 10 +- R/{lexisDS3.R => lexis3DS.R} | 10 +- R/{lmerSLMADS2.R => lmerSLMA2DS.R} | 10 +- R/lmerSLMADS.assign.R | 2 +- R/{matrixDetDS1.R => matrixDet1DS.R} | 4 +- R/{matrixDetDS2.R => matrixDet2DS.R} | 4 +- R/{skewnessDS1.R => skewness1DS.R} | 4 +- R/{skewnessDS2.R => skewness2DS.R} | 4 +- R/{tableDS2.R => table2DS.R} | 4 +- docs/404.html | 7 +- docs/LICENSE.html | 6 +- docs/authors.html | 10 +- docs/authors.md | 4 +- docs/bootstrap-toc.css | 60 --- docs/bootstrap-toc.js | 159 -------- ...=> 109cfdfecabbfbf5e2364aaceece5d12.woff2} | Bin ...=> 5cd426f27cf61d86c207d97f8db6cf8a.woff2} | Bin ...=> a8e2cb7ac3da2c4d38cd7c8c06ca5e46.woff2} | Bin ...=> c0540813382b64c1dde636c1fa0b592a.woff2} | Bin ...=> e0243c1a22ed284bb57c07b3ac886694.woff2} | Bin docs/docsearch.css | 148 ------- docs/docsearch.js | 85 ---- docs/index.html | 19 +- docs/llms.txt | 116 ++---- docs/pkgdown.css | 384 ------------------ docs/pkgdown.yml | 6 +- docs/reference/BooleDS.html | 7 +- docs/reference/BooleDS.md | 2 + docs/reference/absDS.html | 7 +- docs/reference/absDS.md | 2 + docs/reference/asCharacterDS.html | 7 +- docs/reference/asCharacterDS.md | 2 + docs/reference/asDataMatrixDS.html | 7 +- docs/reference/asDataMatrixDS.md | 2 + .../{asFactorDS1.html => asFactor1DS.html} | 14 +- .../{asFactorDS1.md => asFactor1DS.md} | 6 +- .../{asFactorDS2.html => asFactor2DS.html} | 14 +- .../{asFactorDS2.md => asFactor2DS.md} | 6 +- docs/reference/asFactorSimpleDS.html | 10 +- docs/reference/asFactorSimpleDS.md | 4 + docs/reference/asIntegerDS.html | 7 +- docs/reference/asIntegerDS.md | 2 + docs/reference/asListDS.html | 32 +- docs/reference/asListDS.md | 29 +- docs/reference/asLogicalDS.html | 15 +- docs/reference/asLogicalDS.md | 10 +- docs/reference/asMatrixDS.html | 7 +- docs/reference/asMatrixDS.md | 2 + docs/reference/asNumericDS.html | 7 +- docs/reference/asNumericDS.md | 2 + docs/reference/aucDS.html | 7 +- docs/reference/aucDS.md | 2 + docs/reference/blackBoxDS.html | 138 ------- docs/reference/blackBoxDS.md | 81 ---- docs/reference/blackBoxRanksDS.html | 132 ------ docs/reference/blackBoxRanksDS.md | 71 ---- docs/reference/boxPlotGGDS.html | 16 +- docs/reference/boxPlotGGDS.md | 12 +- .../reference/boxPlotGG_data_TreatmentDS.html | 16 +- docs/reference/boxPlotGG_data_TreatmentDS.md | 11 +- .../boxPlotGG_data_Treatment_numericDS.html | 18 +- .../boxPlotGG_data_Treatment_numericDS.md | 13 +- docs/reference/bp_standardsDS.html | 7 +- docs/reference/bp_standardsDS.md | 2 + docs/reference/cDS.html | 13 +- docs/reference/cDS.md | 8 +- docs/reference/cbindDS.html | 7 +- docs/reference/cbindDS.md | 2 + docs/reference/changeRefGroupDS.html | 15 +- docs/reference/changeRefGroupDS.md | 10 +- docs/reference/checkNegValueDS.html | 6 +- .../checkPermissivePrivacyControlLevel.html | 6 +- docs/reference/classDS.html | 7 +- docs/reference/classDS.md | 2 + docs/reference/colnamesDS.html | 6 +- docs/reference/completeCasesDS.html | 7 +- docs/reference/completeCasesDS.md | 2 + docs/reference/corDS.html | 10 +- docs/reference/corDS.md | 5 +- docs/reference/corTestDS.html | 10 +- docs/reference/corTestDS.md | 5 +- docs/reference/covDS.html | 10 +- docs/reference/covDS.md | 6 +- docs/reference/dataFrameDS.html | 7 +- docs/reference/dataFrameDS.md | 2 + docs/reference/dataFrameFillDS.html | 109 ----- docs/reference/dataFrameFillDS.md | 56 --- docs/reference/dataFrameSortDS.html | 7 +- docs/reference/dataFrameSortDS.md | 2 + ...SubsetDS1.html => dataFrameSubset1DS.html} | 31 +- ...rameSubsetDS1.md => dataFrameSubset1DS.md} | 24 +- ...SubsetDS2.html => dataFrameSubset2DS.html} | 29 +- ...rameSubsetDS2.md => dataFrameSubset2DS.md} | 22 +- docs/reference/densityGridDS.html | 24 +- docs/reference/densityGridDS.md | 25 +- docs/reference/dimDS.html | 10 +- docs/reference/dimDS.md | 6 +- docs/reference/dmtC2SDS.html | 6 +- docs/reference/dsBase-package.html | 6 +- docs/reference/elsplineDS.html | 7 +- docs/reference/elsplineDS.md | 2 + .../{testObjExistsDS.html => expDS.html} | 32 +- docs/reference/expDS.md | 32 ++ docs/reference/extract.html | 90 ---- docs/reference/extractQuantilesDS1.html | 123 ------ docs/reference/extractQuantilesDS1.md | 66 --- docs/reference/extractQuantilesDS2.html | 121 ------ docs/reference/extractQuantilesDS2.md | 65 --- docs/reference/fixClassDS.html | 6 +- docs/reference/fixColsDS.html | 6 +- docs/reference/fixLevelsDS.html | 6 +- docs/reference/gamlssDS.html | 15 +- docs/reference/gamlssDS.md | 2 + docs/reference/getAllLevelsDS.html | 6 +- docs/reference/getClassAllColsDS.html | 6 +- docs/reference/getWGSRDS.html | 7 +- docs/reference/getWGSRDS.md | 2 + docs/reference/{glmDS1.html => glm1DS.html} | 15 +- docs/reference/{glmDS1.md => glm1DS.md} | 8 +- docs/reference/{glmDS2.html => glm2DS.html} | 17 +- docs/reference/{glmDS2.md => glm2DS.md} | 10 +- docs/reference/glmPredictDS.ag.html | 7 +- docs/reference/glmPredictDS.ag.md | 2 + docs/reference/glmPredictDS.as.html | 7 +- docs/reference/glmPredictDS.as.md | 2 + .../{glmSLMADS1.html => glmSLMA11DS.html} | 13 +- .../{glmSLMADS1.md => glmSLMA11DS.md} | 6 +- .../{glmSLMADS2.html => glmSLMA2DS.html} | 13 +- .../{glmSLMADS2.md => glmSLMA2DS.md} | 6 +- docs/reference/glmSLMADS.assign.html | 8 +- docs/reference/glmSLMADS.assign.md | 4 +- docs/reference/glmSummaryDS.ag.html | 7 +- docs/reference/glmSummaryDS.ag.md | 2 + docs/reference/glmSummaryDS.as.html | 7 +- docs/reference/glmSummaryDS.as.md | 2 + .../{glmerSLMADS2.html => glmerSLMA2DS.html} | 17 +- .../{glmerSLMADS2.md => glmerSLMA2DS.md} | 8 +- docs/reference/glmerSLMADS.assign.html | 11 +- docs/reference/glmerSLMADS.assign.md | 4 +- docs/reference/glmerSLMADS.assing.html | 231 ----------- docs/reference/heatmapPlotDS.html | 20 +- docs/reference/heatmapPlotDS.md | 17 +- docs/reference/hetcorDS.html | 7 +- docs/reference/hetcorDS.md | 2 + .../{histogramDS1.html => histogram1DS.html} | 18 +- .../{histogramDS1.md => histogram1DS.md} | 14 +- .../{histogramDS2.html => histogram2DS.html} | 15 +- .../{histogramDS2.md => histogram2DS.md} | 9 +- docs/reference/igb_standardsDS.html | 7 +- docs/reference/igb_standardsDS.md | 2 + docs/reference/index.html | 199 +++------ docs/reference/index.md | 116 ++---- docs/reference/isNaDS.html | 17 +- docs/reference/isNaDS.md | 12 +- docs/reference/isValidDS.html | 18 +- docs/reference/isValidDS.md | 13 +- .../{kurtosisDS1.html => kurtosis1DS.html} | 13 +- .../{kurtosisDS1.md => kurtosis1DS.md} | 7 +- .../{kurtosisDS2.html => kurtosis2DS.html} | 16 +- .../{kurtosisDS2.md => kurtosis2DS.md} | 9 +- docs/reference/lengthDS.html | 11 +- docs/reference/lengthDS.md | 6 +- docs/reference/levelsDS.html | 12 +- docs/reference/levelsDS.md | 7 +- .../{lexisDS1.html => lexis1DS.html} | 13 +- docs/reference/{lexisDS1.md => lexis1DS.md} | 6 +- .../{lexisDS2.html => lexis2DS.html} | 15 +- docs/reference/{lexisDS2.md => lexis2DS.md} | 8 +- .../{lexisDS3.html => lexis3DS.html} | 16 +- docs/reference/{lexisDS3.md => lexis3DS.md} | 8 +- docs/reference/listDS.html | 15 +- docs/reference/listDS.md | 10 +- docs/reference/listDisclosureSettingsDS.html | 6 +- .../{lmerSLMADS2.html => lmerSLMA2DS.html} | 19 +- .../{lmerSLMADS2.md => lmerSLMA2DS.md} | 10 +- docs/reference/lmerSLMADS.assign.html | 11 +- docs/reference/lmerSLMADS.assign.md | 4 +- docs/reference/logDS.html | 92 +++++ docs/reference/logDS.md | 37 ++ docs/reference/lsDS.html | 6 +- docs/reference/lsplineDS.html | 7 +- docs/reference/lsplineDS.md | 2 + docs/reference/matrixDS.html | 7 +- docs/reference/matrixDS.md | 2 + .../{matrixDetDS1.html => matrixDet1DS.html} | 11 +- .../{matrixDetDS1.md => matrixDet1DS.md} | 4 +- .../{matrixDetDS2.html => matrixDet2DS.html} | 11 +- .../{matrixDetDS2.md => matrixDet2DS.md} | 4 +- docs/reference/matrixDiagDS.html | 7 +- docs/reference/matrixDiagDS.md | 2 + docs/reference/matrixDimnamesDS.html | 7 +- docs/reference/matrixDimnamesDS.md | 2 + docs/reference/matrixInvertDS.html | 7 +- docs/reference/matrixInvertDS.md | 2 + docs/reference/matrixMultDS.html | 7 +- docs/reference/matrixMultDS.md | 2 + docs/reference/matrixTransposeDS.html | 7 +- docs/reference/matrixTransposeDS.md | 2 + docs/reference/mdPatternDS.html | 10 +- docs/reference/mdPatternDS.md | 6 + docs/reference/meanDS.html | 17 +- docs/reference/meanDS.md | 12 +- docs/reference/meanSdGpDS.html | 13 +- docs/reference/meanSdGpDS.md | 8 +- docs/reference/mergeDS.html | 7 +- docs/reference/mergeDS.md | 2 + docs/reference/messageDS.html | 102 ----- docs/reference/messageDS.md | 46 --- docs/reference/metadataDS.html | 7 +- docs/reference/metadataDS.md | 2 + docs/reference/miceDS.html | 7 +- docs/reference/miceDS.md | 2 + docs/reference/minMaxRandDS.html | 99 ----- docs/reference/minMaxRandDS.md | 40 -- docs/reference/namesDS.html | 7 +- docs/reference/namesDS.md | 2 + docs/reference/nsDS.html | 7 +- docs/reference/nsDS.md | 2 + docs/reference/numNaDS.html | 17 +- docs/reference/numNaDS.md | 12 +- docs/reference/qlsplineDS.html | 7 +- docs/reference/qlsplineDS.md | 2 + docs/reference/quantileMeanDS.html | 17 +- docs/reference/quantileMeanDS.md | 12 +- docs/reference/rBinomDS.html | 18 +- docs/reference/rBinomDS.md | 13 +- docs/reference/rNormDS.html | 19 +- docs/reference/rNormDS.md | 14 +- docs/reference/rPoisDS.html | 18 +- docs/reference/rPoisDS.md | 13 +- docs/reference/rUnifDS.html | 19 +- docs/reference/rUnifDS.md | 14 +- docs/reference/rangeDS.html | 13 +- docs/reference/rangeDS.md | 8 +- docs/reference/ranksSecureDS1.html | 92 ----- docs/reference/ranksSecureDS1.md | 37 -- docs/reference/ranksSecureDS2.html | 113 ------ docs/reference/ranksSecureDS2.md | 45 -- docs/reference/ranksSecureDS3.html | 105 ----- docs/reference/ranksSecureDS3.md | 49 --- docs/reference/ranksSecureDS4.html | 121 ------ docs/reference/ranksSecureDS4.md | 62 --- docs/reference/ranksSecureDS5.html | 121 ------ docs/reference/ranksSecureDS5.md | 61 --- docs/reference/rbindDS.html | 7 +- docs/reference/rbindDS.md | 2 + docs/reference/reShapeDS.html | 12 +- docs/reference/reShapeDS.md | 7 +- docs/reference/recodeLevelsDS.html | 86 ---- docs/reference/recodeLevelsDS.md | 28 -- docs/reference/recodeValuesDS.html | 7 +- docs/reference/recodeValuesDS.md | 2 + docs/reference/repDS.html | 7 +- docs/reference/repDS.md | 2 + docs/reference/replaceNaDS.html | 11 +- docs/reference/replaceNaDS.md | 6 +- docs/reference/rmDS.html | 6 +- docs/reference/rowColCalcDS.html | 13 +- docs/reference/rowColCalcDS.md | 9 +- docs/reference/sampleDS.html | 7 +- docs/reference/sampleDS.md | 2 + docs/reference/scatterPlotDS.html | 20 +- docs/reference/scatterPlotDS.md | 17 +- docs/reference/seqDS.html | 7 +- docs/reference/seqDS.md | 2 + docs/reference/setFilterDS.html | 98 ----- docs/reference/setSeedDS.html | 7 +- docs/reference/setSeedDS.md | 2 + .../{skewnessDS1.html => skewness1DS.html} | 13 +- .../{skewnessDS1.md => skewness1DS.md} | 7 +- .../{skewnessDS2.html => skewness2DS.html} | 16 +- .../{skewnessDS2.md => skewness2DS.md} | 9 +- docs/reference/sqrtDS.html | 7 +- docs/reference/sqrtDS.md | 2 + docs/reference/subsetByClassDS.html | 98 ----- docs/reference/subsetByClassDS.md | 41 -- docs/reference/subsetByClassHelper1.html | 102 ----- docs/reference/subsetByClassHelper2.html | 107 ----- docs/reference/subsetByClassHelper3.html | 105 ----- docs/reference/subsetDS.html | 133 ------ docs/reference/subsetDS.md | 86 ---- docs/reference/table1DDS.html | 6 +- docs/reference/table2DDS.html | 95 ----- docs/reference/table2DDS.md | 42 -- .../{tableDS2.html => table2DS.html} | 11 +- docs/reference/{tableDS2.md => table2DS.md} | 4 +- docs/reference/tableDS.assign.html | 7 +- docs/reference/tableDS.assign.md | 2 + docs/reference/tableDS.html | 7 +- docs/reference/tableDS.md | 2 + docs/reference/tapplyDS.assign.html | 7 +- docs/reference/tapplyDS.assign.md | 2 + docs/reference/tapplyDS.html | 7 +- docs/reference/tapplyDS.md | 2 + docs/reference/testObjExistsDS.md | 30 -- docs/reference/unListDS.html | 7 +- docs/reference/unListDS.md | 2 + docs/reference/uniqueDS.html | 7 +- docs/reference/uniqueDS.md | 2 + docs/reference/varDS.html | 17 +- docs/reference/varDS.md | 13 +- docs/reference/vectorDS.html | 6 +- docs/search.json | 2 +- docs/sitemap.xml | 69 ++-- inst/DATASHIELD | 44 +- man/BooleDS.Rd | 2 +- man/{asFactorDS1.Rd => asFactor1DS.Rd} | 8 +- man/{asFactorDS2.Rd => asFactor2DS.Rd} | 8 +- ...rameSubsetDS1.Rd => dataFrameSubset1DS.Rd} | 28 +- ...rameSubsetDS2.Rd => dataFrameSubset2DS.Rd} | 26 +- man/{glmDS1.Rd => glm1DS.Rd} | 12 +- man/{glmDS2.Rd => glm2DS.Rd} | 14 +- man/{glmSLMADS1.Rd => glmSLMA11DS.Rd} | 10 +- man/{glmSLMADS2.Rd => glmSLMA2DS.Rd} | 10 +- man/glmSLMADS.assign.Rd | 2 +- man/{glmerSLMADS2.Rd => glmerSLMA2DS.Rd} | 12 +- man/glmerSLMADS.assign.Rd | 2 +- man/{histogramDS1.Rd => histogram1DS.Rd} | 8 +- man/{histogramDS2.Rd => histogram2DS.Rd} | 8 +- man/{kurtosisDS1.Rd => kurtosis1DS.Rd} | 8 +- man/{kurtosisDS2.Rd => kurtosis2DS.Rd} | 8 +- man/{lexisDS1.Rd => lexis1DS.Rd} | 10 +- man/{lexisDS2.Rd => lexis2DS.Rd} | 12 +- man/{lexisDS3.Rd => lexis3DS.Rd} | 14 +- man/{lmerSLMADS2.Rd => lmerSLMA2DS.Rd} | 14 +- man/lmerSLMADS.assign.Rd | 2 +- man/{matrixDetDS1.Rd => matrixDet1DS.Rd} | 8 +- man/{matrixDetDS2.Rd => matrixDet2DS.Rd} | 8 +- man/{skewnessDS1.Rd => skewness1DS.Rd} | 8 +- man/{skewnessDS2.Rd => skewness2DS.Rd} | 8 +- man/{tableDS2.Rd => table2DS.Rd} | 8 +- 349 files changed, 1797 insertions(+), 5775 deletions(-) rename R/{asFactorDS1.R => asFactor1DS.R} (97%) rename R/{asFactorDS2.R => asFactor2DS.R} (96%) rename R/{BooleDS.R => booleDS.R} (100%) rename R/{dataFrameSubsetDS1.R => dataFrameSubset1DS.R} (95%) rename R/{dataFrameSubsetDS2.R => dataFrameSubset2DS.R} (94%) rename R/{glmDS1.R => glm1DS.R} (97%) rename R/{glmDS2.R => glm2DS.R} (98%) rename R/{glmSLMADS1.R => glmSLMA1DS.R} (96%) rename R/{glmSLMADS2.R => glmSLMA2DS.R} (98%) rename R/{glmerSLMADS2.R => glmerSLMA2DS.R} (98%) rename R/{histogramDS1.R => histogram1DS.R} (97%) rename R/{histogramDS2.R => histogram2DS.R} (99%) rename R/{kurtosisDS1.R => kurtosis1DS.R} (97%) rename R/{kurtosisDS2.R => kurtosis2DS.R} (97%) rename R/{lexisDS1.R => lexis1DS.R} (95%) rename R/{lexisDS2.R => lexis2DS.R} (98%) rename R/{lexisDS3.R => lexis3DS.R} (71%) rename R/{lmerSLMADS2.R => lmerSLMA2DS.R} (98%) rename R/{matrixDetDS1.R => matrixDet1DS.R} (96%) rename R/{matrixDetDS2.R => matrixDet2DS.R} (95%) rename R/{skewnessDS1.R => skewness1DS.R} (97%) rename R/{skewnessDS2.R => skewness2DS.R} (97%) rename R/{tableDS2.R => table2DS.R} (97%) delete mode 100644 docs/bootstrap-toc.css delete mode 100644 docs/bootstrap-toc.js rename docs/deps/bootstrap-5.3.8/fonts/{ee91700cdbf7ce16c054c2bb8946c736.woff2 => 109cfdfecabbfbf5e2364aaceece5d12.woff2} (100%) rename docs/deps/bootstrap-5.3.8/fonts/{c2f002b3a87d3f9bfeebb23d32cfd9f8.woff2 => 5cd426f27cf61d86c207d97f8db6cf8a.woff2} (100%) rename docs/deps/bootstrap-5.3.8/fonts/{07d40e985ad7c747025dabb9f22142c4.woff2 => a8e2cb7ac3da2c4d38cd7c8c06ca5e46.woff2} (100%) rename docs/deps/bootstrap-5.3.8/fonts/{1f5e011d6aae0d98fc0518e1a303e99a.woff2 => c0540813382b64c1dde636c1fa0b592a.woff2} (100%) rename docs/deps/bootstrap-5.3.8/fonts/{626330658504e338ee86aec8e957426b.woff2 => e0243c1a22ed284bb57c07b3ac886694.woff2} (100%) delete mode 100644 docs/docsearch.css delete mode 100644 docs/docsearch.js delete mode 100644 docs/pkgdown.css rename docs/reference/{asFactorDS1.html => asFactor1DS.html} (66%) rename docs/reference/{asFactorDS1.md => asFactor1DS.md} (84%) rename docs/reference/{asFactorDS2.html => asFactor2DS.html} (73%) rename docs/reference/{asFactorDS2.md => asFactor2DS.md} (94%) delete mode 100644 docs/reference/blackBoxDS.html delete mode 100644 docs/reference/blackBoxDS.md delete mode 100644 docs/reference/blackBoxRanksDS.html delete mode 100644 docs/reference/blackBoxRanksDS.md delete mode 100644 docs/reference/dataFrameFillDS.html delete mode 100644 docs/reference/dataFrameFillDS.md rename docs/reference/{dataFrameSubsetDS1.html => dataFrameSubset1DS.html} (72%) rename docs/reference/{dataFrameSubsetDS1.md => dataFrameSubset1DS.md} (83%) rename docs/reference/{dataFrameSubsetDS2.html => dataFrameSubset2DS.html} (75%) rename docs/reference/{dataFrameSubsetDS2.md => dataFrameSubset2DS.md} (86%) rename docs/reference/{testObjExistsDS.html => expDS.html} (52%) create mode 100644 docs/reference/expDS.md delete mode 100644 docs/reference/extract.html delete mode 100644 docs/reference/extractQuantilesDS1.html delete mode 100644 docs/reference/extractQuantilesDS1.md delete mode 100644 docs/reference/extractQuantilesDS2.html delete mode 100644 docs/reference/extractQuantilesDS2.md rename docs/reference/{glmDS1.html => glm1DS.html} (70%) rename docs/reference/{glmDS1.md => glm1DS.md} (86%) rename docs/reference/{glmDS2.html => glm2DS.html} (70%) rename docs/reference/{glmDS2.md => glm2DS.md} (81%) rename docs/reference/{glmSLMADS1.html => glmSLMA11DS.html} (69%) rename docs/reference/{glmSLMADS1.md => glmSLMA11DS.md} (91%) rename docs/reference/{glmSLMADS2.html => glmSLMA2DS.html} (74%) rename docs/reference/{glmSLMADS2.md => glmSLMA2DS.md} (92%) rename docs/reference/{glmerSLMADS2.html => glmerSLMA2DS.html} (79%) rename docs/reference/{glmerSLMADS2.md => glmerSLMA2DS.md} (92%) delete mode 100644 docs/reference/glmerSLMADS.assing.html rename docs/reference/{histogramDS1.html => histogram1DS.html} (70%) rename docs/reference/{histogramDS1.md => histogram1DS.md} (80%) rename docs/reference/{histogramDS2.html => histogram2DS.html} (71%) rename docs/reference/{histogramDS2.md => histogram2DS.md} (86%) rename docs/reference/{kurtosisDS1.html => kurtosis1DS.html} (65%) rename docs/reference/{kurtosisDS1.md => kurtosis1DS.md} (79%) rename docs/reference/{kurtosisDS2.html => kurtosis2DS.html} (69%) rename docs/reference/{kurtosisDS2.md => kurtosis2DS.md} (82%) rename docs/reference/{lexisDS1.html => lexis1DS.html} (65%) rename docs/reference/{lexisDS1.md => lexis1DS.md} (78%) rename docs/reference/{lexisDS2.html 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histogram1DS.Rd} (93%) rename man/{histogramDS2.Rd => histogram2DS.Rd} (92%) rename man/{kurtosisDS1.Rd => kurtosis1DS.Rd} (89%) rename man/{kurtosisDS2.Rd => kurtosis2DS.Rd} (91%) rename man/{lexisDS1.Rd => lexis1DS.Rd} (79%) rename man/{lexisDS2.Rd => lexis2DS.Rd} (93%) rename man/{lexisDS3.Rd => lexis3DS.Rd} (59%) rename man/{lmerSLMADS2.Rd => lmerSLMA2DS.Rd} (87%) rename man/{matrixDetDS1.Rd => matrixDet1DS.Rd} (88%) rename man/{matrixDetDS2.Rd => matrixDet2DS.Rd} (88%) rename man/{skewnessDS1.Rd => skewness1DS.Rd} (89%) rename man/{skewnessDS2.Rd => skewness2DS.Rd} (91%) rename man/{tableDS2.Rd => table2DS.Rd} (93%) diff --git a/NAMESPACE b/NAMESPACE index 4efc223c..afd88f19 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,8 +4,8 @@ export(BooleDS) export(absDS) export(asCharacterDS) export(asDataMatrixDS) -export(asFactorDS1) -export(asFactorDS2) +export(asFactor1DS) +export(asFactor2DS) export(asFactorSimpleDS) export(asIntegerDS) export(asListDS) @@ -30,8 +30,8 @@ export(corTestDS) export(covDS) export(dataFrameDS) export(dataFrameSortDS) -export(dataFrameSubsetDS1) -export(dataFrameSubsetDS2) +export(dataFrameSubset1DS) +export(dataFrameSubset2DS) export(densityGridDS) export(dimDS) export(dmtC2SDS) @@ -44,41 +44,41 @@ export(gamlssDS) export(getAllLevelsDS) export(getClassAllColsDS) export(getWGSRDS) -export(glmDS1) -export(glmDS2) +export(glm1DS) +export(glm2DS) export(glmPredictDS.ag) export(glmPredictDS.as) +export(glmSLMA11DS) +export(glmSLMA2DS) export(glmSLMADS.assign) -export(glmSLMADS1) -export(glmSLMADS2) export(glmSummaryDS.ag) export(glmSummaryDS.as) +export(glmerSLMA2DS) export(glmerSLMADS.assign) -export(glmerSLMADS2) export(heatmapPlotDS) export(hetcorDS) -export(histogramDS1) -export(histogramDS2) +export(histogram1DS) +export(histogram2DS) export(igb_standardsDS) export(isNaDS) export(isValidDS) -export(kurtosisDS1) -export(kurtosisDS2) +export(kurtosis1DS) +export(kurtosis2DS) export(lengthDS) export(levelsDS) -export(lexisDS1) -export(lexisDS2) -export(lexisDS3) +export(lexis1DS) +export(lexis2DS) +export(lexis3DS) export(listDS) export(listDisclosureSettingsDS) +export(lmerSLMA2DS) export(lmerSLMADS.assign) -export(lmerSLMADS2) export(logDS) export(lsDS) export(lsplineDS) export(matrixDS) -export(matrixDetDS1) -export(matrixDetDS2) +export(matrixDet1DS) +export(matrixDet2DS) export(matrixDiagDS) export(matrixDimnamesDS) export(matrixInvertDS) @@ -111,13 +111,13 @@ export(sampleDS) export(scatterPlotDS) export(seqDS) export(setSeedDS) -export(skewnessDS1) -export(skewnessDS2) +export(skewness1DS) +export(skewness2DS) export(sqrtDS) export(table1DDS) +export(table2DS) export(tableDS) export(tableDS.assign) -export(tableDS2) export(tapplyDS) export(tapplyDS.assign) export(unListDS) diff --git a/R/asFactorDS1.R b/R/asFactor1DS.R similarity index 97% rename from R/asFactorDS1.R rename to R/asFactor1DS.R index c6c0445a..ad1714b2 100644 --- a/R/asFactorDS1.R +++ b/R/asFactor1DS.R @@ -10,7 +10,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -asFactorDS1 <- function(input.var.name=NULL){ +asFactor1DS <- function(input.var.name=NULL){ ################################################################## #MODULE 1: CAPTURE THE nfilter SETTINGS # thr<-dsBase::listDisclosureSettingsDS() # @@ -49,5 +49,5 @@ asFactorDS1 <- function(input.var.name=NULL){ } #AGGREGATE FUNCTION -# asFactorDS1 +# asFactor1DS diff --git a/R/asFactorDS2.R b/R/asFactor2DS.R similarity index 96% rename from R/asFactorDS2.R rename to R/asFactor2DS.R index af45a47f..838d5108 100644 --- a/R/asFactorDS2.R +++ b/R/asFactor2DS.R @@ -18,7 +18,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -asFactorDS2 <- function(input.var.name=NULL, all.unique.levels.transmit=NULL, fixed.dummy.vars=NULL, baseline.level=NULL){ +asFactor2DS <- function(input.var.name=NULL, all.unique.levels.transmit=NULL, fixed.dummy.vars=NULL, baseline.level=NULL){ input.var <- .loadServersideObject(input.var.name) @@ -48,4 +48,4 @@ asFactorDS2 <- function(input.var.name=NULL, all.unique.levels.transmit=NULL, fi } #ASSIGN FUNCTION -# asFactorDS2 \ No newline at end of file +# asFactor2DS diff --git a/R/BooleDS.R b/R/booleDS.R similarity index 100% rename from R/BooleDS.R rename to R/booleDS.R diff --git a/R/dataFrameSubsetDS1.R b/R/dataFrameSubset1DS.R similarity index 95% rename from R/dataFrameSubsetDS1.R rename to R/dataFrameSubset1DS.R index 5f5e0c52..011a2cc2 100644 --- a/R/dataFrameSubsetDS1.R +++ b/R/dataFrameSubset1DS.R @@ -1,46 +1,46 @@ #' -#' @title dataFrameSubsetDS1 an aggregate function called by ds.dataFrameSubset +#' @title dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset #' @description First serverside function for subsetting a data frame by row or by column. #' @details A data frame is a list of variables all with the same number of rows, #' which is of class 'data.frame'. For all details see the help header for ds.dataFrameSubset #' @param df.name a character string providing the name for the data.frame #' to be sorted. argument generated and passed directly to -#' dataFrameSubsetDS1 by ds.dataFrameSubset +#' dataFrameSubset1DS by ds.dataFrameSubset #' @param V1.name A character string specifying the name of a subsetting vector #' to which a Boolean operator will be applied to define the subset to be created. #' argument generated and passed directly to -#' dataFrameSubsetDS1 by ds.dataFrameSubset +#' dataFrameSubset1DS by ds.dataFrameSubset #' @param V2.name A character string specifying the name of the vector #' or scalar to which the values in the vector specified by the argument #' is to be compared. #' argument generated and passed directly to -#' dataFrameSubsetDS1 by ds.dataFrameSubset +#' dataFrameSubset1DS by ds.dataFrameSubset #' @param Boolean.operator.n A character string specifying one of six possible Boolean operators: #' '==', '!=', '>', '>=', '<', '<=' #' argument generated and passed directly to -#' dataFrameSubsetDS1 by ds.dataFrameSubset +#' dataFrameSubset1DS by ds.dataFrameSubset #' @param keep.cols a numeric vector specifying the numbers of the columns to be kept in the #' final subset when subsetting by column. For example: keep.cols=c(2:5,7,12) will keep #' columns 2,3,4,5,7 and 12. #' argument generated and passed directly to -#' dataFrameSubsetDS1 by ds.dataFrameSubset +#' dataFrameSubset1DS by ds.dataFrameSubset #' @param rm.cols a numeric vector specifying the numbers of the columns to be removed before #' creating the final subset when subsetting by column. For example: rm.cols=c(2:5,7,12) #' will remove columns 2,3,4,5,7 and 12. #' argument generated and passed directly to -#' dataFrameSubsetDS1 by ds.dataFrameSubset +#' dataFrameSubset1DS by ds.dataFrameSubset #' @param keep.NAs logical, if TRUE any NAs in the vector holding the final Boolean vector #' indicating whether a given row should be included in the subset will be converted into #' 1s and so they will be included in the subset. Such NAs could be caused by NAs in #' either or . If FALSE or NULL NAs in the final Boolean vector will #' be converted to 0s and the corresponding row will therefore be excluded from the subset. #' argument generated and passed directly to -#' dataFrameSubsetDS1 by ds.dataFrameSubset +#' dataFrameSubset1DS by ds.dataFrameSubset #' @return This first serverside function called by ds.dataFrameSubset provides #' first level traps for a comprehensive series of disclosure risks which can be -#' returned directly to the clientside because dataFrameSubsetDS1 is an aggregate +#' returned directly to the clientside because dataFrameSubset1DS is an aggregate #' function. The second serverside function called by ds.dataFrameSubset -#' (dataFrameSubsetDS2) carries out most of the same disclosure tests, but it is +#' (dataFrameSubset2DS) carries out most of the same disclosure tests, but it is #' an assign function because it writes the subsetted data.frame to the serverside. #' In consequence, it records error messages as studysideMessages which can only be #' retrieved using ds.message @@ -48,7 +48,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -dataFrameSubsetDS1 <- function(df.name=NULL,V1.name=NULL,V2.name=NULL,Boolean.operator.n=NULL,keep.cols=NULL,rm.cols=NULL,keep.NAs=NULL){ +dataFrameSubset1DS <- function(df.name=NULL,V1.name=NULL,V2.name=NULL,Boolean.operator.n=NULL,keep.cols=NULL,rm.cols=NULL,keep.NAs=NULL){ # Check Permissive Privacy Control Level. dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot')) @@ -303,4 +303,4 @@ if(sum(is.na(keep.code.n))>0){ } # AGGREGATE FUNCTION -# dataFrameSubsetDS1 +# dataFrameSubset1DS diff --git a/R/dataFrameSubsetDS2.R b/R/dataFrameSubset2DS.R similarity index 94% rename from R/dataFrameSubsetDS2.R rename to R/dataFrameSubset2DS.R index ff1f2bee..84008883 100644 --- a/R/dataFrameSubsetDS2.R +++ b/R/dataFrameSubset2DS.R @@ -1,42 +1,41 @@ -###############################################################################|###################| 80 and 100 - -#' @title dataFrameSubsetDS2 an assign function called by ds.dataFrameSubset +#' +#' @title dataFrameSubset2DS an assign function called by ds.dataFrameSubset #' @description Second serverside function for subsetting a data frame by row or by column. #' @details A data frame is a list of variables all with the same number of rows, #' which is of class 'data.frame'. For all details see the help header for ds.dataFrameSubset #' @param df.name a character string providing the name for the data.frame #' to be sorted. argument generated and passed directly to -#' dataFrameSubsetDS2 by ds.dataFrameSubset +#' dataFrameSubset2DS by ds.dataFrameSubset #' @param V1.name A character string specifying the name of a subsetting vector #' to which a Boolean operator will be applied to define the subset to be created. #' argument generated and passed directly to -#' dataFrameSubsetDS2 by ds.dataFrameSubset +#' dataFrameSubset2DS by ds.dataFrameSubset #' @param V2.name A character string specifying the name of the vector #' or scalar to which the values in the vector specified by the argument #' is to be compared. #' argument generated and passed directly to -#' dataFrameSubsetDS2 by ds.dataFrameSubset +#' dataFrameSubset2DS by ds.dataFrameSubset #' @param Boolean.operator.n A character string specifying one of six possible Boolean operators: #' '==', '!=', '>', '>=', '<', '<=' #' argument generated and passed directly to -#' dataFrameSubsetDS2 by ds.dataFrameSubset +#' dataFrameSubset2DS by ds.dataFrameSubset #' @param keep.cols a numeric vector specifying the numbers of the columns to be kept in the #' final subset when subsetting by column. For example: keep.cols=c(2:5,7,12) will keep #' columns 2,3,4,5,7 and 12. #' argument generated and passed directly to -#' dataFrameSubsetDS2 by ds.dataFrameSubset +#' dataFrameSubset2DS by ds.dataFrameSubset #' @param rm.cols a numeric vector specifying the numbers of the columns to be removed before #' creating the final subset when subsetting by column. For example: rm.cols=c(2:5,7,12) #' will remove columns 2,3,4,5,7 and 12. #' argument generated and passed directly to -#' dataFrameSubsetDS2 by ds.dataFrameSubset +#' dataFrameSubset2DS by ds.dataFrameSubset #' @param keep.NAs logical, if TRUE any NAs in the vector holding the final Boolean vector #' indicating whether a given row should be included in the subset will be converted into #' 1s and so they will be included in the subset. Such NAs could be caused by NAs in #' either or . If FALSE or NULL NAs in the final Boolean vector will #' be converted to 0s and the corresponding row will therefore be excluded from the subset. #' argument generated and passed directly to -#' dataFrameSubsetDS2 by ds.dataFrameSubset +#' dataFrameSubset2DS by ds.dataFrameSubset #' @return the object specified by the argument (or default name '_subset') #' initially specified in calling ds.dataFrameSubset. The output object (the required #' subsetted data.frame called is written to the serverside. In addition, @@ -44,7 +43,7 @@ #' indicating whether has been created in each data source and if so whether #' it is in a valid form. If its form is not valid in at least one study - e.g. because #' a disclosure trap was tripped and creation of the full output object was blocked - -#' dataFrameSubsetDS2 (via ds.dataFrame()) also returns any studysideMessages +#' dataFrameSubset2DS (via ds.dataFrame()) also returns any studysideMessages #' that can explain the error in creating #' the full output object. As well as appearing on the screen at run time,if you wish to #' see the relevant studysideMessages at a later date you can use the \code{ds.message} @@ -57,7 +56,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -dataFrameSubsetDS2<-function(df.name=NULL,V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL,keep.cols=NULL, rm.cols=NULL, keep.NAs=NULL){ +dataFrameSubset2DS<-function(df.name=NULL,V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL,keep.cols=NULL, rm.cols=NULL, keep.NAs=NULL){ # Check Permissive Privacy Control Level. dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot')) @@ -327,4 +326,4 @@ return(df.subset) } #ASSIGN FUNCTION -# dataFrameSubsetDS2 +# dataFrameSubset2DS diff --git a/R/glmDS1.R b/R/glm1DS.R similarity index 97% rename from R/glmDS1.R rename to R/glm1DS.R index 3fc2ab3c..38760036 100644 --- a/R/glmDS1.R +++ b/R/glm1DS.R @@ -1,9 +1,9 @@ #' -#' @title glmDS1 called by ds.glm +#' @title glm1DS called by ds.glm #' @description This is the first server-side aggregate function called by ds.glm #' @details It is an #' aggregation function that sets up the model structure -#' and creates the starting beta.vector that feeds, via ds.glm, into glmDS2 to enable +#' and creates the starting beta.vector that feeds, via ds.glm, into glm2DS to enable #' iterative fitting of the generalized linear model that has been #' been specified. For more details please see the extensive header for ds.glm. #' @param formula a glm() formula consistent with R syntax eg U~x+y+Z to regress @@ -22,7 +22,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -glmDS1 <- function(formula, family, weights, offset, data){ +glm1DS <- function(formula, family, weights, offset, data){ ############################################################# @@ -202,11 +202,11 @@ if(!is.null(offsetvar)) } } - #If y, X or w data are invalid, or the model is overparameterized, this will be detected by glmDS1 + #If y, X or w data are invalid, or the model is overparameterized, this will be detected by glm1DS #and passed to ds.glm resulting in a warning and a controlled shut down of the function. #But in case someone modifies the client side function to circumvent the trap, so the - #error is only apparent once the main main iterations have started via glmDS2 - #the equivalent tests in glmDS2 will destroy the info.matrix and score.vector in the affected study so + #error is only apparent once the main main iterations have started via glm2DS + #the equivalent tests in glm2DS will destroy the info.matrix and score.vector in the affected study so #the model fitting will simply terminate. if(!(y.invalid>0||w.invalid>0||o.invalid>0||sum(Xpar.invalid)>0||glm.saturation.invalid>0)){ @@ -221,6 +221,6 @@ if(!is.null(offsetvar)) } #AGGREGATE FUNCTION -# glmDS1 +# glm1DS diff --git a/R/glmDS2.R b/R/glm2DS.R similarity index 98% rename from R/glmDS2.R rename to R/glm2DS.R index caff48f0..17dc1bb0 100644 --- a/R/glmDS2.R +++ b/R/glm2DS.R @@ -1,9 +1,9 @@ #' -#' @title glmDS2 called by ds.glm +#' @title glm2DS called by ds.glm #' @description This is the second server-side aggregate function called by ds.glm. #' @details It is an aggregate function that uses the model structure and starting -#' beta.vector constructed by glmDS1 to iteratively fit the generalized linear model -#' that has been specified. The function glmDS2 also carries out a series of disclosure +#' beta.vector constructed by glm1DS to iteratively fit the generalized linear model +#' that has been specified. The function glm2DS also carries out a series of disclosure #' checks and if the arguments or data fail any of those tests, #' model construction is blocked and an appropriate serverside error message is #' created and returned to ds.glm on the clientside. @@ -25,7 +25,7 @@ #' @return List with values from GLM model #' @export #' -glmDS2 <- function (formula, family, beta.vect, offset, weights, dataName) { +glm2DS <- function (formula, family, beta.vect, offset, weights, dataName) { ############################################################# #MODULE 1: CAPTURE THE nfilter SETTINGS @@ -266,7 +266,7 @@ glmDS2 <- function (formula, family, beta.vect, offset, weights, dataName) { #score.vector and information.matrix in the study with the problem. #So this will make model fail without explanation - #Disclosure code from glmDS1 + #Disclosure code from glm1DS errorMessage.combined <- NULL @@ -335,7 +335,7 @@ glmDS2 <- function (formula, family, beta.vect, offset, weights, dataName) { #CHECK W VECTOR VALIDITY w.invalid <- 0 - #Keep same object name as in glmDS1 + #Keep same object name as in glm1DS w.vect <- weightsvar unique.values.noNA.w <- unique(w.vect[stats::complete.cases(w.vect)]) @@ -390,4 +390,4 @@ glmDS2 <- function (formula, family, beta.vect, offset, weights, dataName) { } # AGGREGATE FUNCTION -# glmDS2 +# glm2DS diff --git a/R/glmSLMADS1.R b/R/glmSLMA1DS.R similarity index 96% rename from R/glmSLMADS1.R rename to R/glmSLMA1DS.R index 5e594bf4..05e2d4e8 100644 --- a/R/glmSLMADS1.R +++ b/R/glmSLMA1DS.R @@ -2,7 +2,7 @@ #' @description Fits a generalized linear model (GLM) on data from single or multiple sources #' with pooled co-analysis across studies being based on SLMA (Study Level Meta Analysis). #' @details glmSLMADS.assign is an aggregate function called by clientside function ds.glmSLMA. -#' ds.glmSLMA also calls another aggregate function glmSLMADS2 +#' ds.glmSLMA also calls another aggregate function glmSLMA2DS #' and an assign function glmSLMADS.assign #' For more detailed information see help for ds.glmSLMA. #' @param formula a glm formula, specified in call to ds.glmSLMA @@ -20,7 +20,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export -glmSLMADS1<- function(formula, family, weights, offset, data){ +glmSLMA11DS<- function(formula, family, weights, offset, data){ errorMessage="No errors" @@ -198,11 +198,11 @@ if(!is.null(offsetvar)) } } - #If y, X, weights or offset data are invalid, or the model is overparameterized, this will be detected by glmDS1 + #If y, X, weights or offset data are invalid, or the model is overparameterized, this will be detected by glm1DS #and passed to ds.glm resulting in a warning and a controlled shut down of the function. #But in case someone modifies the client side function to circumvent the trap, so the - #error is only apparent once the main main iterations have started via glmDS2 - #the equivalent tests in glmDS2 will destroy the info.matrix and score.vector in the affected study so + #error is only apparent once the main main iterations have started via glm2DS + #the equivalent tests in glm2DS will destroy the info.matrix and score.vector in the affected study so #the model fitting will simply terminate. if(!(y.invalid>0||w.invalid>0||o.invalid>0||sum(Xpar.invalid)>0||glm.saturation.invalid>0)){ @@ -218,4 +218,4 @@ if(!is.null(offsetvar)) } #AGGREGATE FUNCTION -# glmSLMADS1 +# glmSLMA1DS diff --git a/R/glmSLMADS2.R b/R/glmSLMA2DS.R similarity index 98% rename from R/glmSLMADS2.R rename to R/glmSLMA2DS.R index 20d698ae..6ba6a478 100644 --- a/R/glmSLMADS2.R +++ b/R/glmSLMA2DS.R @@ -2,7 +2,7 @@ #' @description Fits a generalized linear model (GLM) on data from single or multiple sources #' with pooled co-analysis across studies being based on SLMA (Study Level Meta Analysis). #' @details glmSLMADS.assign is an aggregate function called by clientside function ds.glmSLMA. -#' ds.glmSLMA also calls another aggregate function glmSLMADS2 +#' ds.glmSLMA also calls another aggregate function glmSLMA2DS #' and an assign function glmSLMADS.assign #' For more detailed information see help for ds.glmSLMA. #' @param formula a glm formula, specified in call to ds.glmSLMA @@ -24,7 +24,7 @@ #' @author Paul Burton for DataSHIELD Development Team (14/7/20) #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export -glmSLMADS2 <- function(formula, family, offset, weights, newobj, dataName){ +glmSLMA2DS <- function(formula, family, offset, weights, newobj, dataName){ ############################################################# #MODULE 1: CAPTURE THE nfilter SETTINGS # @@ -286,4 +286,4 @@ if(disclosure.risk==0) } # AGGREGATE FUNCTION -# glmSLMADS2 +# glmSLMA2DS diff --git a/R/glmSLMADS.assign.R b/R/glmSLMADS.assign.R index 3448aed3..4e21edaf 100644 --- a/R/glmSLMADS.assign.R +++ b/R/glmSLMADS.assign.R @@ -2,7 +2,7 @@ #' @description Fits a generalized linear model (GLM) on data from single or multiple sources #' with pooled co-analysis across studies being based on SLMA (Study Level Meta Analysis). #' @details glmSLMADS.assign is an assign function called by clientside function ds.glmSLMA. -#' ds.glmSLMA also calls two aggregate functions glmSLMADS1 and glmSLMADS2. +#' ds.glmSLMA also calls two aggregate functions glmSLMA1DS and glmSLMA2DS. #' For more detailed information see help for ds.glmSLMA. #' @param formula a glm formula, specified in call to ds.glmSLMA #' @param family a glm family, specified in call to ds.glmSLMA diff --git a/R/glmerSLMADS2.R b/R/glmerSLMA2DS.R similarity index 98% rename from R/glmerSLMADS2.R rename to R/glmerSLMA2DS.R index 480db660..c00875b8 100644 --- a/R/glmerSLMADS2.R +++ b/R/glmerSLMA2DS.R @@ -1,8 +1,8 @@ #' @title Fitting generalized linear mixed effect models - serverside function -#' @description glmerSLMADS2 fits a generalized linear mixed effects model +#' @description glmerSLMA2DS fits a generalized linear mixed effects model #' (glme) - e.g. a logistic or Poisson regression model including both fixed and random effects #' - on data from one or multiple sources with pooling via SLMA (study level meta-analysis) -#' @details glmerSLMADS2 is a serverside function called by ds.glmerSLMA on the clientside. +#' @details glmerSLMA2DS is a serverside function called by ds.glmerSLMA on the clientside. #' The analytic work engine is the glmer function in R which sits in the lme4 package. #' ds.glmerSLMA fits a generalized linear mixed effects model (glme) - e.g. a logistic or #' Poisson regression model including both fixed and random effects - on data @@ -38,7 +38,7 @@ #' @author Tom Bishop, with some additions by Paul Burton #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export -glmerSLMADS2 <- function(formula, offset, weights, dataName, family, +glmerSLMA2DS <- function(formula, offset, weights, dataName, family, control_type=NULL, control_value.transmit=NULL, nAGQ=1L, verbose = 0, theta = NULL, fixef = NULL){ errorMessage <- "No errors" @@ -445,4 +445,4 @@ if(control_type=="check.conv.grad") } # AGGREGATE FUNCTION -# glmerSLMADS2 +# glmerSLMA2DS diff --git a/R/glmerSLMADS.assign.R b/R/glmerSLMADS.assign.R index 36c7159c..11088f17 100644 --- a/R/glmerSLMADS.assign.R +++ b/R/glmerSLMADS.assign.R @@ -1,5 +1,5 @@ #' @title Fitting generalized linear mixed effect models - serverside function -#' @description glmerSLMADS.assign is the same as glmerSLMADS2 which fits a generalized linear +#' @description glmerSLMADS.assign is the same as glmerSLMA2DS which fits a generalized linear #' mixed effects model (glme) per study and saves the outcomes in each study #' @details glmerSLMADS.assign is a serverside function called by ds.glmerSLMA on the clientside. #' The analytic work engine is the glmer function in R which sits in the lme4 package. diff --git a/R/histogramDS1.R b/R/histogram1DS.R similarity index 97% rename from R/histogramDS1.R rename to R/histogram1DS.R index 97e09780..9bc5137e 100644 --- a/R/histogramDS1.R +++ b/R/histogram1DS.R @@ -22,7 +22,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -histogramDS1 <- function(x, method.indicator, k, noise){ +histogram1DS <- function(x, method.indicator, k, noise){ xvect <- .loadServersideObject(x) .checkClass(obj = xvect, obj_name = x, permitted_classes = c("numeric", "integer")) @@ -53,7 +53,7 @@ histogramDS1 <- function(x, method.indicator, k, noise){ # the study-specific seed for random number generation seed <- getOption("datashield.seed") if (is.null(seed)) - stop("histogramDS1 requires 'datashield.seed' R option to operate", call.=FALSE) + stop("histogram1DS requires 'datashield.seed' R option to operate", call.=FALSE) set.seed(seed) rr <- c(min(xvect, na.rm=TRUE), max(xvect, na.rm=TRUE)) @@ -147,4 +147,4 @@ histogramDS1 <- function(x, method.indicator, k, noise){ } # AGGREGATE FUNCTION -# histogramDS1 +# histogram1DS diff --git a/R/histogramDS2.R b/R/histogram2DS.R similarity index 99% rename from R/histogramDS2.R rename to R/histogram2DS.R index 4e85b83f..f70bb46c 100644 --- a/R/histogramDS2.R +++ b/R/histogram2DS.R @@ -23,7 +23,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -histogramDS2 <- function (x, num.breaks, min, max, method.indicator, k, noise){ +histogram2DS <- function (x, num.breaks, min, max, method.indicator, k, noise){ xvect <- .loadServersideObject(x) .checkClass(obj = xvect, obj_name = x, permitted_classes = c("numeric", "integer")) @@ -177,4 +177,4 @@ histogramDS2 <- function (x, num.breaks, min, max, method.indicator, k, noise){ } # AGGREGATE FUNCTION -# histogramDS2 +# histogram2DS diff --git a/R/kurtosisDS1.R b/R/kurtosis1DS.R similarity index 97% rename from R/kurtosisDS1.R rename to R/kurtosis1DS.R index a51caa43..7ca858bd 100644 --- a/R/kurtosisDS1.R +++ b/R/kurtosis1DS.R @@ -12,7 +12,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -kurtosisDS1 <- function (x, method){ +kurtosis1DS <- function (x, method){ ############################################################# # MODULE 1: CAPTURE THE nfilter SETTINGS @@ -48,4 +48,4 @@ kurtosisDS1 <- function (x, method){ } #AGGREGATE FUNCTION -# kurtosisDS1 +# kurtosis1DS diff --git a/R/kurtosisDS2.R b/R/kurtosis2DS.R similarity index 97% rename from R/kurtosisDS2.R rename to R/kurtosis2DS.R index e7790329..23ea2cf8 100644 --- a/R/kurtosisDS2.R +++ b/R/kurtosis2DS.R @@ -15,7 +15,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -kurtosisDS2 <- function(x, global.mean){ +kurtosis2DS <- function(x, global.mean){ ############################################################# # MODULE 1: CAPTURE THE nfilter SETTINGS @@ -39,4 +39,4 @@ kurtosisDS2 <- function(x, global.mean){ } #AGGREGATE FUNCTION -# kurtosisDS2 +# kurtosis2DS diff --git a/R/lexisDS1.R b/R/lexis1DS.R similarity index 95% rename from R/lexisDS1.R rename to R/lexis1DS.R index 45bea015..7ebaf90f 100644 --- a/R/lexisDS1.R +++ b/R/lexis1DS.R @@ -1,5 +1,5 @@ #' -#' @title lexisDS1 +#' @title lexis1DS #' #' @description The first server-side function called by ds.lexis. #' @details This is an aggregate function. @@ -12,7 +12,7 @@ #' @return List with `max.time` #' @export #' -lexisDS1 <- function(exitCol=NULL){ +lexis1DS <- function(exitCol=NULL){ ############################################################# #MODULE 1: CAPTURE THE nfilter SETTINGS @@ -42,4 +42,4 @@ lexisDS1 <- function(exitCol=NULL){ } #AGGREGATE FUNCTION -# lexisDS1 +# lexis1DS diff --git a/R/lexisDS2.R b/R/lexis2DS.R similarity index 98% rename from R/lexisDS2.R rename to R/lexis2DS.R index d4366720..f6a33004 100644 --- a/R/lexisDS2.R +++ b/R/lexis2DS.R @@ -1,10 +1,10 @@ #' -#' @title lexisDS2 +#' @title lexis2DS #' @description The second serverside function called by ds.lexis. #' @details This is the assign #' function which actually creates #' the expanded dataframe containing survival data for a piecewise exponential -#' regression. lexisDS2 also +#' regression. lexis2DS also #' carries out a series of disclosure checks and if the arguments or data fail any of #' those tests, #' creation of the expanded dataframe is blocked and an appropriate serverside error @@ -36,7 +36,7 @@ #' @return List with `expanded.table` #' @export #' -lexisDS2 <- function(datatext=NULL, intervalWidth, maxmaxtime, idCol, entryCol, exitCol, statusCol, vartext=NULL){ +lexis2DS <- function(datatext=NULL, intervalWidth, maxmaxtime, idCol, entryCol, exitCol, statusCol, vartext=NULL){ ############################################################# #MODULE 1: CAPTURE THE nfilter SETTINGS @@ -217,7 +217,7 @@ lexisDS2 <- function(datatext=NULL, intervalWidth, maxmaxtime, idCol, entryCol, idSeq.matrix<-matrix(0,totsubs,totints) - #ERROR IN ORIGINAL lexisDS2 CORRECTED + #ERROR IN ORIGINAL lexis2DS CORRECTED ###ERR numperiods.exposed<-rep(0,totsubs) first.int.exposed<-rep(1,totsubs) @@ -316,4 +316,4 @@ lexisDS2 <- function(datatext=NULL, intervalWidth, maxmaxtime, idCol, entryCol, } #ASSIGN FUNCTION -# lexisDS2 +# lexis2DS diff --git a/R/lexisDS3.R b/R/lexis3DS.R similarity index 71% rename from R/lexisDS3.R rename to R/lexis3DS.R index 75a31906..409f4270 100644 --- a/R/lexisDS3.R +++ b/R/lexis3DS.R @@ -1,18 +1,18 @@ #' #' @title -#' lexisDS3 +#' lexis3DS #' #' @description #' The third serverside function called by ds.lexis. #' @details This is an assign function that simplifies the -#' returned output from ds.lexis. Specifically, without lexisDS3 the output consists of a table within -#' a list, but lexisDS3 converts this directly into a dataframe. +#' returned output from ds.lexis. Specifically, without lexis3DS the output consists of a table within +#' a list, but lexis3DS converts this directly into a dataframe. #' For more details see the extensive header for ds.lexis. #' #' @return Data frame with `messageobj` object #' @export #' -lexisDS3 <- function(){ +lexis3DS <- function(){ outobj <- data.frame(base::get("messageobj", envir = parent.frame())$expanded.table) @@ -20,4 +20,4 @@ lexisDS3 <- function(){ } #ASSIGN FUNCTION -# lexisDS3 +# lexis3DS diff --git a/R/lmerSLMADS2.R b/R/lmerSLMA2DS.R similarity index 98% rename from R/lmerSLMADS2.R rename to R/lmerSLMA2DS.R index 7a1142d1..e962fba4 100644 --- a/R/lmerSLMADS2.R +++ b/R/lmerSLMA2DS.R @@ -1,8 +1,8 @@ #' @title Fitting linear mixed effect models - serverside function -#' @description lmerSLMADS2 is a serverside function which fits a linear mixed +#' @description lmerSLMA2DS is a serverside function which fits a linear mixed #' effects model (lme) - i.e. can include both fixed and random effects - on data from #' one or multiple sources with pooling via SLMA (study level meta-analysis) -#' @details lmerSLMADS2 is a serverside function called by ds.lmerSLMA on the clientside. +#' @details lmerSLMA2DS is a serverside function called by ds.lmerSLMA on the clientside. #' The analytic work engine is the lmer function in R which sits in the lme4 package. #' ds.lmerSLMA fits a linear mixed effects model (lme) - can include both fixed and random #' effects - on data from a single or multiple sources. When there are multiple data sources, @@ -12,7 +12,7 @@ #' using the metafor package, but as the SLMA occurs on the clientside which, as far #' as the user is concerned is just a standard R environment, the user can choose to use #' any approach to meta-analysis they choose. For more detailed help about any aspect -#' of lmerSLMDS2 please see the extensive help for ds.lmerSLMA. Additional information +#' of lmerSLM2DS please see the extensive help for ds.lmerSLMA. Additional information #' about fitting lmes using the lmer engine can be obtained using R help for lmer and #' the lme4 package #' @param formula see help for ds.lmerSLMA @@ -29,7 +29,7 @@ #' @author Tom Bishop, with some additions by Paul Burton #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export -lmerSLMADS2 <- function(formula, offset, weights, dataName, REML = TRUE, +lmerSLMA2DS <- function(formula, offset, weights, dataName, REML = TRUE, control_type, control_value.transmit, optimizer, verbose=0){ errorMessage <- "No errors" @@ -435,4 +435,4 @@ if(!is.null(optimizer)&&optimizer!="nloptwrap") } # AGGREGATE FUNCTION -# lmerSLMADS2 +# lmerSLMA2DS diff --git a/R/lmerSLMADS.assign.R b/R/lmerSLMADS.assign.R index 7731c552..ab732ae7 100644 --- a/R/lmerSLMADS.assign.R +++ b/R/lmerSLMADS.assign.R @@ -1,5 +1,5 @@ #' @title Fitting linear mixed effect models - serverside function -#' @description lmerSLMADS.assign is the same as lmerSLMADS2 which fits a linear +#' @description lmerSLMADS.assign is the same as lmerSLMA2DS which fits a linear #' mixed effects model (lme) per study and saves the outcomes in each study #' @details lmerSLMADS.assign is a serverside function called by ds.lmerSLMA on the clientside. #' The analytic work engine is the lmer function in R which sits in the lme4 package. diff --git a/R/matrixDetDS1.R b/R/matrixDet1DS.R similarity index 96% rename from R/matrixDetDS1.R rename to R/matrixDet1DS.R index b6fb40ce..f647589e 100644 --- a/R/matrixDetDS1.R +++ b/R/matrixDet1DS.R @@ -14,7 +14,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export -matrixDetDS1 <- function(M1.name=NULL,logarithm){ +matrixDet1DS <- function(M1.name=NULL,logarithm){ dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'avocado', 'banana')) @@ -53,4 +53,4 @@ return(list(matrix.determinant=output)) } #AGGREGATE FUNCTION -# matrixDetDS1 +# matrixDet1DS diff --git a/R/matrixDetDS2.R b/R/matrixDet2DS.R similarity index 95% rename from R/matrixDetDS2.R rename to R/matrixDet2DS.R index 6e15e7d8..36b3d1df 100644 --- a/R/matrixDetDS2.R +++ b/R/matrixDet2DS.R @@ -14,7 +14,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export -matrixDetDS2 <- function(M1.name=NULL,logarithm){ +matrixDet2DS <- function(M1.name=NULL,logarithm){ M1 <- .loadServersideObject(M1.name) .checkClass(obj = M1, obj_name = M1.name, permitted_classes = c("matrix", "data.frame")) @@ -42,4 +42,4 @@ return(output) } #ASSIGN FUNCTION -# matrixDetDS2 +# matrixDet2DS diff --git a/R/skewnessDS1.R b/R/skewness1DS.R similarity index 97% rename from R/skewnessDS1.R rename to R/skewness1DS.R index 64375375..5ae11dd1 100644 --- a/R/skewnessDS1.R +++ b/R/skewness1DS.R @@ -12,7 +12,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -skewnessDS1 <- function(x, method){ +skewness1DS <- function(x, method){ ############################################################# # MODULE 1: CAPTURE THE nfilter SETTINGS @@ -48,5 +48,5 @@ skewnessDS1 <- function(x, method){ } #AGGREGATE FUNCTION -# skewnessDS1 +# skewness1DS diff --git a/R/skewnessDS2.R b/R/skewness2DS.R similarity index 97% rename from R/skewnessDS2.R rename to R/skewness2DS.R index aad3088d..75554111 100644 --- a/R/skewnessDS2.R +++ b/R/skewness2DS.R @@ -15,7 +15,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export #' -skewnessDS2 <- function(x, global.mean){ +skewness2DS <- function(x, global.mean){ ############################################################# # MODULE 1: CAPTURE THE nfilter SETTINGS @@ -39,4 +39,4 @@ skewnessDS2 <- function(x, global.mean){ } #AGGREGATE FUNCTION -# skewnessDS2 +# skewness2DS diff --git a/R/tableDS2.R b/R/table2DS.R similarity index 97% rename from R/tableDS2.R rename to R/table2DS.R index 81886679..878d0b47 100644 --- a/R/tableDS2.R +++ b/R/table2DS.R @@ -30,7 +30,7 @@ #' @author Paul Burton for DataSHIELD Development Team, 13/11/2019 #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export -tableDS2 <- function(newobj,rvar.transmit,cvar.transmit,stvar.transmit){ +table2DS <- function(newobj,rvar.transmit,cvar.transmit,stvar.transmit){ table.obj <- .loadServersideObject(newobj) @@ -64,4 +64,4 @@ return(out.list) } #AGGREGATE FUNCTION -# tableDS2 +# table2DS diff --git a/docs/404.html b/docs/404.html index 17940f30..ae004152 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,8 +1,7 @@ - - + Page not found (404) • dsBase @@ -20,7 +19,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 - - - - - -
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Secure ranking of "V2BR" (vector to be ranked) across all sources

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blackBoxDS.Rd
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The first key serverside function that sets up the V2BR for -ranking in the client.

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Usage

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blackBoxDS(input.var.name = NULL, shared.seedval, synth.real.ratio, NA.manage)
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Arguments

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input.var.name
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a character string specifying the name of V2BR. This -argument is set by the argument with the same name in the clientside function -ds.ranksSecure

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shared.seedval
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a pseudorandom number seed that ensures that the -processes generating the order and parameterisation of the encryption -algorithms are the same in each study. This argument is set by the argument -<shared.seed.value> in the clientside function ds.ranksSecure. For more -details, including future plans to share this starting seed in a more secure -way, please see the associated document entitled "secure.global.ranking.docx" -and the header file for ds.ranksSecure.

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synth.real.ratio
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an integer value representing -the ratio of synthetic (pseudo-data) values to the real number of -values in V2BR. This argument is set by the argument with the same name -in the clientside function ds.ranksSecure. For more details, please see the -associated document entitled "secure.global.ranking.docx" and the header file -for ds.ranksSecure.

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NA.manage
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character string indicating how missing values (NAs) in -V2BR should be managed. It takes three possible values: "NA.delete", -"NA.low","NA.hi". This argument is set by the argument with the same name -in the clientside function ds.ranksSecure. For more details, please see the -associated document entitled "secure.global.ranking.docx" and the header file -for ds.ranksSecure.

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Value

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writes a data frame object entitled blackbox.output.df to the -serverside. In each study this contains the encrypted -"combined real+pseudo data vector" and a range of other key components -from the first stage of the ranking procedure. For more details see the -associated document entitled "secure.global.ranking.docx"

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Details

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Severside assign function called by ds.ranksSecure. -Creates pseudo-data by using the real distribution of values in V2BR -to create a large number of synthetic data with a similar distribution to -the values in V2BR but with a slightly broader distribution at both ends -to ensure that any extreme values in the "combined real+pseudo data vector" -are all pseudo-data. Also ensures that the number of decimal places of -the values in the V2BR is reflected by the number of decimal places in -the pseudodata. Finally, takes the "combined real+pseudo data vector" through -seven rounds of rank consistent encryption that involves algorithms -themselves generated by a pseudorandom process that selects which -transformation to apply and with what parameters. The encryption algorithms -are the same in each study ensuring that ranks also remain consistent between -studies. After encryption the encrypted "combined real+pseudo data vector" is -written to the serverside as a dataframe also including other key component -vectors from the first stage of the ranking procedure. -For more details about the cluster of functions that -collectively enable secure global ranking and estimation of global quantiles -see the associated document entitled "secure.global.ranking.docx". Also -see the header file for ds.ranksSecure

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Author

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Paul Burton 9th November, 2021

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Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

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Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/blackBoxDS.md b/docs/reference/blackBoxDS.md deleted file mode 100644 index 5261428c..00000000 --- a/docs/reference/blackBoxDS.md +++ /dev/null @@ -1,81 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources - -The first key serverside function that sets up the V2BR for ranking in -the client. - -## Usage - -``` r -blackBoxDS(input.var.name = NULL, shared.seedval, synth.real.ratio, NA.manage) -``` - -## Arguments - -- input.var.name: - - a character string specifying the name of V2BR. This argument is set - by the argument with the same name in the clientside function - ds.ranksSecure - -- shared.seedval: - - a pseudorandom number seed that ensures that the processes generating - the order and parameterisation of the encryption algorithms are the - same in each study. This argument is set by the argument - \ in the clientside function ds.ranksSecure. For - more details, including future plans to share this starting seed in a - more secure way, please see the associated document entitled - "secure.global.ranking.docx" and the header file for ds.ranksSecure. - -- synth.real.ratio: - - an integer value representing the ratio of synthetic (pseudo-data) - values to the real number of values in V2BR. This argument is set by - the argument with the same name in the clientside function - ds.ranksSecure. For more details, please see the associated document - entitled "secure.global.ranking.docx" and the header file for - ds.ranksSecure. - -- NA.manage: - - character string indicating how missing values (NAs) in V2BR should be - managed. It takes three possible values: "NA.delete", - "NA.low","NA.hi". This argument is set by the argument with the same - name in the clientside function ds.ranksSecure. For more details, - please see the associated document entitled - "secure.global.ranking.docx" and the header file for ds.ranksSecure. - -## Value - -writes a data frame object entitled blackbox.output.df to the -serverside. In each study this contains the encrypted "combined -real+pseudo data vector" and a range of other key components from the -first stage of the ranking procedure. For more details see the -associated document entitled "secure.global.ranking.docx" - -## Details - -Severside assign function called by ds.ranksSecure. Creates pseudo-data -by using the real distribution of values in V2BR to create a large -number of synthetic data with a similar distribution to the values in -V2BR but with a slightly broader distribution at both ends to ensure -that any extreme values in the "combined real+pseudo data vector" are -all pseudo-data. Also ensures that the number of decimal places of the -values in the V2BR is reflected by the number of decimal places in the -pseudodata. Finally, takes the "combined real+pseudo data vector" -through seven rounds of rank consistent encryption that involves -algorithms themselves generated by a pseudorandom process that selects -which transformation to apply and with what parameters. The encryption -algorithms are the same in each study ensuring that ranks also remain -consistent between studies. After encryption the encrypted "combined -real+pseudo data vector" is written to the serverside as a dataframe -also including other key component vectors from the first stage of the -ranking procedure. For more details about the cluster of functions that -collectively enable secure global ranking and estimation of global -quantiles see the associated document entitled -"secure.global.ranking.docx". Also see the header file for -ds.ranksSecure - -## Author - -Paul Burton 9th November, 2021 diff --git a/docs/reference/blackBoxRanksDS.html b/docs/reference/blackBoxRanksDS.html deleted file mode 100644 index dbf3c955..00000000 --- a/docs/reference/blackBoxRanksDS.html +++ /dev/null @@ -1,132 +0,0 @@ - -Secure ranking of "V2BR" (vector to be ranked) across all sources — blackBoxRanksDS • dsBase - Skip to contents - - -
-
-
- -

Secure ranking of "V2BR" (vector to be ranked) across all sources

- -
blackBoxRanksDS.Rd
-
- -
-

The second key serverside function that prepares the global -ranks of the the real data only generated in the first stage of the -ranking procedure and encrypts them in preparation for generating global -ranks that correspond 1 to 1 with only the real data in V2BR.

-
- -
-

Usage

- 
blackBoxRanksDS(input.var.name = NULL, shared.seedval)
-
- -
-

Arguments

- - -
input.var.name
-

a character string specifying the name of the -vector holding the global ranks. This argument is set automatically by -the clientside function ds.ranksSecure

- - -
shared.seedval
-

a pseudorandom number seed that ensures that the -processes generating the order and parameterisation of the encryption -algorithms are the same in each study. This argument is set by the argument -<shared.seed.value> in the clientside function ds.ranksSecure. The -seed value shared by all studies in setting up the encryption procedures -in blackBoxRanksDS is arbitrarily changed from that used to set up the -encryption procedures in blackBoxDS, so the the set of 7 encryption -algorithms is deliberately different. For more -details, including future plans to share this starting seed in a more secure -way, please see the associated document entitled "secure.global.ranking.docx" -and the header file for ds.ranksSecure.

- -
-
-

Value

-

writes a data frame object entitled blackbox.ranks.df to the -serverside. In each study this contains the encrypted global ranks -and a range of other key components from the second stage (ranking of global -ranks for real observations only) of the ranking procedure. For more details -see the associated document entitled "secure.global.ranking.docx"

-
-
-

Details

-

Severside assign function called by ds.ranksSecure. It takes the -global ranks currently held in sR5.df which reflect the global ranks based on -the "combined real+pseudo data vector" as encrypted by blackBoxDS -but with all pseudo-data stripped out. It then uses these global ranks (of -the real data) as if they were a new variable to be ranked. This is then -equivalent to blackBoxDS with the primary difference that no -pseudo-data are needed. This is because the global ranks are fundamentally -non-disclosive and so can be transferred to the clientside with no risk of -disclosure. However, in order to ensure that the client cannot compare -the list of global.ranks in sR4.df (after initial global ranking based on -ranking of real and pseudo-data combined) with the global.ranks to be -generated by blackBoxRanksDS (based solely on the real data they are -processed through seven more rounds of encryption as before in blackBoxDS. -In consequence the client remains unable to determine which of the original -global ranks corresponded to real data and which to pseudo-data. In -addition, blackBoxRanksDS does not need to determine the number of decimal -places in the data because it is only applied to ranks which are assumed to -be integers. For more details about the cluster of functions that -collectively enable secure global ranking and estimation of global quantiles -see the associated document entitled "secure.global.ranking.docx". Also -see the header file for ds.ranksSecure and the header file for blackBoxDS

-
-
-

Author

-

Paul Burton 9th November, 2021

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/blackBoxRanksDS.md b/docs/reference/blackBoxRanksDS.md deleted file mode 100644 index 5634fd90..00000000 --- a/docs/reference/blackBoxRanksDS.md +++ /dev/null @@ -1,71 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources - -The second key serverside function that prepares the global ranks of the -the real data only generated in the first stage of the ranking procedure -and encrypts them in preparation for generating global ranks that -correspond 1 to 1 with only the real data in V2BR. - -## Usage - -``` r -blackBoxRanksDS(input.var.name = NULL, shared.seedval) -``` - -## Arguments - -- input.var.name: - - a character string specifying the name of the vector holding the - global ranks. This argument is set automatically by the clientside - function ds.ranksSecure - -- shared.seedval: - - a pseudorandom number seed that ensures that the processes generating - the order and parameterisation of the encryption algorithms are the - same in each study. This argument is set by the argument - \ in the clientside function ds.ranksSecure. The - seed value shared by all studies in setting up the encryption - procedures in blackBoxRanksDS is arbitrarily changed from that used to - set up the encryption procedures in blackBoxDS, so the the set of 7 - encryption algorithms is deliberately different. For more details, - including future plans to share this starting seed in a more secure - way, please see the associated document entitled - "secure.global.ranking.docx" and the header file for ds.ranksSecure. - -## Value - -writes a data frame object entitled blackbox.ranks.df to the serverside. -In each study this contains the encrypted global ranks and a range of -other key components from the second stage (ranking of global ranks for -real observations only) of the ranking procedure. For more details see -the associated document entitled "secure.global.ranking.docx" - -## Details - -Severside assign function called by ds.ranksSecure. It takes the global -ranks currently held in sR5.df which reflect the global ranks based on -the "combined real+pseudo data vector" as encrypted by blackBoxDS but -with all pseudo-data stripped out. It then uses these global ranks (of -the real data) as if they were a new variable to be ranked. This is then -equivalent to blackBoxDS with the primary difference that no pseudo-data -are needed. This is because the global ranks are fundamentally -non-disclosive and so can be transferred to the clientside with no risk -of disclosure. However, in order to ensure that the client cannot -compare the list of global.ranks in sR4.df (after initial global ranking -based on ranking of real and pseudo-data combined) with the global.ranks -to be generated by blackBoxRanksDS (based solely on the real data they -are processed through seven more rounds of encryption as before in -blackBoxDS. In consequence the client remains unable to determine which -of the original global ranks corresponded to real data and which to -pseudo-data. In addition, blackBoxRanksDS does not need to determine the -number of decimal places in the data because it is only applied to ranks -which are assumed to be integers. For more details about the cluster of -functions that collectively enable secure global ranking and estimation -of global quantiles see the associated document entitled -"secure.global.ranking.docx". Also see the header file for -ds.ranksSecure and the header file for blackBoxDS - -## Author - -Paul Burton 9th November, 2021 diff --git a/docs/reference/boxPlotGGDS.html b/docs/reference/boxPlotGGDS.html index ed19da2e..5d8056c2 100644 --- a/docs/reference/boxPlotGGDS.html +++ b/docs/reference/boxPlotGGDS.html @@ -1,5 +1,5 @@ -Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS • dsBaseCreate the identity stats and necessary data to draw a plot on the client — boxPlotGGDS • dsBasedsBase - 6.3.6.9000 + 7.0.0.9000 - - - - - -
-
-
- -

dataFrameFillDS

- -
dataFrameFillDS.Rd
-
- -
-

An assign function called by the clientside ds.dataFrameFill function.

-
- -
-

Usage

- 
dataFrameFillDS(
-  df.name,
-  allNames.transmit,
-  class.vect.transmit,
-  levels.vec.transmit
-)
-
- -
-

Arguments

- - -
df.name
-

a character string representing the name of the input data frame that will be -filled with extra columns with missing values if a number of variables is missing from it -compared to the data frames of the other studies used in the analysis.

- - -
allNames.transmit
-

unique names of all the variables that are included in the input -data frames from all the used datasources.

- - -
class.vect.transmit
-

the classes of all the variables that are included in the vector -allNames.transmit.

- - -
levels.vec.transmit
-

the levels of all factor variables. -The classes supported are 'numeric', 'integer', 'character', 'factor' and 'logical'.

- -
-
-

Value

-

Nothing is returned to the client. The generated object is written to the serverside.

-
-
-

Details

-

This function checks if each study has all the variables compared to the other studies -in the analysis. If a study does not have some of the variables, the function generates those -variables as vectors of missing values and combines them as columns to the input data frame. -Then, the "complete" in terms of the columns dataframe is saved in each server with a name -specified by the argument newobj on the clientside.

-
-
-

Author

-

Demetris Avraam for DataSHIELD Development Team

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/dataFrameFillDS.md b/docs/reference/dataFrameFillDS.md deleted file mode 100644 index 5741f242..00000000 --- a/docs/reference/dataFrameFillDS.md +++ /dev/null @@ -1,56 +0,0 @@ -# dataFrameFillDS - -An assign function called by the clientside ds.dataFrameFill function. - -## Usage - -``` r -dataFrameFillDS( - df.name, - allNames.transmit, - class.vect.transmit, - levels.vec.transmit -) -``` - -## Arguments - -- df.name: - - a character string representing the name of the input data frame that - will be filled with extra columns with missing values if a number of - variables is missing from it compared to the data frames of the other - studies used in the analysis. - -- allNames.transmit: - - unique names of all the variables that are included in the input data - frames from all the used datasources. - -- class.vect.transmit: - - the classes of all the variables that are included in the vector - `allNames.transmit`. - -- levels.vec.transmit: - - the levels of all factor variables. The classes supported are - 'numeric', 'integer', 'character', 'factor' and 'logical'. - -## Value - -Nothing is returned to the client. The generated object is written to -the serverside. - -## Details - -This function checks if each study has all the variables compared to the -other studies in the analysis. If a study does not have some of the -variables, the function generates those variables as vectors of missing -values and combines them as columns to the input data frame. Then, the -"complete" in terms of the columns dataframe is saved in each server -with a name specified by the argument `newobj` on the clientside. - -## Author - -Demetris Avraam for DataSHIELD Development Team diff --git a/docs/reference/dataFrameSortDS.html b/docs/reference/dataFrameSortDS.html index 9f5a25ac..16c61ef5 100644 --- a/docs/reference/dataFrameSortDS.html +++ b/docs/reference/dataFrameSortDS.html @@ -1,5 +1,5 @@ -Sorting and reordering data frames, vectors or matrices — dataFrameSortDS • dsBase +Sorting and reordering data frames, vectors or matrices — dataFrameSortDS • dsBase Skip to contents @@ -7,7 +7,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 - - dsBase - 6.3.3 - - - - - - - - - -
-
-
-

Splits character by '$' and returns the single characters

- - -
- -
-

This is an internal function.

-
- -
- 
extract(input)
-
- -
-

Arguments

- - -
input
-

a vector or a list of characters

- -
-
-

Value

-

a vector of characters

-
-
-

Details

-

Not required

-
- -
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.1.3.

-
- -
- - - - - - - - diff --git a/docs/reference/extractQuantilesDS1.html b/docs/reference/extractQuantilesDS1.html deleted file mode 100644 index 757856e3..00000000 --- a/docs/reference/extractQuantilesDS1.html +++ /dev/null @@ -1,123 +0,0 @@ - -Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies — extractQuantilesDS1 • dsBase - Skip to contents - - -
-
-
- -

Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies

- -
extractQuantilesDS1.Rd
-
- -
-

identify the global values of V2BR (i.e. the values across all -studies) that relate to a set of quantiles to be evaluated.

-
- -
-

Usage

- 
extractQuantilesDS1(extract.quantiles, extract.summary.output.ranks.df)
-
- -
-

Arguments

- - -
extract.quantiles
-

one of a restricted set of character strings that -fix the set of quantile values for which the corresponding values across -all studies are to be estimated. For more details -see the associated document entitled "secure.global.ranking.docx", the -header for ds.ranksSecure and ds.extractQuantiles functions. -The value of this argument is set in choosing the value of the argument -<quantiles.for.estimation> in ds.ranksSecure.

- - -
extract.summary.output.ranks.df
-

character string specifying optional -name for the data.frame written to the serverside on each data source that -contains 5 of the key output variables from the ranking procedure pertaining -to that particular data source. This data frame represents the key source of -information - including global ranks - that determines the values of V2BR -that are identified as corresponding to the particular set of quantiles to -be estimated as specified by the <quantiles.for.estimation> argument of -function ds.ranksSecure (and the <extract.quantiles> argument of -ds.extractQuantiles).

- -
-
-

Value

-

as a first step in creating the vector of values of values of V2BR -that correspond to each quantile value, extractQuantilesDS1 identifies the -two closest quantile values across all studies that span each key quantile -value. These are saved as the data frame "closest.bounds.df" on the -clientside and then saved on the serverside by ds.dmtC2S into the data frame -"global.bounds.df". Also if the number of observations across all studies is -too small, and a disclosure risk exists if the final.quantile.vector is made -available via the client, this function stops the processing and returns a -warning/error message.

-
-
-

Details

-

Severside aggregate function called by ds.extractQuantiles via -ds.ranksSecure. As well as estimating the key values of V2BR that correspond -to the selected quantiles, this function also implements a disclosure control -trap. If the ratio of the total number of all observations across all studies -divided by the number of quantile values to be estimated is less than or -equal to nfilter.subset (which specifies the minimum size of a subset) the -process stops and an error message is returned suggesting that you might -try selecting a narrower range of quantiles with less quantile values to be -estimated as specified by the argument <quantiles.for.estimation> of the -function ds.ranksSecure. For more details about the cluster of functions that -collectively enable secure global ranking and estimation of global quantiles -see the associated document entitled "secure.global.ranking.docx"

-
-
-

Author

-

Paul Burton 11th November, 2021

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/extractQuantilesDS1.md b/docs/reference/extractQuantilesDS1.md deleted file mode 100644 index b828396a..00000000 --- a/docs/reference/extractQuantilesDS1.md +++ /dev/null @@ -1,66 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies - -identify the global values of V2BR (i.e. the values across all studies) -that relate to a set of quantiles to be evaluated. - -## Usage - -``` r -extractQuantilesDS1(extract.quantiles, extract.summary.output.ranks.df) -``` - -## Arguments - -- extract.quantiles: - - one of a restricted set of character strings that fix the set of - quantile values for which the corresponding values across all studies - are to be estimated. For more details see the associated document - entitled "secure.global.ranking.docx", the header for ds.ranksSecure - and ds.extractQuantiles functions. The value of this argument is set - in choosing the value of the argument \ in - ds.ranksSecure. - -- extract.summary.output.ranks.df: - - character string specifying optional name for the data.frame written - to the serverside on each data source that contains 5 of the key - output variables from the ranking procedure pertaining to that - particular data source. This data frame represents the key source of - information - including global ranks - that determines the values of - V2BR that are identified as corresponding to the particular set of - quantiles to be estimated as specified by the - \ argument of function ds.ranksSecure (and - the \ argument of ds.extractQuantiles). - -## Value - -as a first step in creating the vector of values of values of V2BR that -correspond to each quantile value, extractQuantilesDS1 identifies the -two closest quantile values across all studies that span each key -quantile value. These are saved as the data frame "closest.bounds.df" on -the clientside and then saved on the serverside by ds.dmtC2S into the -data frame "global.bounds.df". Also if the number of observations across -all studies is too small, and a disclosure risk exists if the -final.quantile.vector is made available via the client, this function -stops the processing and returns a warning/error message. - -## Details - -Severside aggregate function called by ds.extractQuantiles via -ds.ranksSecure. As well as estimating the key values of V2BR that -correspond to the selected quantiles, this function also implements a -disclosure control trap. If the ratio of the total number of all -observations across all studies divided by the number of quantile values -to be estimated is less than or equal to nfilter.subset (which specifies -the minimum size of a subset) the process stops and an error message is -returned suggesting that you might try selecting a narrower range of -quantiles with less quantile values to be estimated as specified by the -argument \ of the function ds.ranksSecure. -For more details about the cluster of functions that collectively enable -secure global ranking and estimation of global quantiles see the -associated document entitled "secure.global.ranking.docx" - -## Author - -Paul Burton 11th November, 2021 diff --git a/docs/reference/extractQuantilesDS2.html b/docs/reference/extractQuantilesDS2.html deleted file mode 100644 index e1d6d96c..00000000 --- a/docs/reference/extractQuantilesDS2.html +++ /dev/null @@ -1,121 +0,0 @@ - -Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies — extractQuantilesDS2 • dsBase - Skip to contents - - -
-
-
- -

Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies

- -
extractQuantilesDS2.Rd
-
- -
-

identify the global values of V2BR (i.e. the values across all -studies) that relate to a set of quantiles to be evaluated.

-
- -
-

Usage

- 
extractQuantilesDS2(extract.summary.output.ranks.df)
-
- -
-

Arguments

- - -
extract.summary.output.ranks.df
-

character string specifies an optional -name for the data.frame written to the serverside on each data source that -contains 5 of the key output variables from the ranking procedure pertaining -to that particular data source. This data frame represents the key source of -information - including global ranks - that determines the values of V2BR -that are identified as corresponding to the particular set of quantiles to -be estimated as specified by the <quantiles.for.estimation> argument of -function ds.ranksSecure (and the <extract.quantiles> argument of -ds.extractQuantiles).

- -
-
-

Value

-

the single value of V2BR which best corresponds to each key quantile -value to be estimated as specified by the argument <quantiles.for.estimation> -A data frame (final.quantile.df)summarising the results of this analysis -is written to the clientside. This data frame consists of two vectors. The -first is named "evaluation.quantiles". It lists the full set of quantiles -you have requested for evaluation as specified by the argument -"quantiles.for.estimation" The second vector which is called -"final.quantile.vector" details the values of V2BR that correspond to the -the key quantiles listed in vector 1.

-
-
-

Details

-

Severside aggregate function called by ds.extractQuantiles via -ds.ranksSecure. This takes the "global.bounds.df" data frame saved on the -serverside following construction by extractQuantilesDS1. This -data frame includes the two quantile values that most closely span each -quartile value to be estimated. If either of the values had been the correct -value for a given quantile, both the bounding values would have taken that -value in global.bounds.df. This is because the upper bound was defined as -the lowest value that was equal to or greater than the true value for that -quantile while the lower bound was defined as the highest value that was -equal to or lower than the true value. Next, the function extractQuantileDS2 -goes round study by study to identify the values of V2BR that actually -correspond to each of the spanning values around each quantile. Then the -function goes quantile by quantile and estimates the mean of the -two values of V2BR that correspond to the the spanning quantiles. If these -two values are the same it means that that value of V2BR is the -"true" value and the mean of two (or potentially several) instances of that -value is inevitably also equal to that true value. If the upper and lower -bounding values of V2BR differ, neither can be the precisely correct single -value of V2BR for that quantile (see above for explanation) and so the mean -of the two is a reasonable interpolated summary.

-
-
-

Author

-

Paul Burton 11th November, 2021

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/extractQuantilesDS2.md b/docs/reference/extractQuantilesDS2.md deleted file mode 100644 index 99e4e20a..00000000 --- a/docs/reference/extractQuantilesDS2.md +++ /dev/null @@ -1,65 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies - -identify the global values of V2BR (i.e. the values across all studies) -that relate to a set of quantiles to be evaluated. - -## Usage - -``` r -extractQuantilesDS2(extract.summary.output.ranks.df) -``` - -## Arguments - -- extract.summary.output.ranks.df: - - character string specifies an optional name for the data.frame written - to the serverside on each data source that contains 5 of the key - output variables from the ranking procedure pertaining to that - particular data source. This data frame represents the key source of - information - including global ranks - that determines the values of - V2BR that are identified as corresponding to the particular set of - quantiles to be estimated as specified by the - \ argument of function ds.ranksSecure (and - the \ argument of ds.extractQuantiles). - -## Value - -the single value of V2BR which best corresponds to each key quantile -value to be estimated as specified by the argument -\ A data frame (final.quantile.df)summarising -the results of this analysis is written to the clientside. This data -frame consists of two vectors. The first is named -"evaluation.quantiles". It lists the full set of quantiles you have -requested for evaluation as specified by the argument -"quantiles.for.estimation" The second vector which is called -"final.quantile.vector" details the values of V2BR that correspond to -the the key quantiles listed in vector 1. - -## Details - -Severside aggregate function called by ds.extractQuantiles via -ds.ranksSecure. This takes the "global.bounds.df" data frame saved on -the serverside following construction by extractQuantilesDS1. This data -frame includes the two quantile values that most closely span each -quartile value to be estimated. If either of the values had been the -correct value for a given quantile, both the bounding values would have -taken that value in global.bounds.df. This is because the upper bound -was defined as the lowest value that was equal to or greater than the -true value for that quantile while the lower bound was defined as the -highest value that was equal to or lower than the true value. Next, the -function extractQuantileDS2 goes round study by study to identify the -values of V2BR that actually correspond to each of the spanning values -around each quantile. Then the function goes quantile by quantile and -estimates the mean of the two values of V2BR that correspond to the the -spanning quantiles. If these two values are the same it means that that -value of V2BR is the "true" value and the mean of two (or potentially -several) instances of that value is inevitably also equal to that true -value. If the upper and lower bounding values of V2BR differ, neither -can be the precisely correct single value of V2BR for that quantile (see -above for explanation) and so the mean of the two is a reasonable -interpolated summary. - -## Author - -Paul Burton 11th November, 2021 diff --git a/docs/reference/fixClassDS.html b/docs/reference/fixClassDS.html index 35697eae..862ebd43 100644 --- a/docs/reference/fixClassDS.html +++ b/docs/reference/fixClassDS.html @@ -1,5 +1,5 @@ -Change Class of Target Variables in a Data Frame — fixClassDS • dsBase +Change Class of Target Variables in a Data Frame — fixClassDS • dsBase Skip to contents @@ -7,7 +7,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 - - dsBase - 6.1.1 - - - - - - - - - - - -
-
-
-

Fitting generalized linear mixed effect models - serverside function

- - -
- -
-

glmerSLMADS.assing is the same as glmerSLMADS2 which fits a generalized linear -mixed effects model (glme) per study and saves the outcomes in each study

-
- - 
glmerSLMADS.assing(
-  formula,
-  offset,
-  weights,
-  dataName,
-  family,
-  control_type = NULL,
-  control_value.transmit = NULL,
-  nAGQ = 1L,
-  verbose = 0,
-  theta = NULL,
-  fixef = NULL
-)
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
formula

see help for ds.glmerSLMA

offset

see help for ds.glmerSLMA

weights

see help for ds.glmerSLMA

dataName

see help for ds.glmerSLMA

family

see help for ds.glmerSLMA

control_type

see help for ds.glmerSLMA

control_value.transmit

see help for argument <control_value> for -function ds.glmerSLMA

nAGQ

integer scalar, defaulting to 1L. IN PRACTICE, IT MAY BE NECESSARY -TO SET nAGQ TO 0L when the model appears to converge perfectly well (e.g. verbose=2 -demonstrates good initial convergence of both the log-likelihood and -regression coefficients) but formal convergence does not get declared - -so no output is produced - despite running the model for many iterations. -The nAGQ argument is set by the nAGQ argument for ds.glmerSLMA and further -details can be found in help(ds.glmerSLMA) and in the native R help for glmer()

verbose

see help for ds.glmerSLMA

theta

see help for argument <start_theta> for -function ds.glmerSLMA

fixef

see help for argument <start_fixef> for -function ds.glmerSLMA

- -

Value

- -

writes glmerMod object summarising the fitted model to the serverside. -For more detailed information see help for ds.glmerSLMA.

-

Details

- -

glmerSLMADS.assign is a serverside function called by ds.glmerSLMA on the clientside. -The analytic work engine is the glmer function in R which sits in the lme4 package. -glmerSLMADS.assign fits a generalized linear mixed effects model (glme) - e.g. a logistic or -Poisson regression model including both fixed and random effects - on data -from each single data source and saves the regression outcomes on the serveside.

-

Author

- -

Demetris Avraam for DataSHIELD Development Team

- -
- -
- - -
-
-

Developed by DataSHIELD Developers.

-
- -
-

Site built with pkgdown 1.6.1.

-
- -
- - - - - - - - - diff --git a/docs/reference/heatmapPlotDS.html b/docs/reference/heatmapPlotDS.html index 6a5f6f19..c60f18df 100644 --- a/docs/reference/heatmapPlotDS.html +++ b/docs/reference/heatmapPlotDS.html @@ -1,5 +1,5 @@ -Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS • dsBase +Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS • dsBase Skip to contents @@ -7,7 +7,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 + + + + + +
+
+
+ +

Computes the logarithm values of the input variable

+ +
logDS.Rd
+
+ +
+

This function is similar to R function log.

+
+ +
+

Usage

+ 
logDS(x, base = exp(1))
+
+ +
+

Arguments

+ + +
x
+

a string character, the name of a numeric or integer vector

+ + +
base
+

a positive number, the base for which logarithms are computed. +Default exp(1).

+ +
+
+

Value

+

the object specified by the newobj argument +of ds.log (or default name log.newobj) +which is written to the serverside. The output object is of class numeric.

+
+
+

Details

+

The function computes the logarithm values of an input numeric +or integer vector. By default natural logarithms are computed.

+
+
+

Author

+

DataSHIELD Development Team

+

Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands

+
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.1.

+
+ +
+ + + + + + + diff --git a/docs/reference/logDS.md b/docs/reference/logDS.md new file mode 100644 index 00000000..570e548a --- /dev/null +++ b/docs/reference/logDS.md @@ -0,0 +1,37 @@ +# Computes the logarithm values of the input variable + +This function is similar to R function `log`. + +## Usage + +``` r +logDS(x, base = exp(1)) +``` + +## Arguments + +- x: + + a string character, the name of a numeric or integer vector + +- base: + + a positive number, the base for which logarithms are computed. Default + `exp(1)`. + +## Value + +the object specified by the `newobj` argument of `ds.log` (or default +name `log.newobj`) which is written to the serverside. The output object +is of class numeric. + +## Details + +The function computes the logarithm values of an input numeric or +integer vector. By default natural logarithms are computed. + +## Author + +DataSHIELD Development Team + +Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands diff --git a/docs/reference/lsDS.html b/docs/reference/lsDS.html index 8fdea6b9..b5d1487b 100644 --- a/docs/reference/lsDS.html +++ b/docs/reference/lsDS.html @@ -1,5 +1,5 @@ -lists all objects on a serverside environment — lsDS • dsBaselists all objects on a serverside environment — lsDS • dsBase Skip to contents @@ -9,7 +9,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 - - - - - -
-
-
- -

messageDS

- -
messageDS.Rd
-
- -
-

This function allows for error messages arising from the -running of a server-side assign function to be returned to the client-side

-
- -
-

Usage

- 
messageDS(message.object.name)
-
- -
-

Arguments

- - -
message.object.name
-

is a character string, containing the name of the list containing the -message. See the header of the client-side function ds.message for more details.

- -
-
-

Value

-

a list object from each study, containing whatever message has been written by -DataSHIELD into $studysideMessage.

-
-
-

Details

-

Errors arising from aggregate server-side functions can be returned -directly to the client-side. But this is not possible for server-side assign -functions because they are designed specifically to write objects to the -server-side and to return no meaningful information to the client-side. -Otherwise, users may be able to use assign functions to return disclosive -output to the client-side. ds.message calls messageDS which looks -specifically for an object called $serversideMessage in a designated list on -the server-side. Server-side functions from which error messages are to be made -available, are designed to be able to write the designated error message to -the $serversideMessage object into the list that is saved on the server-side -as the primary output of that function. So only valid server-side functions of -DataSHIELD can write a $studysideMessage, and as additional protection against -unexpected ways that someone may try to get round this limitation, a -$studysideMessage is a string that cannot exceed a length of nfilter.string -a default of 80 characters.

-
-
-

Author

-

Burton PR

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/messageDS.md b/docs/reference/messageDS.md deleted file mode 100644 index d0580a9f..00000000 --- a/docs/reference/messageDS.md +++ /dev/null @@ -1,46 +0,0 @@ -# messageDS - -This function allows for error messages arising from the running of a -server-side assign function to be returned to the client-side - -## Usage - -``` r -messageDS(message.object.name) -``` - -## Arguments - -- message.object.name: - - is a character string, containing the name of the list containing the - message. See the header of the client-side function ds.message for - more details. - -## Value - -a list object from each study, containing whatever message has been -written by DataSHIELD into \$studysideMessage. - -## Details - -Errors arising from aggregate server-side functions can be returned -directly to the client-side. But this is not possible for server-side -assign functions because they are designed specifically to write objects -to the server-side and to return no meaningful information to the -client-side. Otherwise, users may be able to use assign functions to -return disclosive output to the client-side. ds.message calls messageDS -which looks specifically for an object called \$serversideMessage in a -designated list on the server-side. Server-side functions from which -error messages are to be made available, are designed to be able to -write the designated error message to the \$serversideMessage object -into the list that is saved on the server-side as the primary output of -that function. So only valid server-side functions of DataSHIELD can -write a \$studysideMessage, and as additional protection against -unexpected ways that someone may try to get round this limitation, a -\$studysideMessage is a string that cannot exceed a length of -nfilter.string a default of 80 characters. - -## Author - -Burton PR diff --git a/docs/reference/metadataDS.html b/docs/reference/metadataDS.html index 6c2b4036..f819de78 100644 --- a/docs/reference/metadataDS.html +++ b/docs/reference/metadataDS.html @@ -1,5 +1,5 @@ -Returns the metadata, if any, about the specified variable — metadataDS • dsBase +Returns the metadata, if any, about the specified variable — metadataDS • dsBase Skip to contents @@ -7,7 +7,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 - - - - - -
-
-
- -

Secure ranking of "V2BR" (vector to be ranked) across all sources

- -
minMaxRandDS.Rd
-
- -
-

Creates a minimum value that is more negative, and less positive -than any real value in V2BR and a maximum value that is more positive and -less negative than any value of V2BR.

-
- -
-

Usage

- 
minMaxRandDS(input.var.name)
-
- -
-

Arguments

- - -
input.var.name
-

a character string specifying the name of V2BR. This -argument is set by the argument with the same name in the clientside function -ds.ranksSecure

- -
-
-

Value

-

the data frame objects containing the global ranks and quantiles. -For more details see the associated document entitled -"secure.global.ranking.docx"

-
-
-

Details

-

Severside aggregate function called by ds.ranksSecure. The minimum -and maximum values it creates are used to replace missing values -(NAs) in V2BR if the argument <NA.manag>e is set to "NA.low" or "NA.hi" -respectively. For more details about the cluster of functions that -collectively enable secure global ranking and estimation of global quantiles -see the associated document entitled "secure.global.ranking.docx". Also -see the header file for ds.ranksSecure

-
-
-

Author

-

Paul Burton 9th November, 2021

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/minMaxRandDS.md b/docs/reference/minMaxRandDS.md deleted file mode 100644 index d937070b..00000000 --- a/docs/reference/minMaxRandDS.md +++ /dev/null @@ -1,40 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources - -Creates a minimum value that is more negative, and less positive than -any real value in V2BR and a maximum value that is more positive and -less negative than any value of V2BR. - -## Usage - -``` r -minMaxRandDS(input.var.name) -``` - -## Arguments - -- input.var.name: - - a character string specifying the name of V2BR. This argument is set - by the argument with the same name in the clientside function - ds.ranksSecure - -## Value - -the data frame objects containing the global ranks and quantiles. For -more details see the associated document entitled -"secure.global.ranking.docx" - -## Details - -Severside aggregate function called by ds.ranksSecure. The minimum and -maximum values it creates are used to replace missing values (NAs) in -V2BR if the argument \e is set to "NA.low" or "NA.hi" -respectively. For more details about the cluster of functions that -collectively enable secure global ranking and estimation of global -quantiles see the associated document entitled -"secure.global.ranking.docx". Also see the header file for -ds.ranksSecure - -## Author - -Paul Burton 9th November, 2021 diff --git a/docs/reference/namesDS.html b/docs/reference/namesDS.html index fc6d2abd..843841e8 100644 --- a/docs/reference/namesDS.html +++ b/docs/reference/namesDS.html @@ -1,5 +1,5 @@ -Return the names of a list object — namesDS • dsBase +Return the names of a list object — namesDS • dsBase Skip to contents @@ -7,7 +7,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 - - - - - -
-
-
- -

Secure ranking of "V2BR" (vector to be ranked) across all sources

- -
ranksSecureDS1.Rd
-
- -
-

takes key non-disclosive components of the serverside data frame -blackbox.output.df over to the clientside to enable global ranking.

-
- -
-

Usage

- 
ranksSecureDS1()
-
- -
-

Value

-

the non-disclosive elements of blackbox.output.df (see details) -on the serverside as a data frame object (called blackbox.output) -on the clientside. After processing to create the global ranks across all -studies, this is returned to the serverside as the data frame sR4.df using -the clientside function ds.dmtC2S

-
-
-

Details

-

Severside aggregate function called by ds.ranksSecure. The -non-disclosive components of blackbox.output.df that are transmitted to the -clientside are: (1) final values of the "combined real+pseudo data vector" -after all seven rounds of encryption have been completed; (2) a set of -sequential IDs allocated after sorting the "combined real+pseudo data vector" -by value (in ascending order). This allows later re-linkage of values back on -the serverside and confirmation that that linkage is correct. For more -details about the cluster of functions that collectively enable secure global -ranking and estimation of global quantiles see the associated document -entitled "secure.global.ranking.docx". Also see the header file -for ds.ranksSecure

-
-
-

Author

-

Paul Burton 9th November, 2021

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/ranksSecureDS1.md b/docs/reference/ranksSecureDS1.md deleted file mode 100644 index db7bb40f..00000000 --- a/docs/reference/ranksSecureDS1.md +++ /dev/null @@ -1,37 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources - -takes key non-disclosive components of the serverside data frame -blackbox.output.df over to the clientside to enable global ranking. - -## Usage - -``` r -ranksSecureDS1() -``` - -## Value - -the non-disclosive elements of blackbox.output.df (see details) on the -serverside as a data frame object (called blackbox.output) on the -clientside. After processing to create the global ranks across all -studies, this is returned to the serverside as the data frame sR4.df -using the clientside function ds.dmtC2S - -## Details - -Severside aggregate function called by ds.ranksSecure. The -non-disclosive components of blackbox.output.df that are transmitted to -the clientside are: (1) final values of the "combined real+pseudo data -vector" after all seven rounds of encryption have been completed; (2) a -set of sequential IDs allocated after sorting the "combined real+pseudo -data vector" by value (in ascending order). This allows later re-linkage -of values back on the serverside and confirmation that that linkage is -correct. For more details about the cluster of functions that -collectively enable secure global ranking and estimation of global -quantiles see the associated document entitled -"secure.global.ranking.docx". Also see the header file for -ds.ranksSecure - -## Author - -Paul Burton 9th November, 2021 diff --git a/docs/reference/ranksSecureDS2.html b/docs/reference/ranksSecureDS2.html deleted file mode 100644 index 6aab7b75..00000000 --- a/docs/reference/ranksSecureDS2.html +++ /dev/null @@ -1,113 +0,0 @@ - -Secure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS2 • dsBase - Skip to contents - - -
-
-
- -

Secure ranking of "V2BR" (vector to be ranked) across all sources

- -
ranksSecureDS2.Rd
-
- -
-

Checks that the data frame produced in creating the initial -global ranks (ranks based on real and pseudo-data after the running of -blackBoxDS)has the correct dimensions and order as the serverside data frames -to which it will now be appended. If either the number of rows or the order -of the rows are inconsistent with the pre-existing data frames on the -serverside an error message is returned and the processing stops. Then -strips out the pseudo-data leaving solely the global ranks based just on -the real data

-
- -
-

Usage

- 
ranksSecureDS2()
-
- -
-

Value

-

creates a new data frame sR5.df on the serverside containing -solely the real data and including key elements needed for next stage of the -ranking process. Most crucially these include "global.rank" and "ID.by.val" -sorted in ascending order of the magnitude of V2BR

-
-
-

Details

-

Severside assign function called by ds.ranksSecure. -It works on the on the output created by serverside function ranksSecureDS1 -and saved on the serverside in data frame sR4.df by ds.dmtC2S. Having -checked QA it strips out all rows corresponding to pseudo-data. The resultant -data frame contains the following vectors: (1) the fully encrypted V2BR -(after application of blackBoxDS);(2) "ID.by.val" the sequential -ID associated with the "combined real+pseudo data vector" sorted by -value (ascending); (3) "studyid", a vector consisting solely of value n in -the nth study; (4) "global.rank" the vector containing global ranks created by -the clientside code in ds.ranksSecure after ranksSecureDS1 is called and up -to the point where ds.dmtC2S sends sR4.df to the serverside. For more -details about the cluster of functions that collectively enable secure global -ranking and estimation of global quantiles see the associated document -entitled "secure.global.ranking.docx". Also see the header file -for ds.ranksSecure

-
-
-

Author

-

Paul Burton 9th November, 2021

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/ranksSecureDS2.md b/docs/reference/ranksSecureDS2.md deleted file mode 100644 index 78febe60..00000000 --- a/docs/reference/ranksSecureDS2.md +++ /dev/null @@ -1,45 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources - -Checks that the data frame produced in creating the initial global ranks -(ranks based on real and pseudo-data after the running of blackBoxDS)has -the correct dimensions and order as the serverside data frames to which -it will now be appended. If either the number of rows or the order of -the rows are inconsistent with the pre-existing data frames on the -serverside an error message is returned and the processing stops. Then -strips out the pseudo-data leaving solely the global ranks based just on -the real data - -## Usage - -``` r -ranksSecureDS2() -``` - -## Value - -creates a new data frame sR5.df on the serverside containing solely the -real data and including key elements needed for next stage of the -ranking process. Most crucially these include "global.rank" and -"ID.by.val" sorted in ascending order of the magnitude of V2BR - -## Details - -Severside assign function called by ds.ranksSecure. It works on the on -the output created by serverside function ranksSecureDS1 and saved on -the serverside in data frame sR4.df by ds.dmtC2S. Having checked QA it -strips out all rows corresponding to pseudo-data. The resultant data -frame contains the following vectors: (1) the fully encrypted V2BR -(after application of blackBoxDS);(2) "ID.by.val" the sequential ID -associated with the "combined real+pseudo data vector" sorted by value -(ascending); (3) "studyid", a vector consisting solely of value n in the -nth study; (4) "global.rank" the vector containing global ranks created -by the clientside code in ds.ranksSecure after ranksSecureDS1 is called -and up to the point where ds.dmtC2S sends sR4.df to the serverside. For -more details about the cluster of functions that collectively enable -secure global ranking and estimation of global quantiles see the -associated document entitled "secure.global.ranking.docx". Also see the -header file for ds.ranksSecure - -## Author - -Paul Burton 9th November, 2021 diff --git a/docs/reference/ranksSecureDS3.html b/docs/reference/ranksSecureDS3.html deleted file mode 100644 index 7740a6d8..00000000 --- a/docs/reference/ranksSecureDS3.html +++ /dev/null @@ -1,105 +0,0 @@ - -Secure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS3 • dsBase - Skip to contents - - -
-
-
- -

Secure ranking of "V2BR" (vector to be ranked) across all sources

- -
ranksSecureDS3.Rd
-
- -
-

takes key non-disclosive components of the serverside data frame -blackbox.ranks.df over to the clientside to enable global re-ranking of the -global ranks just applying to the real data (not the pseudo-data).

-
- -
-

Usage

- 
ranksSecureDS3()
-
- -
-

Value

-

the non-disclosive elements of blackbox.output.df (see details) -on the serverside as a data frame object (called sR6.df) -on the clientside. After processing within ds.ranksSecure to create the -global ranks and global quantiles (of real data only) across all studies, -this is returned to the serverside as data frame "global.ranks.quantiles.df" -using the clientside function ds.dmtC2S. To illustrate the difference between -ranks and quantiles, if there are a total of 1000 original real observations -across all studies and one particular observation has the rank 250, it will -have quantile value 0.25 (i.e. 25 -increasing value). Both ranks and quantiles can have ties. For more details -about the cluster of functions that collectively enable secure global ranking -and estimation of global quantiles see the associated document entitled -"secure.global.ranking.docx". Also see the header file for ds.ranksSecure

-
-
-

Details

-

Severside aggregate function called by ds.ranksSecure. The -non-disclosive components of blackbox.ranks.df that are transmitted to the -clientside are: (1) final values of the encrypted global ranks vector -after all seven rounds of encryption have been completed; (2) a set of -sequential IDs allocated to the global ranks vector in each study in their -current order based on increasing value of V2BR. This allows later re-linkage -of values back on the serverside and confirmation that that linkage is -correct. (3) a studyid vector with all values n in the nth study. This -facilitates data management on the serverside during the global ranking -of global ranks. For more details about the cluster of functions that -collectively enable secure global ranking and estimation of global quantiles -see the associated document entitled "secure.global.ranking.docx". Also see -the header file for ds.ranksSecure

-
-
-

Author

-

Paul Burton 9th November, 2021

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/ranksSecureDS3.md b/docs/reference/ranksSecureDS3.md deleted file mode 100644 index 5602ce29..00000000 --- a/docs/reference/ranksSecureDS3.md +++ /dev/null @@ -1,49 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources - -takes key non-disclosive components of the serverside data frame -blackbox.ranks.df over to the clientside to enable global re-ranking of -the global ranks just applying to the real data (not the pseudo-data). - -## Usage - -``` r -ranksSecureDS3() -``` - -## Value - -the non-disclosive elements of blackbox.output.df (see details) on the -serverside as a data frame object (called sR6.df) on the clientside. -After processing within ds.ranksSecure to create the global ranks and -global quantiles (of real data only) across all studies, this is -returned to the serverside as data frame "global.ranks.quantiles.df" -using the clientside function ds.dmtC2S. To illustrate the difference -between ranks and quantiles, if there are a total of 1000 original real -observations across all studies and one particular observation has the -rank 250, it will have quantile value 0.25 (i.e. 25 increasing value). -Both ranks and quantiles can have ties. For more details about the -cluster of functions that collectively enable secure global ranking and -estimation of global quantiles see the associated document entitled -"secure.global.ranking.docx". Also see the header file for -ds.ranksSecure - -## Details - -Severside aggregate function called by ds.ranksSecure. The -non-disclosive components of blackbox.ranks.df that are transmitted to -the clientside are: (1) final values of the encrypted global ranks -vector after all seven rounds of encryption have been completed; (2) a -set of sequential IDs allocated to the global ranks vector in each study -in their current order based on increasing value of V2BR. This allows -later re-linkage of values back on the serverside and confirmation that -that linkage is correct. (3) a studyid vector with all values n in the -nth study. This facilitates data management on the serverside during the -global ranking of global ranks. For more details about the cluster of -functions that collectively enable secure global ranking and estimation -of global quantiles see the associated document entitled -"secure.global.ranking.docx". Also see the header file for -ds.ranksSecure - -## Author - -Paul Burton 9th November, 2021 diff --git a/docs/reference/ranksSecureDS4.html b/docs/reference/ranksSecureDS4.html deleted file mode 100644 index 60c03845..00000000 --- a/docs/reference/ranksSecureDS4.html +++ /dev/null @@ -1,121 +0,0 @@ - -Secure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS4 • dsBase - Skip to contents - - -
-
-
- -

Secure ranking of "V2BR" (vector to be ranked) across all sources

- -
ranksSecureDS4.Rd
-
- -
-

Creates a data frame "sR8.df" by cbinding the data frame -"blackBox.ranks.df" with the global ranks and global quantiles vectors in -"global.ranks.quantiles.df". Performs QA on this matrix and orders the -sR8.df data frame according to the argument <ranks.sort.by> in ds.ranksSecure

-
- -
-

Usage

- 
ranksSecureDS4(ranks.sort.by)
-
- -
-

Arguments

- - -
ranks.sort.by
-

a character string taking two possible values. These -are "ID.orig" and "vals.orig". These define the order in which the -output.ranks.df and summary.output.ranks.df data frames are presented. This -argument is set by the argument with the same name in ds.ranksSecure. -Default value is "ID.orig".

- -
-
-

Value

-

Creates the data frame identified by the name given by the argument -(<output.ranks.df>) of the ds.ranksSecure function and writes it to the -serverside. If the argument <output.ranks.df> is NULL or unspecified the -output data frame is called "main.ranks.df". The data frame is ordered -according to the argument <ranks.sort.by> in ds.ranksSecure.

-
-
-

Details

-

Severside assign function called by ds.ranksSecure. -Creates a data frame "sR8.df" by cbinding the data frame "blackBox.ranks.df" -with the global ranks and global quantiles vectors in -"global.ranks.quantiles.df". Checks that all components of sR8.df have the -correct dimensions and are consistent in their ordering. If either the -number of rows or the order of the rows are inconsistent with those in -"blackBox.ranks.df" an error message is returned and the processing stops. -If sR8.df passes all QA tests it is written to the serverside as a data -frame with its name identified by the argument <output.ranks.df> in -ds.ranksSecure. If that argument is NULL or unspecified the data frame -is called "main.ranks.df". The ranksSecureDS4 function also orders the -combined data frame (<output.ranks.df>) in one of two ways: if -the argument <ranks.sort.by> in ds.ranksSecure is set to "ID.orig" the -combined data frame is ordered in the same way as the original V2BR vector; -if the argument <ranks.sort.by> is set to vals.orig" the combined data frame -is ordered by the magnitude of the values of V2BR (ascending). Having -created the data frame (<output.ranks.df>) in this manner it can now be -directly cbinded to either the V2BR vector itself or to a data frame, tibble -or matrix containing V2BR (assuming they are also in the order corresponding -to the argument <ranks.sort.by>) and this combined object can be used as the -basis of analysis based on the global ranks or quantiles including a range -of types of non-parametric analysis.

-
-
-

Author

-

Paul Burton 9th November, 2021

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/ranksSecureDS4.md b/docs/reference/ranksSecureDS4.md deleted file mode 100644 index 814907c9..00000000 --- a/docs/reference/ranksSecureDS4.md +++ /dev/null @@ -1,62 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources - -Creates a data frame "sR8.df" by cbinding the data frame -"blackBox.ranks.df" with the global ranks and global quantiles vectors -in "global.ranks.quantiles.df". Performs QA on this matrix and orders -the sR8.df data frame according to the argument \ in -ds.ranksSecure - -## Usage - -``` r -ranksSecureDS4(ranks.sort.by) -``` - -## Arguments - -- ranks.sort.by: - - a character string taking two possible values. These are "ID.orig" and - "vals.orig". These define the order in which the output.ranks.df and - summary.output.ranks.df data frames are presented. This argument is - set by the argument with the same name in ds.ranksSecure. Default - value is "ID.orig". - -## Value - -Creates the data frame identified by the name given by the argument -(\) of the ds.ranksSecure function and writes it to -the serverside. If the argument \ is NULL or -unspecified the output data frame is called "main.ranks.df". The data -frame is ordered according to the argument \ in -ds.ranksSecure. - -## Details - -Severside assign function called by ds.ranksSecure. Creates a data frame -"sR8.df" by cbinding the data frame "blackBox.ranks.df" with the global -ranks and global quantiles vectors in "global.ranks.quantiles.df". -Checks that all components of sR8.df have the correct dimensions and are -consistent in their ordering. If either the number of rows or the order -of the rows are inconsistent with those in "blackBox.ranks.df" an error -message is returned and the processing stops. If sR8.df passes all QA -tests it is written to the serverside as a data frame with its name -identified by the argument \ in ds.ranksSecure. If -that argument is NULL or unspecified the data frame is called -"main.ranks.df". The ranksSecureDS4 function also orders the combined -data frame (\) in one of two ways: if the argument -\ in ds.ranksSecure is set to "ID.orig" the combined -data frame is ordered in the same way as the original V2BR vector; if -the argument \ is set to vals.orig" the combined data -frame is ordered by the magnitude of the values of V2BR (ascending). -Having created the data frame (\) in this manner it -can now be directly cbinded to either the V2BR vector itself or to a -data frame, tibble or matrix containing V2BR (assuming they are also in -the order corresponding to the argument \) and this -combined object can be used as the basis of analysis based on the global -ranks or quantiles including a range of types of non-parametric -analysis. - -## Author - -Paul Burton 9th November, 2021 diff --git a/docs/reference/ranksSecureDS5.html b/docs/reference/ranksSecureDS5.html deleted file mode 100644 index 1bb7537d..00000000 --- a/docs/reference/ranksSecureDS5.html +++ /dev/null @@ -1,121 +0,0 @@ - -Secure ranking of "V2BR" (vector to be ranked) across all sources — ranksSecureDS5 • dsBase - Skip to contents - - -
-
-
- -

Secure ranking of "V2BR" (vector to be ranked) across all sources

- -
ranksSecureDS5.Rd
-
- -
-

Summarises the serverside data frame written by ranksSecureDS4 -which is identified by the name given by the argument (<output.ranks.df>) of -the ds.ranksSecure function to produce a new output data frame containing -only 5 key variables.

-
- -
-

Usage

- 
ranksSecureDS5(output.ranks.df)
-
- -
-

Arguments

- - -
output.ranks.df
-

a character string which specifies an optional name -for the data.frame written to the serverside on each data source that -contains 11 of the key output variables from the ranking procedure pertaining -to that particular data source. This argument is set by the argument with -the same name in ds.ranksSecure.

- -
-
-

Value

-

extracts 5 key vectors from the larger data frame created by -ranksSecureDS4 to produce a summary data frame that is written to the -serverside. It is given a name specified by the argument.

-
-
-

Details

-

Serverside assign function called by clientside function -ds.ranksSecure. Takes the serverside data frame written by ranksSecureDS4 -which is identified by the name given by the argument (<output.ranks.df>) of -the ds.ranksSecure function. This holds 11 vectors including the final -global ranks across all studies and final global quantiles. The data frame -is ordered according to the argument <ranks.sort.by> in ds.ranksSecure. The -ranksSecureDS5 function then extracts 5 key vectors from the larger data -frame to produce a summary data frame that is given a name specified by -the argument (<summary.output.ranks.df>) the ds.ranksSecure function. -This data frame includes the following components: (1) The values of a -sequential ID variable (ID.seq.real.orig) created to lie alongside the -original V2BR vector in the same order as that vector was itself ordered. -These ID values therefore reflect which row in the original data corresponds -to a given row in the output. If the argument <ranks.sort.by> in -ds.ranksSecure is set to "ID.orig" the values of the ID.seq.real.orig vector -in the output data frame simply run sequentially from 1 to N where N is the -number of individuals in the corresponding study. If <ranks.sort.by> is -set to "vals.orig" the values of the ID.seq.real.orig vector will be -determined by the magnitude of the corresponding V2BR value and will -appear to be ordered in a haphazard manner; (2) the original values of V2BR; -(3) the global ranks corresponding to the original values in V2BR, with ties -reflected appropriately; (4) the global quantiles corresponding to the -original values in V2BR, with ties reflected appropriately; (5) a studyid -vector in which all elements take the value n in the nth study.

-
-
-

Author

-

Paul Burton 9th November, 2021

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/ranksSecureDS5.md b/docs/reference/ranksSecureDS5.md deleted file mode 100644 index 7c4d964b..00000000 --- a/docs/reference/ranksSecureDS5.md +++ /dev/null @@ -1,61 +0,0 @@ -# Secure ranking of "V2BR" (vector to be ranked) across all sources - -Summarises the serverside data frame written by ranksSecureDS4 which is -identified by the name given by the argument (\) of -the ds.ranksSecure function to produce a new output data frame -containing only 5 key variables. - -## Usage - -``` r -ranksSecureDS5(output.ranks.df) -``` - -## Arguments - -- output.ranks.df: - - a character string which specifies an optional name for the data.frame - written to the serverside on each data source that contains 11 of the - key output variables from the ranking procedure pertaining to that - particular data source. This argument is set by the argument with the - same name in ds.ranksSecure. - -## Value - -extracts 5 key vectors from the larger data frame created by -ranksSecureDS4 to produce a summary data frame that is written to the -serverside. It is given a name specified by the argument. - -## Details - -Serverside assign function called by clientside function ds.ranksSecure. -Takes the serverside data frame written by ranksSecureDS4 which is -identified by the name given by the argument (\) of -the ds.ranksSecure function. This holds 11 vectors including the final -global ranks across all studies and final global quantiles. The data -frame is ordered according to the argument \ in -ds.ranksSecure. The ranksSecureDS5 function then extracts 5 key vectors -from the larger data frame to produce a summary data frame that is given -a name specified by the argument (\) the -ds.ranksSecure function. This data frame includes the following -components: (1) The values of a sequential ID variable -(ID.seq.real.orig) created to lie alongside the original V2BR vector in -the same order as that vector was itself ordered. These ID values -therefore reflect which row in the original data corresponds to a given -row in the output. If the argument \ in ds.ranksSecure -is set to "ID.orig" the values of the ID.seq.real.orig vector in the -output data frame simply run sequentially from 1 to N where N is the -number of individuals in the corresponding study. If \ -is set to "vals.orig" the values of the ID.seq.real.orig vector will be -determined by the magnitude of the corresponding V2BR value and will -appear to be ordered in a haphazard manner; (2) the original values of -V2BR; (3) the global ranks corresponding to the original values in V2BR, -with ties reflected appropriately; (4) the global quantiles -corresponding to the original values in V2BR, with ties reflected -appropriately; (5) a studyid vector in which all elements take the value -n in the nth study. - -## Author - -Paul Burton 9th November, 2021 diff --git a/docs/reference/rbindDS.html b/docs/reference/rbindDS.html index e2a48678..b4497ccc 100644 --- a/docs/reference/rbindDS.html +++ b/docs/reference/rbindDS.html @@ -1,5 +1,5 @@ -rbindDS called by ds.rbind — rbindDS • dsBaserbindDS called by ds.rbind — rbindDS • dsBasedsBase - 6.3.6.9000 + 7.0.0.9000 - - - - - -
-
-
- -

Recodes the levels of a categorical variables

- -
recodeLevelsDS.Rd
-
- -
-

The functions uses the input factor and generates a new factor -with new levels.

-
- -
-

Usage

- 
recodeLevelsDS(x = NULL, classes = NULL)
-
- -
-

Arguments

- - -
x
-

a factor vector

- - -
classes
-

a character vector the levels of the newt factor vector

- -
-
-

Value

-

a factor vector with the new levels

-
-
-

Author

-

Gaye, A.

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/recodeLevelsDS.md b/docs/reference/recodeLevelsDS.md deleted file mode 100644 index f2735ebd..00000000 --- a/docs/reference/recodeLevelsDS.md +++ /dev/null @@ -1,28 +0,0 @@ -# Recodes the levels of a categorical variables - -The functions uses the input factor and generates a new factor with new -levels. - -## Usage - -``` r -recodeLevelsDS(x = NULL, classes = NULL) -``` - -## Arguments - -- x: - - a factor vector - -- classes: - - a character vector the levels of the newt factor vector - -## Value - -a factor vector with the new levels - -## Author - -Gaye, A. diff --git a/docs/reference/recodeValuesDS.html b/docs/reference/recodeValuesDS.html index 540e3a81..42510ae4 100644 --- a/docs/reference/recodeValuesDS.html +++ b/docs/reference/recodeValuesDS.html @@ -1,5 +1,5 @@ -recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS • dsBaserecodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS • dsBase Skip to contents @@ -9,7 +9,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 - - dsBase - 6.3.3 - - - - - - - - - -
-
-
-

Sets the privacy level

- - -
- -
-

This is an internal function that set the number of observation -that are allowed in any table or vector. The function gets the value from the data repository -and if no value was set it uses the default value 5.

-
- -
- 
setFilterDS(x = getOption("datashield.privacyLevel", default = 5))
-
- -
-

Arguments

- - -
x
-

a dummy argument

- -
-
-

Value

-

an integer between 1 and 5

-
-
-

Details

-

The function is called by server side functios

-
-
-

Author

-

Gaye, A.

-
- -
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.1.3.

-
- -
- - - - - - - - diff --git a/docs/reference/setSeedDS.html b/docs/reference/setSeedDS.html index 1d0b9286..56396c10 100644 --- a/docs/reference/setSeedDS.html +++ b/docs/reference/setSeedDS.html @@ -1,5 +1,5 @@ -setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS • dsBasesetSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS • dsBase Skip to contents @@ -9,7 +9,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 - - - - - -
-
-
- -

Breaks down a dataframe or a factor into its sub-classes

- -
subsetByClassDS.Rd
-
- -
-

The function takes a categorical vector or dataframe as input and generates subset(s) -vectors or dataframes for each category. Subsets are considered invalid if they hold between 1 and -4 observations.

-
- -
-

Usage

- 
subsetByClassDS(data = NULL, variables = NULL)
-
- -
-

Arguments

- - -
data
-

a string character, the name of the dataframe or the factor vector

- - -
variables
-

a vector of string characters, the names of the the variables to subset on.

- -
-
-

Value

-

a list which contains the subsetted datasets

-
-
-

Details

-

If the input data object is a dataframe it is possible to specify the variables -to subset on. If a subset is not 'valid' all its the values are reported as missing (i.e. NA), -the name of the subsets is labelled as '_INVALID'. If no variables are specified to subset on, -the dataframe will be subset on each of its factor variables. -And if none of the columns holds a factor variable a message is issued as output. A message is also -issued as output if the input vector is not of type factor.

-
-
-

Author

-

Gaye, A.

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/subsetByClassDS.md b/docs/reference/subsetByClassDS.md deleted file mode 100644 index b4ee99c9..00000000 --- a/docs/reference/subsetByClassDS.md +++ /dev/null @@ -1,41 +0,0 @@ -# Breaks down a dataframe or a factor into its sub-classes - -The function takes a categorical vector or dataframe as input and -generates subset(s) vectors or dataframes for each category. Subsets are -considered invalid if they hold between 1 and 4 observations. - -## Usage - -``` r -subsetByClassDS(data = NULL, variables = NULL) -``` - -## Arguments - -- data: - - a string character, the name of the dataframe or the factor vector - -- variables: - - a vector of string characters, the names of the the variables to - subset on. - -## Value - -a list which contains the subsetted datasets - -## Details - -If the input data object is a dataframe it is possible to specify the -variables to subset on. If a subset is not 'valid' all its the values -are reported as missing (i.e. NA), the name of the subsets is labelled -as '\_INVALID'. If no variables are specified to subset on, the -dataframe will be subset on each of its factor variables. And if none of -the columns holds a factor variable a message is issued as output. A -message is also issued as output if the input vector is not of type -factor. - -## Author - -Gaye, A. diff --git a/docs/reference/subsetByClassHelper1.html b/docs/reference/subsetByClassHelper1.html deleted file mode 100644 index 5f03b8e5..00000000 --- a/docs/reference/subsetByClassHelper1.html +++ /dev/null @@ -1,102 +0,0 @@ - -generates subsets vectors from a factor vector — subsetByClassHelper1 • dsBase - - -
-
- - - -
-
-
-

generates subsets vectors from a factor vector

- - -
- -
-

This is an internal function called by the function 'subsetByClassDS'.

-
- -
- 
subsetByClassHelper1(xvect = NULL, xname = NULL, filter = NULL)
-
- -
-

Arguments

- - -
xvect
-

a vector of type factor.

- - -
xname
-

the name of the vector.

- - -
filter
-

the minimum number observation (i.e. rows) that are allowed.

- -
-
-

Value

-

a list which contains the subsets.

-
-
-

Details

-

The function generates subsets if the input of 'subsetByClassDS' is a factor vector.

-
-
-

Author

-

Gaye, A.

-
- -
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.1.3.

-
- -
- - - - - - - - diff --git a/docs/reference/subsetByClassHelper2.html b/docs/reference/subsetByClassHelper2.html deleted file mode 100644 index 0363307e..00000000 --- a/docs/reference/subsetByClassHelper2.html +++ /dev/null @@ -1,107 +0,0 @@ - -generates subset tables from a data frame — subsetByClassHelper2 • dsBase - - -
-
- - - -
-
-
-

generates subset tables from a data frame

- - -
- -
-

This is an internal function called by the function 'subsetByClassDS'

-
- -
- 
subsetByClassHelper2(df = NULL, iter = NULL, filter = NULL)
-
- -
-

Arguments

- - -
df
-

a data frame.

- - -
iter
-

the indices of columns to loop trough.

- - -
filter
-

the minimum number of observations (i.e. rows) that are allowed.

- -
-
-

Value

-

a list which contains the subsets, their names and an integer that indicates how many columns were -not factors.

-
-
-

Details

-

The function generates subsets if the input of 'subsetByClassDS' is a data frame -and if the number variables(columns) to subset by are greater than 1; i.e. this -function is called if the user specified more than one variable or no variable to subset by -(if no variables are specified the function 'subsetByClassDS' produces a subset for each category -in each variable).

-
-
-

Author

-

Gaye, A.

-
- -
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.1.3.

-
- -
- - - - - - - - diff --git a/docs/reference/subsetByClassHelper3.html b/docs/reference/subsetByClassHelper3.html deleted file mode 100644 index 46aea1ab..00000000 --- a/docs/reference/subsetByClassHelper3.html +++ /dev/null @@ -1,105 +0,0 @@ - -generates subset tables from a data frame — subsetByClassHelper3 • dsBase - - -
-
- - - -
-
-
-

generates subset tables from a data frame

- - -
- -
-

This is an internal function called by the function 'subsetByClassDS'

-
- -
- 
subsetByClassHelper3(df = NULL, indx1 = NULL, filter = NULL)
-
- -
-

Arguments

- - -
df
-

a data frame.

- - -
indx1
-

the column index of the variable specified by the user.

- - -
filter
-

the minimum number of observations (i.e. rows) that are allowed.

- -
-
-

Value

-

a list which contains the subsets, their names and an integer that indicates if -the variable specified by user is a factor.

-
-
-

Details

-

The function generates subsets if the input of 'subsetByClassDS' is a data frame -and if the number of variables (columns) to subset by is 1; i.e. this -function is called if the user specified one variable to subset by.

-
-
-

Author

-

Gaye, A.

-
- -
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.1.3.

-
- -
- - - - - - - - diff --git a/docs/reference/subsetDS.html b/docs/reference/subsetDS.html deleted file mode 100644 index 2d7865a8..00000000 --- a/docs/reference/subsetDS.html +++ /dev/null @@ -1,133 +0,0 @@ - -Generates a valid subset of a table or a vector — subsetDS • dsBase - Skip to contents - - -
-
-
- -

Generates a valid subset of a table or a vector

- -
subsetDS.Rd
-
- -
-

The function uses the R classical subsetting with squared brackets '[]' and allows also to -subset using a logical operator and a threshold. The object to subset from must be a vector (factor, numeric -or character) or a table (data.frame or matrix).

-
- -
-

Usage

- 
subsetDS(
-  dt = NULL,
-  complt = NULL,
-  rs = NULL,
-  cs = NULL,
-  lg = NULL,
-  th = NULL,
-  varname = NULL
-)
-
- -
-

Arguments

- - -
dt
-

a string character, the name of the dataframe or the factor vector and the range of the subset.

- - -
complt
-

a boolean that tells if the subset to subset should include only complete cases

- - -
rs
-

a vector of two integers that give the range of rows de extract.

- - -
cs
-

a vector of two integers or one or more characters; the indices of the columns to extract or the names of the columns (i.e. -names of the variables to extract).

- - -
lg
-

a character, the logical parameter to use if the user wishes to subset a vector using a logical -operator. This parameter is ignored if the input data is not a vector.

- - -
th
-

a numeric, the threshold to use in conjunction with the logical parameter. This parameter is ignored -if the input data is not a vector.

- - -
varname
-

a character, if the input data is a table, if this parameter is provided along with the 'logical' and 'threshold' -parameters, a subtable is based the threshold applied to the specified variable. This parameter is however ignored if the parameter -'rows' and/or 'cols' are provided.

- -
-
-

Value

-

a subset of the vector, matrix or dataframe as specified is stored on the server side

-
-
-

Details

-

If the input data is a table: The user specifies the rows and/or columns to include in the subset if the input -object is a table; the columns can be referred to by their names. The name of a vector (i.e. a variable) can also be provided -with a logical operator and a threshold (see example 3). -If the input data is a vector: when the parameters 'rows', 'logical' and 'threshold' are all provided the last two are ignored ( -'rows' has precedence over the other two parameters then). -If the requested subset is not valid (i.e. contains less than the allowed -number of observations), the subset is not generated, rather a table or a vector of missing values is generated to allow -for any subsequent process using the output of the function to proceed after informing the user via a message.

-
-
-

Author

-

Gaye, A.

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/subsetDS.md b/docs/reference/subsetDS.md deleted file mode 100644 index 11059bdc..00000000 --- a/docs/reference/subsetDS.md +++ /dev/null @@ -1,86 +0,0 @@ -# Generates a valid subset of a table or a vector - -The function uses the R classical subsetting with squared brackets -'\[\]' and allows also to subset using a logical operator and a -threshold. The object to subset from must be a vector (factor, numeric -or character) or a table (data.frame or matrix). - -## Usage - -``` r -subsetDS( - dt = NULL, - complt = NULL, - rs = NULL, - cs = NULL, - lg = NULL, - th = NULL, - varname = NULL -) -``` - -## Arguments - -- dt: - - a string character, the name of the dataframe or the factor vector and - the range of the subset. - -- complt: - - a boolean that tells if the subset to subset should include only - complete cases - -- rs: - - a vector of two integers that give the range of rows de extract. - -- cs: - - a vector of two integers or one or more characters; the indices of the - columns to extract or the names of the columns (i.e. names of the - variables to extract). - -- lg: - - a character, the logical parameter to use if the user wishes to subset - a vector using a logical operator. This parameter is ignored if the - input data is not a vector. - -- th: - - a numeric, the threshold to use in conjunction with the logical - parameter. This parameter is ignored if the input data is not a - vector. - -- varname: - - a character, if the input data is a table, if this parameter is - provided along with the 'logical' and 'threshold' parameters, a - subtable is based the threshold applied to the specified variable. - This parameter is however ignored if the parameter 'rows' and/or - 'cols' are provided. - -## Value - -a subset of the vector, matrix or dataframe as specified is stored on -the server side - -## Details - -If the input data is a table: The user specifies the rows and/or columns -to include in the subset if the input object is a table; the columns can -be referred to by their names. The name of a vector (i.e. a variable) -can also be provided with a logical operator and a threshold (see -example 3). If the input data is a vector: when the parameters 'rows', -'logical' and 'threshold' are all provided the last two are ignored ( -'rows' has precedence over the other two parameters then). If the -requested subset is not valid (i.e. contains less than the allowed -number of observations), the subset is not generated, rather a table or -a vector of missing values is generated to allow for any subsequent -process using the output of the function to proceed after informing the -user via a message. - -## Author - -Gaye, A. diff --git a/docs/reference/table1DDS.html b/docs/reference/table1DDS.html index 9bedc43b..cbdf5cce 100644 --- a/docs/reference/table1DDS.html +++ b/docs/reference/table1DDS.html @@ -1,5 +1,5 @@ -Creates 1-dimensional contingency tables — table1DDS • dsBaseCreates 1-dimensional contingency tables — table1DDS • dsBase Skip to contents @@ -9,7 +9,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 - - - - - -
-
-
- -

table2DDS (aggregate function) called by ds.table2D

- -
table2DDS.Rd
-
- -
-

This function generates a 2-dimensional contingency table where potentially disclosive cells -(based on a set threshold) are replaced by a missing value ('NA').

-
- -
-

Usage

- 
table2DDS(xvect, yvect)
-
- -
-

Arguments

- - -
xvect
-

a numerical vector with discrete values - usually a factor.

- - -
yvect
-

a numerical vector with discrete values - usually a factor.

- -
-
-

Value

-

a list which contains two elements: 'table', the 2-dimensional table and 'message' a message which -informs about the validity of the table.

-
-
-

Details

-

It generates 2-dimensional contingency tables where valid (non-disclosive) tables are defined -as those where none of their cells have counts between 1 and the set threshold "nfilter.tab". When the output table -is invalid all cells except the total counts are replaced by missing values. Only the total counts are visible -on the table returned to the client side. A message is also returned with the 2-dimensional table; the message -says "invalid table - invalid counts present" if the table is invalid and 'valid table' otherwise.

-
-
-

Author

-

Amadou Gaye, Paul Burton, Demetris Avraam for DataSHIELD Development Team

-
- -
- - -
-

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

-
- -
-

Site built with pkgdown 2.2.0.

-
- -
- - - - - - - diff --git a/docs/reference/table2DDS.md b/docs/reference/table2DDS.md deleted file mode 100644 index 655e2396..00000000 --- a/docs/reference/table2DDS.md +++ /dev/null @@ -1,42 +0,0 @@ -# table2DDS (aggregate function) called by ds.table2D - -This function generates a 2-dimensional contingency table where -potentially disclosive cells (based on a set threshold) are replaced by -a missing value ('NA'). - -## Usage - -``` r -table2DDS(xvect, yvect) -``` - -## Arguments - -- xvect: - - a numerical vector with discrete values - usually a factor. - -- yvect: - - a numerical vector with discrete values - usually a factor. - -## Value - -a list which contains two elements: 'table', the 2-dimensional table and -'message' a message which informs about the validity of the table. - -## Details - -It generates 2-dimensional contingency tables where valid -(non-disclosive) tables are defined as those where none of their cells -have counts between 1 and the set threshold "nfilter.tab". When the -output table is invalid all cells except the total counts are replaced -by missing values. Only the total counts are visible on the table -returned to the client side. A message is also returned with the -2-dimensional table; the message says "invalid table - invalid counts -present" if the table is invalid and 'valid table' otherwise. - -## Author - -Amadou Gaye, Paul Burton, Demetris Avraam for DataSHIELD Development -Team diff --git a/docs/reference/tableDS2.html b/docs/reference/table2DS.html similarity index 76% rename from docs/reference/tableDS2.html rename to docs/reference/table2DS.html index 62a1f762..e29b93a0 100644 --- a/docs/reference/tableDS2.html +++ b/docs/reference/table2DS.html @@ -1,5 +1,5 @@ -tableDS is the second of two serverside aggregate functions called by ds.table — tableDS2 • dsBasetableDS is the second of two serverside aggregate functions called by ds.table — table2DS • dsBase Skip to contents @@ -9,7 +9,7 @@ dsBase - 6.3.6.9000 + 7.0.0.9000 + + + + + +
+
+
+ +

booleDS

+ +
booleDS.Rd
+
+ +
+

Converts the individual elements of a vector or other object into +Boolean indicators.

+
+ +
+

Usage

+ 
booleDS(
+  V1.name = NULL,
+  V2.name = NULL,
+  Boolean.operator.n = NULL,
+  na.assign.text,
+  numeric.output = TRUE
+)
+
+ +
+

Arguments

+ + +
V1.name
+

A character string specifying the name of the vector to which the +Boolean operator is to be applied

+ + +
V2.name
+

A character string specifying the name of the vector or scalar to +which <V1> is to be compared.

+ + +
Boolean.operator.n
+

An integer value (1 to 6) providing a numeric coding for +the character string +specifying one of six possible Boolean operators: '==', '!=', '>', '>=','<', '<=' +that could legally be passed +from client to server via DataSHIELD parser

+ + +
na.assign.text
+

A character string taking values 'NA', '1' or '0'. If 'NA' +then any NA values in the +input vector remain as NAs in the output vector. If '1' or '0' NA values in the +input vector are all converted to 1 or 0 respectively.

+ + +
numeric.output
+

a TRUE/FALSE indicator defaulting to TRUE determining whether +the final output variable +should be of class numeric (1/0) or class logical (TRUE/FALSE).

+ +
+
+

Value

+

the levels of the input variable.

+
+
+

Details

+

The function converts the input vector into Boolean indicators.

+
+
+

Author

+

DataSHIELD Development Team

+

Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands

+
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.1.

+
+ +
+ + + + + + + diff --git a/docs/reference/booleDS.md b/docs/reference/booleDS.md new file mode 100644 index 00000000..39c81779 --- /dev/null +++ b/docs/reference/booleDS.md @@ -0,0 +1,62 @@ +# booleDS + +Converts the individual elements of a vector or other object into +Boolean indicators. + +## Usage + +``` r +booleDS( + V1.name = NULL, + V2.name = NULL, + Boolean.operator.n = NULL, + na.assign.text, + numeric.output = TRUE +) +``` + +## Arguments + +- V1.name: + + A character string specifying the name of the vector to which the + Boolean operator is to be applied + +- V2.name: + + A character string specifying the name of the vector or scalar to + which \ is to be compared. + +- Boolean.operator.n: + + An integer value (1 to 6) providing a numeric coding for the character + string specifying one of six possible Boolean operators: '==', '!=', + '\>', '\>=','\<', '\<=' that could legally be passed from client to + server via DataSHIELD parser + +- na.assign.text: + + A character string taking values 'NA', '1' or '0'. If 'NA' then any NA + values in the input vector remain as NAs in the output vector. If '1' + or '0' NA values in the input vector are all converted to 1 or 0 + respectively. + +- numeric.output: + + a TRUE/FALSE indicator defaulting to TRUE determining whether the + final output variable should be of class numeric (1/0) or class + logical (TRUE/FALSE). + +## Value + +the levels of the input variable. + +## Details + +The function converts the input vector into Boolean indicators. + +## Author + +DataSHIELD Development Team + +Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands diff --git a/docs/reference/index.html b/docs/reference/index.html index 3ddd4ba9..3c540198 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -41,13 +41,6 @@

All functionsBooleDS() - - -
BooleDS
- -
- absDS()
@@ -130,6 +123,13 @@

All functionsbooleDS() + + +
booleDS
+
boxPlotGGDS() diff --git a/docs/reference/index.md b/docs/reference/index.md index 7f4f37a2..7e60db06 100644 --- a/docs/reference/index.md +++ b/docs/reference/index.md @@ -2,8 +2,6 @@ ## All functions -- [`BooleDS()`](BooleDS.md) : BooleDS - - [`absDS()`](absDS.md) : Computes the absolute values of the input variable @@ -38,6 +36,8 @@ - [`aucDS()`](aucDS.md) : aucDS an aggregate function called by ds.auc +- [`booleDS()`](booleDS.md) : booleDS + - [`boxPlotGGDS()`](boxPlotGGDS.md) : Create the identity stats and necessary data to draw a plot on the client diff --git a/docs/search.json b/docs/search.json index 7145b9d9..f33cae8f 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Paul Burton. Author. Rebecca Wilson. Author. Olly Butters. Author. Patricia Ryser-Welch. Author. Alex Westerberg. Author. Leire Abarrategui. Author. Roberto Villegas-Diaz. Author. Demetris Avraam. Author. Yannick Marcon. Author. Tom Bishop. Author. Amadou Gaye. Author. Xavier Escribà-Montagut. Author. Stuart Wheater. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg , Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye , Escribà-Montagut X, Wheater S (????). dsBase: 'DataSHIELD' Server Side Base Functions. R package version 7.0.0.9000. Gaye , Marcon Y, Isaeva J, LaFlamme P, Turner , Jones E, Minion J, Boyd , Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir , Doiron D, Giepmans L, Wallace S, Budin-Ljøsne , Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry , Peters , Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier , Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking analysis data, data analysis.” International Journal Epidemiology, 43(6), 1929–1944. doi:10.1093/ije/dyu188. Wilson R, Butters O, Avraam D, Baker J, Tedds J, Turner , Murtagh M, Burton P (2017). “DataSHIELD – New Directions Dimensions.” Data Science Journal, 16(21), 1–21. doi:10.5334/dsj-2017-021. Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan , Murtagh M, Nestor M, Nybo Andersen , Parker S, Pinot de Moira , Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1–21. doi:10.1093/bioadv/vbaf046.","code":"@Manual{, title = {dsBase: 'DataSHIELD' Server Side Base Functions}, author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater}, note = {R package version 7.0.0.9000}, } @Article{, title = {{DataSHIELD: taking the analysis to the data, not the data to the analysis}}, author = {Amadou Gaye and Yannick Marcon and Julia Isaeva and Philippe {LaFlamme} and Andrew Turner and Elinor M Jones and Joel Minion and Andrew W Boyd and Christopher J Newby and Marja-Liisa Nuotio and Rebecca Wilson and Oliver Butters and Barnaby Murtagh and Ipek Demir and Dany Doiron and Lisette Giepmans and Susan E Wallace and Isabelle Budin-Lj{\\o}sne and Carsten O. Schmidt and Paolo Boffetta and Mathieu Boniol and Maria Bota and Kim W Carter and Nick {deKlerk} and Chris Dibben and Richard W Francis and Tero Hiekkalinna and Kristian Hveem and Kirsti Kval{\\o}y and Sean Millar and Ivan J Perry and Annette Peters and Catherine M Phillips and Frank Popham and Gillian Raab and Eva Reischl and Nuala Sheehan and Melanie Waldenberger and Markus Perola and Edwin {{van den Heuvel}} and John Macleod and Bartha M Knoppers and Ronald P Stolk and Isabel Fortier and Jennifer R Harris and Bruce H R Woffenbuttel and Madeleine J Murtagh and Vincent Ferretti and Paul R Burton}, journal = {International Journal of Epidemiology}, year = {2014}, volume = {43}, number = {6}, pages = {1929--1944}, doi = {10.1093/ije/dyu188}, } @Article{, title = {{DataSHIELD – New Directions and Dimensions}}, author = {Rebecca C. Wilson and Oliver W. Butters and Demetris Avraam and James Baker and Jonathan A. Tedds and Andrew Turner and Madeleine Murtagh and Paul R. Burton}, journal = {Data Science Journal}, year = {2017}, volume = {16}, number = {21}, pages = {1--21}, doi = {10.5334/dsj-2017-021}, } @Article{, title = {{DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform}}, author = {Demetris Avraam and Rebecca C Wilson and Noemi {{Aguirre Chan}} and Soumya Banerjee and Tom R P Bishop and Olly Butters and Tim Cadman and Luise Cederkvist and Liesbeth Duijts and Xavier {{Escrib{\\a`a} Montagut}} and Hugh Garner and Gon{\\c c}alo {Gon{\\c c}alves} and Juan R Gonz{\\a'a}lez and Sido Haakma and Mette Hartlev and Jan Hasenauer and Manuel Huth and Eleanor Hyde and Vincent W V Jaddoe and Yannick Marcon and Michaela Th Mayrhofer and Fruzsina Molnar-Gabor and Andrei Scott Morgan and Madeleine Murtagh and Marc Nestor and Anne-Marie {{Nybo Andersen}} and Simon Parker and Angela {{Pinot de Moira}} and Florian Schwarz and Katrine Strandberg-Larsen and Morris A Swertz and Marieke Welten and Stuart Wheater and Paul R Burton}, journal = {Bioinformatics Advances}, year = {2024}, volume = {5}, number = {1}, pages = {1--21}, doi = {10.1093/bioadv/vbaf046}, editor = {Thomas Lengauer}, publisher = {Oxford University Press (OUP)}, }"},{"path":[]},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"DataSHIELD Server Side Base Functions","text":"can install released version dsBase CRAN : development version GitHub : full list development branches, checkout https://github.com/datashield/dsBase/branches","code":"install.packages(\"dsBase\") install.packages(\"remotes\") remotes::install_github(\"datashield/dsBase\", \"\") # Install v6.3.6 with the following remotes::install_github(\"datashield/dsBase\", \"6.3.6\")"},{"path":"/index.html","id":"about","dir":"","previous_headings":"","what":"About","title":"DataSHIELD Server Side Base Functions","text":"DataSHIELD software package allows non-disclosive federated analysis sensitive data. website (https://www.datashield.org) depth descriptions , works install . key point highlight DataSHIELD client-server infrastructure, dsBase package (https://github.com/datashield/dsBase) needs used conjunction dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying use one without makes sense. Detailed instructions install DataSHIELD https://wiki.datashield.org/. code organised :","code":""},{"path":"/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"DataSHIELD Server Side Base Functions","text":"[1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg , Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye , Escribà Montagut X, Wheater S (2025). dsBase: ‘DataSHIELD’ Server Side Base Functions. R package version 6.3.4. https://doi.org/10.32614/CRAN.package.dsBase. [2] Gaye , Marcon Y, Isaeva J, LaFlamme P, Turner , Jones E, Minion J, Boyd , Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir , Doiron D, Giepmans L, Wallace S, Budin-Ljøsne , Oliver Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry , Peters , Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier , Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking analysis data, data analysis.” International Journal Epidemiology, 43(6), 1929-1944. https://doi.org/10.1093/ije/dyu188. [3] Wilson R, W. Butters O, Avraam D, Baker J, Tedds J, Turner , Murtagh M, R. Burton P (2017). “DataSHIELD – New Directions Dimensions.” Data Science Journal, 16(21), 1-21. https://doi.org/10.5334/dsj-2017-021. [4] Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan , Murtagh M, Nestor M, Nybo Andersen , Parker S, Pinot de Moira , Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1-21. https://doi.org/10.1093/bioadv/vbaf046. Note: Apple Mx architecture users, please aware numerical limitations platform, leads unexpected results using base R packages, like stats​. x <- c(0, 3, 7) 1 - cor(x, x)​ result value zero. Also See: details see https://cran.r-project.org/doc/FAQ/R-FAQ.html#-doesn_0027t-R-think--numbers--equal_003f bug report: https://bugs.r-project.org/show_bug.cgi?id=18941","code":""},{"path":"/reference/BooleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"BooleDS — BooleDS","title":"BooleDS — BooleDS","text":"Converts individual elements vector object Boolean indicators.","code":""},{"path":"/reference/BooleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BooleDS — BooleDS","text":"","code":"BooleDS( V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, na.assign.text, numeric.output = TRUE )"},{"path":"/reference/BooleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BooleDS — BooleDS","text":"V1.name character string specifying name vector Boolean operator applied V2.name character string specifying name vector scalar compared. Boolean.operator.n integer value (1 6) providing numeric coding character string specifying one six possible Boolean operators: '==', '!=', '>', '>=','<', '<=' legally passed client server via DataSHIELD parser na.assign.text character string taking values 'NA', '1' '0'. 'NA' NA values input vector remain NAs output vector. '1' '0' NA values input vector converted 1 0 respectively. numeric.output TRUE/FALSE indicator defaulting TRUE determining whether final output variable class numeric (1/0) class logical (TRUE/FALSE).","code":""},{"path":"/reference/BooleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"BooleDS — BooleDS","text":"levels input variable.","code":""},{"path":"/reference/BooleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"BooleDS — BooleDS","text":"function converts input vector Boolean indicators.","code":""},{"path":"/reference/BooleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"BooleDS — BooleDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/absDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the absolute values of the input variable — absDS","title":"Computes the absolute values of the input variable — absDS","text":"function similar R function abs.","code":""},{"path":"/reference/absDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the absolute values of the input variable — absDS","text":"","code":"absDS(x)"},{"path":"/reference/absDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the absolute values of the input variable — absDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/absDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the absolute values of the input variable — absDS","text":"object specified newobj argument ds.abs (default name abs.newobj) written serverside. output object class numeric integer.","code":""},{"path":"/reference/absDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the absolute values of the input variable — absDS","text":"function computes absolute values input numeric integer vector.","code":""},{"path":"/reference/absDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the absolute values of the input variable — absDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asCharacterDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class character — asCharacterDS","title":"Coerces an R object into class character — asCharacterDS","text":"function based native R function .character","code":""},{"path":"/reference/asCharacterDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class character — asCharacterDS","text":"","code":"asCharacterDS(x.name)"},{"path":"/reference/asCharacterDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class character — asCharacterDS","text":"x.name name input object coerced class character. Must specified inverted commas. argument usually specified directly x.name argument clientside function ds.asCharacter","code":""},{"path":"/reference/asCharacterDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class character — asCharacterDS","text":"object specified newobj argument (default name \"ascharacter.newobj\") written serverside. details see help clientside function ds.asCharacter","code":""},{"path":"/reference/asCharacterDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class character — asCharacterDS","text":"See help function .character native R","code":""},{"path":"/reference/asCharacterDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class character — asCharacterDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asDataMatrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"Coerces R object matrix maintaining original class columns data.frames.","code":""},{"path":"/reference/asDataMatrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"","code":"asDataMatrixDS(x.name)"},{"path":"/reference/asDataMatrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"x.name name input object coerced class data.matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asDataMatrix","code":""},{"path":"/reference/asDataMatrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"object specified argument (default name \"asdatamatrix.newobj\") written serverside. details see help clientside function ds.asDataMatrix","code":""},{"path":"/reference/asDataMatrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"assign function based native R function data.matrix applied data.frame, native R function .matrix converts columns character class. contrast, applied data.frame native R function data.matrix converts data.frame matrix maintains data columns original class","code":""},{"path":"/reference/asDataMatrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactor1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Determines the levels of the input variable in each single study — asFactor1DS","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"function aggregate DataSHIELD function returns levels input variable single study client-side function.","code":""},{"path":"/reference/asFactor1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"","code":"asFactor1DS(input.var.name = NULL)"},{"path":"/reference/asFactor1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"input.var.name name variable converted factor.","code":""},{"path":"/reference/asFactor1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"levels input variable.","code":""},{"path":"/reference/asFactor1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"function encodes input vector factor returns levels ascending order levels numerical alphabetical order levels type character.","code":""},{"path":"/reference/asFactor1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactor2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts a numeric vector into a factor — asFactor2DS","title":"Converts a numeric vector into a factor — asFactor2DS","text":"function assign DataSHIELD function converts numeric vector factor type presented vector matrix dummy variables.","code":""},{"path":"/reference/asFactor2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts a numeric vector into a factor — asFactor2DS","text":"","code":"asFactor2DS( input.var.name = NULL, all.unique.levels.transmit = NULL, fixed.dummy.vars = NULL, baseline.level = NULL )"},{"path":"/reference/asFactor2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts a numeric vector into a factor — asFactor2DS","text":"input.var.name name variable converted factor. .unique.levels.transmit levels variable transmitted . fixed.dummy.vars boolean determines whether new object represented vector matrix dummy variables indicating factor level data point. argument set FALSE (default) input variable converted factor assigned vector. set TRUE input variable converted factor assigned matrix dummy variables. baseline.level number indicating baseline level used creation matrix dummy variables.","code":""},{"path":"/reference/asFactor2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts a numeric vector into a factor — asFactor2DS","text":"object class factor","code":""},{"path":"/reference/asFactor2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Converts a numeric vector into a factor — asFactor2DS","text":"functions converts input variable factor presented vector fixed.dummy.vars set FALSE matrix dummy variables fixed.dummy.vars set TRUE (see help file ds.asFactor.b details).","code":""},{"path":"/reference/asFactor2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts a numeric vector into a factor — asFactor2DS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactorSimpleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts a numeric vector into a factor — asFactorSimpleDS","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"function assign DataSHIELD function coerces numeric character vector factor","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"","code":"asFactorSimpleDS(input.var.name = NULL)"},{"path":"/reference/asFactorSimpleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"input.var.name name variable converted factor.","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"object class factor","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"functions converts input variable factor. Unlike ds.asFactor serverside functions, ds.asFactorSimple coerce class variable factor study. check enforce consistency factor levels across sources allow force arbitrary set levels unless levels actually exist sources. addition, allow create array binary dummy variables equivalent factor. need things use ds.asFactor function.","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asIntegerDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class integer — asIntegerDS","title":"Coerces an R object into class integer — asIntegerDS","text":"function based native R function .integer.","code":""},{"path":"/reference/asIntegerDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class integer — asIntegerDS","text":"","code":"asIntegerDS(x.name)"},{"path":"/reference/asIntegerDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class integer — asIntegerDS","text":"x.name name input object coerced class integer. Must specified inverted commas. argument usually specified directly argument clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class integer — asIntegerDS","text":"object specified argument (default name \"asinteger.newobj\") written serverside. details see help clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class integer — asIntegerDS","text":"See help function .integer native R, details section help file clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class integer — asIntegerDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asListDS.html","id":null,"dir":"Reference","previous_headings":"","what":"asListDS a serverside assign function called by ds.asList — asListDS","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"Coerces R object list","code":""},{"path":"/reference/asListDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"","code":"asListDS(x.name)"},{"path":"/reference/asListDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"x.name name input object coerced class data.matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asList","code":""},{"path":"/reference/asListDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"input object coerced list, ds.asList writes serverside. way .list coerces objects list depends class object","code":""},{"path":"/reference/asListDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"assign function based native R function .list additional information can found help .list","code":""},{"path":"/reference/asListDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asLogicalDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class logical — asLogicalDS","title":"Coerces an R object into class logical — asLogicalDS","text":"function based native R function .logical","code":""},{"path":"/reference/asLogicalDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class logical — asLogicalDS","text":"","code":"asLogicalDS(x.name)"},{"path":"/reference/asLogicalDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class logical — asLogicalDS","text":"x.name name input object coerced class logical. Must specified inverted commas. argument usually specified directly argument clientside function ds.asLogical","code":""},{"path":"/reference/asLogicalDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class logical — asLogicalDS","text":"object specified argument (default name .logic) written serverside. details see help clientside function ds.asLogical","code":""},{"path":"/reference/asLogicalDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class logical — asLogicalDS","text":"See help function .logical native R","code":""},{"path":"/reference/asLogicalDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class logical — asLogicalDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asMatrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into a matrix — asMatrixDS","title":"Coerces an R object into a matrix — asMatrixDS","text":"function based native R function .matrix","code":""},{"path":"/reference/asMatrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into a matrix — asMatrixDS","text":"","code":"asMatrixDS(x.name)"},{"path":"/reference/asMatrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into a matrix — asMatrixDS","text":"x.name name input object coerced class matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asMatrix","code":""},{"path":"/reference/asMatrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into a matrix — asMatrixDS","text":"object specified argument (default name .mat) written serverside. details see help clientside function ds.asMatrix","code":""},{"path":"/reference/asMatrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into a matrix — asMatrixDS","text":"See help function .matrix native R","code":""},{"path":"/reference/asMatrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into a matrix — asMatrixDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asNumericDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class numeric — asNumericDS","title":"Coerces an R object into class numeric — asNumericDS","text":"function based native R function .numeric.","code":""},{"path":"/reference/asNumericDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class numeric — asNumericDS","text":"","code":"asNumericDS(x.name)"},{"path":"/reference/asNumericDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class numeric — asNumericDS","text":"x.name name input object coerced class numeric. Must specified inverted commas. argument usually specified directly argument clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class numeric — asNumericDS","text":"object specified argument (default name .num) written serverside. details see help clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class numeric — asNumericDS","text":"See help function .numeric native R, details section help file clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class numeric — asNumericDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/aucDS.html","id":null,"dir":"Reference","previous_headings":"","what":"aucDS an aggregate function called by ds.auc — aucDS","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"function calculates C-statistic AUC logistic regression models.","code":""},{"path":"/reference/aucDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"","code":"aucDS(pred = pred, y = y)"},{"path":"/reference/aucDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"pred name vector predicted values y name outcome variable. Note variable include complete cases used regression model.","code":""},{"path":"/reference/aucDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"returns AUC standard error","code":""},{"path":"/reference/aucDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"AUC determines discriminative ability model.","code":""},{"path":"/reference/aucDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGGDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"order create non disclosive box plot, data passed client purely geometrical aspects plot, ggplot object contains data inside, graphical parameters passed. three different cases depending grouping variables. outliers also removed graphical parameters.","code":""},{"path":"/reference/boxPlotGGDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"","code":"boxPlotGGDS(data_table.name, group = NULL, group2 = NULL)"},{"path":"/reference/boxPlotGGDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"data_table.name character Name server-side data frame holds information plotted, arranged : Column 'x': Names X axis boxplot, aka variables plot Column 'value': Values variable (raw data columns rbinded) Column 'group': (Optional) Values grouping variable Column 'group2': (Optional) Values second grouping variable group character (default NULL) Name first grouping variable. group2 character (default NULL) Name second grouping variable.","code":""},{"path":"/reference/boxPlotGGDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"list : -data frame Geometrical parameters (identity stats ggplot) -character Type plot (single_group, double_group no_group)","code":""},{"path":"/reference/boxPlotGGDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"Arrange data frame pass boxplot function","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"","code":"boxPlotGG_data_TreatmentDS(table.name, variables, group = NULL, group2 = NULL)"},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"table.name character Name server-side data frame holds information plotted later variables character vector Name column(s) data frame include boxplot group character (default NULL) Name first grouping variable. group2 character (default NULL) Name second grouping variable.","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"data frame following structure: Column 'x': Names X axis boxplot, aka variables plot Column 'value': Values variable (raw data columns rbinded) Column 'group': (Optional) Values grouping variable Column 'group2': (Optional) Values second grouping variable","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"Arrange vector pass boxplot function","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"","code":"boxPlotGG_data_Treatment_numericDS(vector.name)"},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"vector.name character Name server-side numeric vector arrange plotted later","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"data frame following structure: Column 'x': Names X axis boxplot, aka name vector (vector.name argument) Column 'value': Values variable","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/bp_standardsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates Blood pressure z-scores — bp_standardsDS","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"function calculates blood pressure z-scores two steps: Step 1. Calculates z-score height according CDC growth chart (growth chart!). Step 2. Calculates z-score BP according fourth report BP management, USA","code":""},{"path":"/reference/bp_standardsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"","code":"bp_standardsDS( sex = sex, age = age, height = height, bp = bp, systolic = systolic )"},{"path":"/reference/bp_standardsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"sex name sex variable. variable coded 1 males 2 females. coded differently (e.g. 0/1), can use ds.recodeValues function recode categories 1/2 use ds.bp_standards age name age variable years. height name height variable cm bp name blood pressure variable. systolic logical. TRUE (default) function assumes conversion systolic blood pressure. FALSE function assumes conversion diastolic blood pressure.","code":""},{"path":"/reference/bp_standardsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"assigns new object server-side. assigned object list two elements: 'Zbp' zscores blood pressure 'perc' percentiles BP zscores.","code":""},{"path":"/reference/bp_standardsDS.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"z-scores height based CDC growth charts calculated sds function childsds R package.","code":""},{"path":"/reference/bp_standardsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/cDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenates objects into a vector or list — cDS","title":"Concatenates objects into a vector or list — cDS","text":"function similar R base function 'c'.","code":""},{"path":"/reference/cDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenates objects into a vector or list — cDS","text":"","code":"cDS(x.names)"},{"path":"/reference/cDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenates objects into a vector or list — cDS","text":"x.names character vector object names concatenate.","code":""},{"path":"/reference/cDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenates objects into a vector or list — cDS","text":"vector list","code":""},{"path":"/reference/cDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Concatenates objects into a vector or list — cDS","text":"Unlike R base function 'c' vector list certain length allowed output","code":""},{"path":"/reference/cDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Concatenates objects into a vector or list — cDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/cbindDS.html","id":null,"dir":"Reference","previous_headings":"","what":"cbindDS called by ds.cbind — cbindDS","title":"cbindDS called by ds.cbind — cbindDS","text":"serverside assign function takes sequence vector, matrix data-frame arguments combines column produce data-frame.","code":""},{"path":"/reference/cbindDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cbindDS called by ds.cbind — cbindDS","text":"","code":"cbindDS(x.names.transmit = NULL, colnames.transmit = NULL)"},{"path":"/reference/cbindDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"cbindDS called by ds.cbind — cbindDS","text":"x.names.transmit vector character strings representing names elemental components combined converted transmittable format. argument fully specified x argument client-side ds.cbind function. colnames.transmit vector character strings representing column names output object converted transmittable format.","code":""},{"path":"/reference/cbindDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"cbindDS called by ds.cbind — cbindDS","text":"object specified newobj argument ds.cbind (default name cbind.newobj) written serverside. output object class data.frame.","code":""},{"path":"/reference/cbindDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"cbindDS called by ds.cbind — cbindDS","text":"sequence vector, matrix data-frame arguments combined column column produce data-frame written serverside. critical requirement length component variables, number rows component data.frames matrices must . output data.frame number rows. details see help ds.cbind native R function cbind.","code":""},{"path":"/reference/cbindDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"cbindDS called by ds.cbind — cbindDS","text":"Paul Burton Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/changeRefGroupDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Changes a reference level of a factor — changeRefGroupDS","title":"Changes a reference level of a factor — changeRefGroupDS","text":"function similar R function relevel,","code":""},{"path":"/reference/changeRefGroupDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Changes a reference level of a factor — changeRefGroupDS","text":"","code":"changeRefGroupDS(x, ref = NULL, reorderByRef = NULL)"},{"path":"/reference/changeRefGroupDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Changes a reference level of a factor — changeRefGroupDS","text":"x character string, name factor vector. ref character, reference level reorderByRef boolean tells whether new vector ordered reference group.","code":""},{"path":"/reference/changeRefGroupDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Changes a reference level of a factor — changeRefGroupDS","text":"factor length input vector","code":""},{"path":"/reference/changeRefGroupDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Changes a reference level of a factor — changeRefGroupDS","text":"addition R function , function allows user re-order vector, putting reference group first. user chooses re-order warning issued can introduce mismatch values vector put back table reordered way. mismatch can render results operations table invalid.","code":""},{"path":"/reference/changeRefGroupDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Changes a reference level of a factor — changeRefGroupDS","text":"Isaeva, J., Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/checkNegValueDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if a numeric variable has negative values — checkNegValueDS","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"function called client function ds.glm.","code":""},{"path":"/reference/checkNegValueDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"","code":"checkNegValueDS(weights)"},{"path":"/reference/checkNegValueDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"weights numeric vector","code":""},{"path":"/reference/checkNegValueDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"boolean; TRUE vector one negative values FALSE otherwise","code":""},{"path":"/reference/checkNegValueDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"user sets parameter 'weights' client side function ds.glm server side function called verify 'weights' vector negative values negative allowed weights.","code":""},{"path":"/reference/checkNegValueDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"Gaye, .","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":null,"dir":"Reference","previous_headings":"","what":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"server-side function check server running \"permissive\" privacy control level.","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"","code":"checkPermissivePrivacyControlLevel(privacyControlLevels)"},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"privacyControlLevels vector strings contains privacy control level names permitted calling method.","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"return value, called side effects","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"Tests whether R option \"datashield.privacyControlLevel\" set \"permissive\", cause call stop() message \"BLOCKED: server running 'non-permissive' mode caused method blocked\".","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"Wheater, Dr SM., DataSHIELD Development Team.","code":""},{"path":"/reference/classDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the class of an object — classDS","title":"Returns the class of an object — classDS","text":"function similar R function class.","code":""},{"path":"/reference/classDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the class of an object — classDS","text":"","code":"classDS(x)"},{"path":"/reference/classDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the class of an object — classDS","text":"x string character, name object","code":""},{"path":"/reference/classDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the class of an object — classDS","text":"class input object","code":""},{"path":"/reference/classDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the class of an object — classDS","text":"function returns class object","code":""},{"path":"/reference/classDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the class of an object — classDS","text":"Stuart Wheater, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/colnamesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the column names of a data frame or matrix — colnamesDS","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"function similar R function colnames.","code":""},{"path":"/reference/colnamesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"","code":"colnamesDS(x)"},{"path":"/reference/colnamesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"x string character, name dataframe matrix","code":""},{"path":"/reference/colnamesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"column names input object","code":""},{"path":"/reference/colnamesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"function returns column names input dataframe matrix","code":""},{"path":"/reference/colnamesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"Demetris Avraam, DataSHIELD Development Team","code":""},{"path":"/reference/completeCasesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"Identifies strips rows data.frame, matrix vector contain NAs.","code":""},{"path":"/reference/completeCasesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"","code":"completeCasesDS(x1.transmit)"},{"path":"/reference/completeCasesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"x1.transmit argument determines input data.frame, matrix vector rows NAs stripped. argument fully specified argument ds.completeCases function.","code":""},{"path":"/reference/completeCasesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"modified data.frame, matrix vector rows containing least one NA deleted. modified object written serverside source. addition, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.completeCases also returns studysideMessages can help explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/completeCasesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"case data.frame matrix, completeCasesDS identifies rows containing one NAs deletes rows altogether. one variable NA given row lead deletion whole row. case vector, completeCasesDS acts equivalent manner equivalent 'row' simply strips observations recorded NA. ds.completeCASES analogous complete.cases function native R. Limited additional information can therefore found help(\"complete.cases\") native R.","code":""},{"path":"/reference/completeCasesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/corDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"function computes sum vector variable sum products two variables (.e. scalar product two vectors).","code":""},{"path":"/reference/corDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"","code":"corDS(x = NULL, y = NULL)"},{"path":"/reference/corDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"x character, name vector, matrix dataframe variables(s) correlation(s) () going calculated . y NULL (default) name vector, matrix dataframe compatible dimensions x.","code":""},{"path":"/reference/corDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"list includes matrix elements sum products two variables, matrix elements sum values variable, matrix elements number complete cases pair variables, list number missing values variable separately (columnwise) number missing values casewise, vector elements sum squares variable. first disclosure control checks number variables bigger percentage individual-level records (allowed percentage pre-specified 'nfilter.glm'). second disclosure control checks none dichotomous level fewer counts pre-specified 'nfilter.tab' threshold. list also includes class, class input object client-side consistency checking.","code":""},{"path":"/reference/corDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"computes sum vector variable sum products two variables","code":""},{"path":"/reference/corDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/corTestDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests for correlation between paired samples — corTestDS","title":"Tests for correlation between paired samples — corTestDS","text":"function similar R function cor.test.","code":""},{"path":"/reference/corTestDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests for correlation between paired samples — corTestDS","text":"","code":"corTestDS(x, y, method, exact, conf.level)"},{"path":"/reference/corTestDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests for correlation between paired samples — corTestDS","text":"x character string providing name numerical vector. y character string providing name numerical vector. method character string indicating correlation coefficient used test. One \"pearson\", \"kendall\", \"spearman\", can abbreviated. exact logical indicating whether exact p-value computed. Used Kendall's tau Spearman's rho. conf.level confidence level returned confidence interval. Currently used Pearson product moment correlation coefficient least 4 complete pairs observations.","code":""},{"path":"/reference/corTestDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tests for correlation between paired samples — corTestDS","text":"list results correlation test class, class input object client-side consistency checking.","code":""},{"path":"/reference/corTestDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tests for correlation between paired samples — corTestDS","text":"function runs two-sided correlation test","code":""},{"path":"/reference/corTestDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Tests for correlation between paired samples — corTestDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/covDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"function computes sum vector variable sum products two variables (.e. scalar product two vectors).","code":""},{"path":"/reference/covDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"","code":"covDS(x = NULL, y = NULL, use = NULL)"},{"path":"/reference/covDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"x character, name vector, matrix dataframe variable(s) covariance(s) correlation(s) () going calculated . y NULL (default) name vector, matrix dataframe compatible dimensions x. use character string giving method computing covariances presence missing values. must one strings \"casewise.complete\" \"pairwise.complete\". use set 'casewise.complete' rows missing values omitted vector, matrix dataframe calculations sums. use set 'pairwise.complete' (default case set client-side), sums products computed two variables using complete pairs observations two variables.","code":""},{"path":"/reference/covDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"list includes matrix elements sum products two variables, matrix elements sum values variable, matrix elements number complete cases pair variables, list number missing values variable separately (columnwise) number missing values casewise pairwise depending argument use, error message indicates whether input variables pass disclosure controls. first disclosure control checks number variables bigger percentage individual-level records (allowed percentage pre-specified 'nfilter.glm'). second disclosure control checks none dichotomous level fewer counts pre-specified 'nfilter.tab' threshold. input variables pass disclosure controls output values replaced NAs. list also includes class, class input object client-side consistency checking.","code":""},{"path":"/reference/covDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"computes sum vector variable sum products two variables","code":""},{"path":"/reference/covDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameDS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameDS called by ds.dataFrame — dataFrameDS","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"serverside function creates data frame elemental components. : pre-existing data frames; single variables; /matrices","code":""},{"path":"/reference/dataFrameDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"","code":"dataFrameDS( vectors = NULL, r.names = NULL, ch.rows = FALSE, ch.names = TRUE, clnames = NULL, strAsFactors = TRUE, completeCases = FALSE )"},{"path":"/reference/dataFrameDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"vectors list contains elemental components combine. correspond vector character strings specified argument x clientside function ds.dataFrame() r.names NULL character vector specifying names rows. Default NULL. ch.rows logical, TRUE rows checked consistency length names. Default FALSE. ch.names logical, TRUE names variables data frame checked ensure syntactically valid variable names duplicated. Default TRUE. fact, clientside function ensures duplicated names can presented dataFrameDS argument kept check forms syntactic validity. clnames list characters, column names output data frame. generated clientside function names vectors, column names data.frames matrices combined producing output data.frame strAsFactors logical, TRUE determines whether character vectors automatically converted factors? Default TRUE. completeCases logical. TRUE indicates complete cases included: rows missing values component excluded. Default FALSE.","code":""},{"path":"/reference/dataFrameDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"dataframe composed specified elemental components created serverside named according argument clientside function ds.dataFrame()","code":""},{"path":"/reference/dataFrameDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"data frame list variables number rows unique row names, class 'data.frame'. ds.dataFrame create data frame combining series elemental components may pre-existing data.frames, matrices variables. critical requirement length component variables, number rows component data.frames matrices must . output data.frame number rows. serverside function dataFrameDS() calls native R function data.frame() several arguments precisely data.frame(). consequence, additional information can sought help() data.frame().","code":""},{"path":"/reference/dataFrameDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSortDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Sorts data frame using specified alphanumeric numeric sort key","code":""},{"path":"/reference/dataFrameSortDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"","code":"dataFrameSortDS( df.name = NULL, sort.key.name = NULL, sort.descending, sort.method )"},{"path":"/reference/dataFrameSortDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"df.name character string providing name serverside data.frame sorted. parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.key.name character string providing name sort key. serverside vector may sit inside data frame sorted independently serverside analysis environment. , sits outside data frame must length data frame. parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.descending logical, TRUE data.frame sorted sort key descending order. Default = FALSE (sort order ascending). parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.method character string taking one values: \"default\", \"d\", \"alphabetic\", \"\", \"numeric\", \"n\", NULL. Default value \"default\". parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\").","code":""},{"path":"/reference/dataFrameSortDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"appropriately re-sorted data.frame written serverside R environment data.frame named according argument(default name 'dataframesort.newobj') name specified","code":""},{"path":"/reference/dataFrameSortDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Serverside assign function dataFrameSortDS called clientside function ds.dataFrameSort. vector matrix can added , coerced , data frame (using function [ds.dataFrame]) means can sorted/reordered using ds.dataFrameSort. Fundamentally, function [ds.dataFrameSort] sort specified data frame serverside using sort key also serverside. details see help clientside function: [ds.dataFrameShort]","code":""},{"path":"/reference/dataFrameSortDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Paul Burton, critical error identification Leire Abarrategui-Martinez, DataSHIELD Development Team, 2/4/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"First serverside function subsetting data frame row column.","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"","code":"dataFrameSubset1DS( df.name = NULL, V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, keep.cols = NULL, rm.cols = NULL, keep.NAs = NULL )"},{"path":"/reference/dataFrameSubset1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"df.name character string providing name data.frame sorted. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset V1.name character string specifying name subsetting vector Boolean operator applied define subset created. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset V2.name character string specifying name vector scalar values vector specified argument compared. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset Boolean.operator.n character string specifying one six possible Boolean operators: '==', '!=', '>', '>=', '<', '<=' argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset keep.cols numeric vector specifying numbers columns kept final subset subsetting column. example: keep.cols=c(2:5,7,12) keep columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset rm.cols numeric vector specifying numbers columns removed creating final subset subsetting column. example: rm.cols=c(2:5,7,12) remove columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset keep.NAs logical, TRUE NAs vector holding final Boolean vector indicating whether given row included subset converted 1s included subset. NAs caused NAs either . FALSE NULL NAs final Boolean vector converted 0s corresponding row therefore excluded subset. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"first serverside function called ds.dataFrameSubset provides first level traps comprehensive series disclosure risks can returned directly clientside dataFrameSubset1DS aggregate function. second serverside function called ds.dataFrameSubset (dataFrameSubset2DS) carries disclosure tests, assign function writes subsetted data.frame serverside. consequence, records error messages studysideMessages can retrieved using ds.message","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"data frame list variables number rows, class 'data.frame'. details see help header ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"Second serverside function subsetting data frame row column.","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"","code":"dataFrameSubset2DS( df.name = NULL, V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, keep.cols = NULL, rm.cols = NULL, keep.NAs = NULL )"},{"path":"/reference/dataFrameSubset2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"df.name character string providing name data.frame sorted. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset V1.name character string specifying name subsetting vector Boolean operator applied define subset created. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset V2.name character string specifying name vector scalar values vector specified argument compared. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset Boolean.operator.n character string specifying one six possible Boolean operators: '==', '!=', '>', '>=', '<', '<=' argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset keep.cols numeric vector specifying numbers columns kept final subset subsetting column. example: keep.cols=c(2:5,7,12) keep columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset rm.cols numeric vector specifying numbers columns removed creating final subset subsetting column. example: rm.cols=c(2:5,7,12) remove columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset keep.NAs logical, TRUE NAs vector holding final Boolean vector indicating whether given row included subset converted 1s included subset. NAs caused NAs either . FALSE NULL NAs final Boolean vector converted 0s corresponding row therefore excluded subset. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"object specified argument (default name '_subset') initially specified calling ds.dataFrameSubset. output object (required subsetted data.frame called written serverside. addition, two validity messages returned via ds.dataFrameSubset indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - dataFrameSubset2DS (via ds.dataFrame()) also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"data frame list variables number rows, class 'data.frame'. details see help header ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/densityGridDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates a density grid with or without a priori defined limits — densityGridDS","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Generates density grid can used heatmap contour plots.","code":""},{"path":"/reference/densityGridDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"","code":"densityGridDS( x, y, limits = FALSE, x.min = NULL, x.max = NULL, y.min = NULL, y.max = NULL, numints = 20 )"},{"path":"/reference/densityGridDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"x character string providing name server-side numerical vector y character string providing name server-side numerical vector limits logical expression whether limits density grid defined user. limits set \"FALSE\", min max x y used range. limits set \"TRUE\", limits defined x.min, x.max, y.min y.max used. x.min minimum value x axis grid density object, needed x.max maximum value x axis grid density object, needed y.min minimum value y axis grid density object, needed y.max maximum value y axis grid density object, needed numints number intervals grid density object, default 20","code":""},{"path":"/reference/densityGridDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"list grid density matrix (grid) classes x y inputs (class.x class.y)","code":""},{"path":"/reference/densityGridDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Invalid cells (cells count < set filter value minimum allowed counts table cells) turn 0.","code":""},{"path":"/reference/densityGridDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Julia Isaeva, Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dimDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the dimension of a data frame or matrix — dimDS","title":"Returns the dimension of a data frame or matrix — dimDS","text":"function similar R function dim.","code":""},{"path":"/reference/dimDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the dimension of a data frame or matrix — dimDS","text":"","code":"dimDS(x)"},{"path":"/reference/dimDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the dimension of a data frame or matrix — dimDS","text":"x string character, name dataframe matrix","code":""},{"path":"/reference/dimDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the dimension of a data frame or matrix — dimDS","text":"list two elements: dim (dimension input object) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/dimDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the dimension of a data frame or matrix — dimDS","text":"function returns dimension input dataframe matrix","code":""},{"path":"/reference/dimDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the dimension of a data frame or matrix — dimDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dmtC2SDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"Creates data.frame, matrix tibble serverside equivalent data.frame, matrix tibble (DMT) clientside.","code":""},{"path":"/reference/dmtC2SDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"","code":"dmtC2SDS( dfdata.mat.transmit, inout.object.transmit, from, nrows.transmit, ncols.transmit, colnames.transmit, colclass.transmit, byrow )"},{"path":"/reference/dmtC2SDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"dfdata.mat.transmit character string format can pass DataSHIELD R parser specifies name DMT copied clientside serverside. Value fully specified argument ds.dmtC2S. inout.object.transmit character string taking values \"DF\", \"MAT\" \"TBL\". value argument automatically set ds.dmtC2S depending whether clientside DMT data.frame, matrix tibble. Correspondingly, value determines whether object created serverside data.frame, matrix tibble. unlikely always work (class misspecifications may occur) works test cases. character string specifying source . Fixed clientside function \"clientside.matdftbl\". nrows.transmit specifies number rows matrix created. Fixed clientside function equal number rows clientside DMT transferred. ncols.transmit specifies number columns matrix created. Fixed clientside function equal number columns clientside DMT transferred. colnames.transmit parser-transmissible vector specifying name column DMT transferred clientside serverside. Generated automatically clientside function colnames clientside DMT. colclass.transmit parser-transmissible vector specifying class vector representing individual column DMT transferred. Generated automatically clientside function. allows transmission DMTs containing columns different classes.something going go wrong class misspecification (see inout.object.transmit) DMT complex combination data/column types likely cause. suggests always check class serverside DMT individual columns (latter important). situation arises class columns crucial function needed please contact DataSHIELD forum can try remedy problem. byrow logical value specifying whether DMT created serverside filled row row column column. fixed clientside function FALSE (fill column column).","code":""},{"path":"/reference/dmtC2SDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"object specified argument (default name \"matdftbl.copied.C2S\") written data.frame, matrix tibble serverside.","code":""},{"path":"/reference/dmtC2SDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"dmtC2SDS serverside assign function called ds.dmtC2S. information works see help ds.dmtC2S","code":""},{"path":"/reference/dmtC2SDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"Paul Burton DataSHIELD Development Team - 3rd June, 2021","code":""},{"path":"/reference/dsBase-package.html","id":null,"dir":"Reference","previous_headings":"","what":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","title":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","text":"Base 'DataSHIELD' functions server side. 'DataSHIELD' software package allows non-disclosive federated analysis sensitive data. 'DataSHIELD' analytic functions designed share non disclosive summary statistics, built automated output checking based statistical disclosure control. data sites setting threshold values automated output checks. details, see 'citation(\"dsBase\")'.","code":""},{"path":"/reference/dsBase-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","text":"Maintainer: Stuart Wheater stuart.wheater@arjuna.com (ORCID) Authors: Stuart Wheater stuart.wheater@arjuna.com (ORCID) Paul Burton (ORCID) Rebecca Wilson (ORCID) Olly Butters (ORCID) Patricia Ryser-Welch (ORCID) Alex Westerberg Leire Abarrategui Roberto Villegas-Diaz (ORCID) Demetris Avraam (ORCID) Yannick Marcon yannick.marcon@obiba.org (ORCID) Tom Bishop Amadou Gaye (ORCID) Xavier Escribà-Montagut (ORCID)","code":""},{"path":"/reference/elsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"function based native R function elspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/elsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"","code":"elsplineDS(x = x, n = n, marginal = FALSE, names = NULL)"},{"path":"/reference/elsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"x name input numeric variable n integer greater 2, knots computed cut n equally-spaced intervals along range x marginal logical, parametrize spline, see Details names character, vector names constructed variables","code":""},{"path":"/reference/elsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"elspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/elsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment. Function elspline wraps lspline computes knot positions cut range x n equal-width intervals.","code":""},{"path":"/reference/elsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/expDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the exponential values of the input variable — expDS","title":"Computes the exponential values of the input variable — expDS","text":"function similar R function exp.","code":""},{"path":"/reference/expDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the exponential values of the input variable — expDS","text":"","code":"expDS(x)"},{"path":"/reference/expDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the exponential values of the input variable — expDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/expDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the exponential values of the input variable — expDS","text":"object specified newobj argument ds.exp (default name exp.newobj) written serverside. output object class numeric.","code":""},{"path":"/reference/expDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the exponential values of the input variable — expDS","text":"function computes exponential values input numeric integer vector.","code":""},{"path":"/reference/expDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the exponential values of the input variable — expDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/fixClassDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Change Class of Target Variables in a Data Frame — fixClassDS","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"Change Class Target Variables Data Frame","code":""},{"path":"/reference/fixClassDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"","code":"fixClassDS(df.name, target_vars, target_class)"},{"path":"/reference/fixClassDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"df.name string representing name data frame. target_vars character vector specifying columns modified. target_class character vector specifying new classes column (1 = factor, 2 = integer, 3 = numeric, 4 = character, 5 = logical).","code":""},{"path":"/reference/fixClassDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"modified data frame specified columns converted target classes.","code":""},{"path":"/reference/fixColsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Missing Columns with NA Values — fixColsDS","title":"Add Missing Columns with NA Values — fixColsDS","text":"Add Missing Columns NA Values","code":""},{"path":"/reference/fixColsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Missing Columns with NA Values — fixColsDS","text":"","code":"fixColsDS(.data, cols)"},{"path":"/reference/fixColsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Missing Columns with NA Values — fixColsDS","text":".data string representing name data frame. cols character vector specifying columns added missing.","code":""},{"path":"/reference/fixColsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Missing Columns with NA Values — fixColsDS","text":"modified data frame missing columns added filled NA.","code":""},{"path":"/reference/fixLevelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"Set Factor Levels Specific Columns Data Frame","code":""},{"path":"/reference/fixLevelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"","code":"fixLevelsDS(df.name, vars, levels)"},{"path":"/reference/fixLevelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"df.name string representing name data frame modify. vars character vector specifying columns modified. levels named list element contains levels corresponding factor variable.","code":""},{"path":"/reference/fixLevelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"modified data frame specified columns converted factors provided levels.","code":""},{"path":"/reference/gamlssDS.html","id":null,"dir":"Reference","previous_headings":"","what":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"function calls gamlssDS wrapper function gamlss R package. function returns object class \"gamlss\", generalized additive model location, scale shape (GAMLSS). function also saves residuals object server-side name specified newobj argument. addition, argument centiles set TRUE, function calls centiles function gamlss package returns sample percentages centile curve.","code":""},{"path":"/reference/gamlssDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"","code":"gamlssDS( formula = formula, sigma.formula = sigma.formula, nu.formula = nu.formula, tau.formula = tau.formula, family = family, data = data, method = method, mu.fix = mu.fix, sigma.fix = sigma.fix, nu.fix = nu.fix, tau.fix = tau.fix, control = control, i.control = i.control, centiles = centiles, xvar = xvar, newobj = newobj )"},{"path":"/reference/gamlssDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"formula formula object, response left ~ operator, terms, separated + operators, right. Nonparametric smoothing terms indicated pb() penalised beta splines, cs smoothing splines, lo loess smooth terms random ra random terms, e.g. y~cs(x,df=5)+x1+x2*x3. sigma.formula formula object fitting model sigma parameter, formula , e.g. sigma.formula=~cs(x,df=5). nu.formula formula object fitting model nu parameter, e.g. nu.formula=~x tau.formula formula object fitting model tau parameter, e.g. tau.formula=~cs(x,df=2) family gamlss.family object, used define distribution link functions various parameters. distribution families supported gamlss() can found gamlss.family. Functions BI() (binomial) produce family object. Also can given without parentheses .e. BI. Family functions can take arguments, BI(mu.link=probit). data data frame containing variables occurring formula. missing, variables parent environment. method character indicating algorithm GAMLSS. Can either 'RS', 'CG' 'mixed'. method='RS' function use Rigby Stasinopoulos algorithm, method='CG' function use Cole Green algorithm, method='mixed' function use RS algorithm twice switching Cole Green algorithm 10 extra iterations. mu.fix logical, indicate whether mu parameter kept fixed fitting processes. sigma.fix logical, indicate whether sigma parameter kept fixed fitting processes. nu.fix logical, indicate whether nu parameter kept fixed fitting processes. tau.fix logical, indicate whether tau parameter kept fixed fitting processes. control sets control parameters outer iterations algorithm using gamlss.control function. vector 7 numeric values: () c.crit (convergence criterion algorithm), (ii) n.cyc (number cycles algorithm), (iii) mu.step (step length parameter mu), (iv) sigma.step (step length parameter sigma), (v) nu.step (step length parameter nu), (vi) tau.step (step length parameter tau), (vii) gd.tol (global deviance tolerance level). default values 7 parameters set c(0.001, 20, 1, 1, 1, 1, Inf). .control sets control parameters inner iterations RS algorithm using glim.control function. vector 4 numeric values: () cc (convergence criterion algorithm), (ii) cyc (number cycles algorithm), (iii) bf.cyc (number cycles backfitting algorithm), (iv) bf.tol (convergence criterion (tolerance level) backfitting algorithm). default values 4 parameters set c(0.001, 50, 30, 0.001). centiles logical, indicating whether function centiles() used tabulate sample percentages centile curve. Default set FALSE. xvar unique explanatory variable used centiles() function. variable used centiles argument set TRUE. restriction centiles function applies models one explanatory variable . newobj character string provides name output object stored data servers. Default gamlss_residuals.","code":""},{"path":"/reference/gamlssDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"gamlss object components native R gamlss function. Individual-level information like components y (response response) residuals (normalised quantile residuals model) disclosed client-side.","code":""},{"path":"/reference/gamlssDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"additional details see help header gamlss centiles functions native R gamlss package.","code":""},{"path":"/reference/gamlssDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/getAllLevelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"Retrieve Factor Levels Specific Columns","code":""},{"path":"/reference/getAllLevelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"","code":"getAllLevelsDS(df.name, factor_vars)"},{"path":"/reference/getAllLevelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"df.name string representing name data frame. factor_vars character vector specifying factor columns.","code":""},{"path":"/reference/getAllLevelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"list factor levels specified columns.","code":""},{"path":"/reference/getClassAllColsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"Get Class Columns Data Frame","code":""},{"path":"/reference/getClassAllColsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"","code":"getClassAllColsDS(df.name)"},{"path":"/reference/getClassAllColsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"df.name string representing name data frame.","code":""},{"path":"/reference/getClassAllColsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"tibble class column data frame.","code":""},{"path":"/reference/getWGSRDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"Calculate Growth Reference z-score given anthropometric measurement function similar R function getWGSR zscorer package.","code":""},{"path":"/reference/getWGSRDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"","code":"getWGSRDS(sex, firstPart, secondPart, index, standing = NA, thirdPart = NA)"},{"path":"/reference/getWGSRDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"sex name binary variable indicates sex subject. must coded 1 = male 2 = female. project variable sex different levels, recode levels 1 males 2 females using ds.recodeValues DataSHIELD function use ds.getWGSR. firstPart Name variable specifying: Weight (kg) BMI/, W/, W/H, W/L Head circumference (cm) HC/Height (cm) H/Length (cm) L/MUAC (cm) MUAC/Sub-scapular skinfold (mm) SSF/Triceps skinfold (mm) TSF/Give quoted variable name (e.g.) \"weight\". careful units (weight kg; height, length, head circumference, MUAC cm, skinfolds mm). secondPart Name variable specifying: Age (days) H/, HC/, L/, MUAC/, SSF/, TSF/Height (cm) BMI/, W/H Length (cm) W/L Give quoted variable name (e.g.) \"age\". careful units (age days; height length cm). index index calculated added data. One : bfa BMI age hca Head circumference age hfa Height age lfa Length age mfa MUAC age ssa Sub-scapular skinfold age tsa Triceps skinfold age wfa Weight age wfh Weight height wfl Weight length Give quoted index name (e.g.) \"wfh\". standing Variable specifying stature measured. NA (default) age (\"hfa\" \"lfa\") height rules (\"wfh\" \"wfl\") applied. must coded 1 = Standing; 2 = Supine; 3 = Unknown. Missing values recoded 3 = Unknown. Give single value (e.g.\"1\"). value specified height age rules applied. thirdPart Name variable specifying age (days) BMI/. Give quoted variable name (e.g.) \"age\". careful units (age days).","code":""},{"path":"/reference/getWGSRDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"ds.getWGSR assigns numeric vector includes z-scores specified index.","code":""},{"path":"/reference/getWGSRDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"function computes Growth Reference z-scores anthropometric data weight, height length, MUAC, head circumference, sub-scapular skinfold triceps skinfold. Note function might fail return NAs variables outside ranges given WGS (Child Growth Standards) reference (.e. 45 120 cm height 0 60 months age). user check ranges units data.","code":""},{"path":"/reference/getWGSRDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glm1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"glm1DS called by ds.glm — glm1DS","title":"glm1DS called by ds.glm — glm1DS","text":"first server-side aggregate function called ds.glm","code":""},{"path":"/reference/glm1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"glm1DS called by ds.glm — glm1DS","text":"","code":"glm1DS(formula, family, weights, offset, data)"},{"path":"/reference/glm1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"glm1DS called by ds.glm — glm1DS","text":"formula glm() formula consistent R syntax eg U~x+y+Z regress variables U x,y Z family glm() family consistent R syntax eg \"gaussian\", \"poisson\", \"binomial\" weights optional variable providing regression weights offset offset data optional character string specifying data.frame object holding data analysed specified model","code":""},{"path":"/reference/glm1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"glm1DS called by ds.glm — glm1DS","text":"List values GLM model.","code":""},{"path":"/reference/glm1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"glm1DS called by ds.glm — glm1DS","text":"aggregation function sets model structure creates starting beta.vector feeds, via ds.glm, glm2DS enable iterative fitting generalized linear model specified. details please see extensive header ds.glm.","code":""},{"path":"/reference/glm1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"glm1DS called by ds.glm — glm1DS","text":"Burton PR DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glm2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"glm2DS called by ds.glm — glm2DS","title":"glm2DS called by ds.glm — glm2DS","text":"second server-side aggregate function called ds.glm.","code":""},{"path":"/reference/glm2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"glm2DS called by ds.glm — glm2DS","text":"","code":"glm2DS(formula, family, beta.vect, offset, weights, dataName)"},{"path":"/reference/glm2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"glm2DS called by ds.glm — glm2DS","text":"formula glm() formula consistent R syntax eg U~x+y+Z regress variables U x, y Z family glm() family consistent R syntax eg \"gaussian\", \"poisson\", \"binomial\" beta.vect numeric vector created clientside function specifying vector regression coefficients current iteration offset optional variable providing regression offset weights optional variable providing regression weights dataName optional character string specifying data.frame object holding data analysed specified model ","code":""},{"path":"/reference/glm2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"glm2DS called by ds.glm — glm2DS","text":"List values GLM model","code":""},{"path":"/reference/glm2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"glm2DS called by ds.glm — glm2DS","text":"aggregate function uses model structure starting beta.vector constructed glm1DS iteratively fit generalized linear model specified. function glm2DS also carries series disclosure checks arguments data fail tests, model construction blocked appropriate serverside error message created returned ds.glm clientside. details please see extensive header ds.glm.","code":""},{"path":"/reference/glm2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"glm2DS called by ds.glm — glm2DS","text":"Paul Burton, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmPredictDS.ag.html","id":null,"dir":"Reference","previous_headings":"","what":"predict regression responses from a glm object — glmPredictDS.ag","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"identify return key components/summaries serverside glm_predict object can safely returned clientside without disclosure risk","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"","code":"glmPredictDS.ag( glmname.transmit, newdataname.transmit, output.type, se.fit, dispersion, terms.transmit, na.action )"},{"path":"/reference/glmPredictDS.ag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"glmname.transmit character string specifying name glm object serverside used prediction. Fully specified glmname argument ds.glmPredict newdataname.transmit character string specifying (optional) dataframe serverside look (potentially) new covariate values base predictions. Fully specified newdataname argument ds.glmPredict. output.type character string taking values 'response', 'link' 'terms'. Fully specified corresponding argument ds.glmPredict. se.fit logical standard errors fitted predictions required. Fully specified corresponding argument ds.glmPredict. dispersion numeric value specifying dispersion GLM fit assumed computing standard errors. Fully specified corresponding argument ds.glmPredict. terms.transmit character vector specifying subset terms return prediction. Fully specified 'terms' argument ds.glmPredict. na.action character string determining done missing values data.frame identified . Fully specified na.action argument ds.glmPredict.","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"components/summarising statistics serverside predict_glm object can safely transmitted clientside without risk disclosure. details see DataSHIELD help ds.glmPredict glmPredict.help native R predict.glm predict.glm native R","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"Serverside aggregate function called ds.glmPredict. called immediately assign function glmPredict.created predict_glm object serverside applying equivalent predict.glm() native R glm object serverside. aggregate function, glmPredict.ag, identifies returns components predict_glm object can safely returned clientside without risk disclosure. details see DataSHIELD help ds.glmPredict glmPredict.help native R predict.glm","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmPredictDS.as.html","id":null,"dir":"Reference","previous_headings":"","what":"predict regression responses from a glm object — glmPredictDS.as","title":"predict regression responses from a glm object — glmPredictDS.as","text":"create predict_glm object serverside applying equivalent predict.glm() native R glm object serverside. Identify return components predict_glm object can safely sent clientside without risk disclosure","code":""},{"path":"/reference/glmPredictDS.as.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"predict regression responses from a glm object — glmPredictDS.as","text":"","code":"glmPredictDS.as( glmname.transmit, newdataname.transmit, output.type, se.fit, dispersion, terms.transmit, na.action )"},{"path":"/reference/glmPredictDS.as.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"predict regression responses from a glm object — glmPredictDS.as","text":"glmname.transmit character string specifying name glm object serverside used prediction. Fully specified glmname argument ds.glmPredict newdataname.transmit character string specifying (optional) dataframe serverside look (potentially) new covariate values base predictions. Fully specified newdataname argument ds.glmPredict. output.type character string taking values 'response', 'link' 'terms'. Fully specified corresponding argument ds.glmPredict. se.fit logical standard errors fitted predictions required. Fully specified corresponding argument ds.glmPredict. dispersion numeric value specifying dispersion GLM fit assumed computing standard errors. Fully specified corresponding argument ds.glmPredict. terms.transmit character vector specifying subset terms return prediction. Fully specified 'terms' argument ds.glmPredict. na.action character string determining done missing values data.frame identified . Fully specified na.action argument ds.glmPredict.","code":""},{"path":"/reference/glmPredictDS.as.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"predict regression responses from a glm object — glmPredictDS.as","text":"glmPredict.writes new object serverside containing output precisely equivalent output predict.glm native R. details see DataSHIELD help ds.glmPredict help predict.glm native R","code":""},{"path":"/reference/glmPredictDS.as.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"predict regression responses from a glm object — glmPredictDS.as","text":"Serverside assign function called ds.glmPredict makes predictions regression responses based serverside glm object already created serverside ds.glmSLMA writes predict_glm object serverside. details see help ds.glmPredict help native R predict.glm","code":""},{"path":"/reference/glmPredictDS.as.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"predict regression responses from a glm object — glmPredictDS.as","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMA11DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMA11DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"","code":"glmSLMA11DS(formula, family, weights, offset, data)"},{"path":"/reference/glmSLMA11DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA weights character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. offset character string specifying variable used offset. Specified call ds.glmSLMA. data character string specifying name data.frame holding data model. Specified dataName call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"assesses returns information failure pass disclosure traps test model complexity (saturation). detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"glmSLMADS.assign aggregate function called clientside function ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS assign function glmSLMADS.assign detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"Paul Burton DataSHIELD Development Team (14/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"","code":"glmSLMA2DS(formula, family, offset, weights, newobj, dataName)"},{"path":"/reference/glmSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA offset character string specifying variable used offset. Specified call ds.glmSLMA. weights character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. newobj character string specifying name glm object written serverside glmSLMADS.assign. either name specified newobj argument ds.glmSLMA newobj unspecified NULL called new.glm.obj. dataName character string specifying name data.frame holding data model. Specified call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"quantitative, Boolean, character objects required enable SLMA pooling separate glm models fitted study - particular including study-specific regression coefficients corresponding standard errors.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"glmSLMADS.assign aggregate function called clientside function ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS assign function glmSLMADS.assign detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"Paul Burton DataSHIELD Development Team (14/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"","code":"glmSLMADS.assign(formula, family, offsetName, weightsName, dataName)"},{"path":"/reference/glmSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA offsetName character string specifying variable used offset. Specified call ds.glmSLMA. weightsName character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. dataName character string specifying name data.frame holding data model. Specified call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"writes glm object summarising fitted model serverside. detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"glmSLMADS.assign assign function called clientside function ds.glmSLMA. ds.glmSLMA also calls two aggregate functions glmSLMA1DS glmSLMA2DS. detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"Paul Burton DataSHIELD Development Team (14/7/20)","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize a glm object on the serverside — glmSummaryDS.ag","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"returns non-disclosive elements clientside glm object corresponding object holding output summary(glm object) serverside.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"","code":"glmSummaryDS.ag(x.transmit)"},{"path":"/reference/glmSummaryDS.ag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"x.transmit character string specifying name glm object serverside summarised. specified x.name argument ds.glmSummary","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"returns clientside non-disclosive elements (non-disclosive elements) specified serverside glm corresponding summary_glm object.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"Serverside aggregate function called ds.glmSummary. ds.glmSummary first calls glmSummaryDS.ag create glm_summary object serverside based applying native R's summary.glm() serverside glm object previously created ds.glmSLMA. calls glmSummaryDS.ag return clientside non-disclosive elements (non-disclosive elements) serverside glm corresponding summary_glm object.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSummaryDS.as.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize a glm object on the serverside — glmSummaryDS.as","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"summarize glm object serverside create summary_glm object. Also identify return components glm object summary_glm object can safely sent clientside without risk disclosure","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"","code":"glmSummaryDS.as(x.transmit)"},{"path":"/reference/glmSummaryDS.as.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"x.transmit character string specifying name glm object serverside summarised. specified x.name argument ds.glmSummary","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"writes object serverside precisely equivalent summary(glm object) native R","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"Serverside assign function called ds.glmSummary summarises glm object already created serverside fitting ds.glmSLMA writes summary_glm object serverside. details see help ds.glmSLMA help native R glm() summary.glm","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmerSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"glmerSLMA2DS fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data one multiple sources pooling via SLMA (study level meta-analysis)","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"","code":"glmerSLMA2DS( formula, offset, weights, dataName, family, control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL )"},{"path":"/reference/glmerSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"formula see help ds.glmerSLMA offset see help ds.glmerSLMA weights see help ds.glmerSLMA dataName see help ds.glmerSLMA family see help ds.glmerSLMA control_type see help ds.glmerSLMA control_value.transmit see help argument function ds.glmerSLMA nAGQ integer scalar, defaulting 1L. PRACTICE, MAY NECESSARY SET nAGQ 0L model appears converge perfectly well (e.g. verbose=2 demonstrates good initial convergence log-likelihood regression coefficients) formal convergence get declared - output produced - despite running model many iterations. nAGQ argument set nAGQ argument ds.glmerSLMA details can found help(ds.glmerSLMA) native R help glmer() verbose see help ds.glmerSLMA theta see help argument function ds.glmerSLMA fixef see help argument function ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"key model components see help ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"glmerSLMA2DS serverside function called ds.glmerSLMA clientside. analytic work engine glmer function R sits lme4 package. ds.glmerSLMA fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data single multiple sources. multiple data sources, glme fitted convergence data source independently estimates standard errors returned client thereby enabling cross-study pooling using study level meta-analysis (SLMA). default SLMA undertaken using metafor package, SLMA occurs clientside , far user concerned just standard R environment, user can choose use approach meta-analysis choose. Additional information fitting glmes using glmer engine can obtained using R help glmer lme4 package","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"Tom Bishop, additions Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"glmerSLMADS.assign glmerSLMA2DS fits generalized linear mixed effects model (glme) per study saves outcomes study","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"","code":"glmerSLMADS.assign( formula, offset, weights, dataName, family, control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL )"},{"path":"/reference/glmerSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"formula see help ds.glmerSLMA offset see help ds.glmerSLMA weights see help ds.glmerSLMA dataName see help ds.glmerSLMA family see help ds.glmerSLMA control_type see help ds.glmerSLMA control_value.transmit see help argument function ds.glmerSLMA nAGQ integer scalar, defaulting 1L. PRACTICE, MAY NECESSARY SET nAGQ 0L model appears converge perfectly well (e.g. verbose=2 demonstrates good initial convergence log-likelihood regression coefficients) formal convergence get declared - output produced - despite running model many iterations. nAGQ argument set nAGQ argument ds.glmerSLMA details can found help(ds.glmerSLMA) native R help glmer() verbose see help ds.glmerSLMA theta see help argument function ds.glmerSLMA fixef see help argument function ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"writes glmerMod object summarising fitted model serverside. detailed information see help ds.glmerSLMA.","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"glmerSLMADS.assign serverside function called ds.glmerSLMA clientside. analytic work engine glmer function R sits lme4 package. glmerSLMADS.assign fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data single data source saves regression outcomes serverside.","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/heatmapPlotDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"function calculates coordinates centroids n nearest neighbours.","code":""},{"path":"/reference/heatmapPlotDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"","code":"heatmapPlotDS(x.name, y.name, k, noise, method.indicator)"},{"path":"/reference/heatmapPlotDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"x.name character string providing name server-side numeric vector, x-variable. y.name character string providing name server-side numeric vector, y-variable. k number nearest neighbours centroid calculated method.indicator equal 1 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 2 (.e. probabilistic method). method.indicator number equal either 1 2. value equal 1 'deterministic' method used. value set 2 'probabilistic' method used.","code":""},{"path":"/reference/heatmapPlotDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"list x y coordinates centroids deterministic method used x y coordinated noisy data probabilistic method used, along classes x y inputs (class.x class.y)","code":""},{"path":"/reference/heatmapPlotDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"function finds n-1 nearest neighbours data point 2-dimensional space. nearest neighbours data points minimum Euclidean distances point interest. point interest n-1 nearest neighbours used calculation coordinates centroid n points. Centroid referred centre mass, .e. x-coordinate centroid average value x-coordinates n nearest neighbours y-coordinate centroid average y-coordinates n nearest neighbours. coordinates centroids return client side function can used plot non-disclosive graphs (e.g. scatter plots, heatmap plots, contour plots, etc).","code":""},{"path":"/reference/heatmapPlotDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/hetcorDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Heterogeneous Correlation Matrix — hetcorDS","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"function based hetcor function R package polycor.","code":""},{"path":"/reference/hetcorDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"","code":"hetcorDS(data, ML, std.err, bins, pd, use)"},{"path":"/reference/hetcorDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"data name data frame consisting factors, ordered factors, logical variables, character variables, /numeric variables, first several variables. ML TRUE, compute maximum-likelihood estimates; FALSE (default), compute quick two-step estimates. std.err TRUE (default), compute standard errors. bins number bins use continuous variables testing bivariate normality; default 4. pd TRUE (default) correlation matrix positive-definite, attempt made adjust positive-definite matrix, using nearPD function Matrix package. Note default arguments nearPD used (except corr=TRUE); control call nearPD directly. use \"complete.obs\", remove observations missing data; \"pairwise.complete.obs\", compute correlation using observations valid data pair variables.","code":""},{"path":"/reference/hetcorDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Returns object class \"hetcor\" following components: correlation matrix; type correlation: \"Pearson\", \"Polychoric\", \"Polyserial\"; standard errors correlations, requested; number (numbers) observations correlations based; p-values tests bivariate normality pair variables; method missing data handled: \"complete.obs\" \"pairwise.complete.obs\"; TRUE ML estimates, FALSE two-step estimates.","code":""},{"path":"/reference/hetcorDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Computes heterogeneous correlation matrix, consisting Pearson product-moment correlations numeric variables, polyserial correlations numeric ordinal variables, polychoric correlations ordinal variables.","code":""},{"path":"/reference/hetcorDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/histogram1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"returns the minimum and the maximum of the input numeric vector — histogram1DS","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"function returns minimum maximum input numeric vector depends argument method.indicator. method.indicator set 1 (.e. 'smallCellsRule' used) computed minimum maximum values multiplied small random number. method.indicator set 2 (.e. 'deterministic' method used) function returns minimum maximum values vector scaled centroids. method.indicator set 3 (.e. 'probabilistic' method used) function returns minimum maximum values generated 'noisy' vector.","code":""},{"path":"/reference/histogram1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"","code":"histogram1DS(x, method.indicator, k, noise)"},{"path":"/reference/histogram1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"x character string providing name server-side numeric vector histogram desired. method.indicator number equal either 1, 2 3 indicating method disclosure control used generation histogram. value equal 1 'smallCellsRule' used. value equal 2 'deterministic' method used. value set 3 'probabilistic' method used. k number nearest neighbours centroid calculated method.indicator equal 2 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 3 (.e. probabilistic method).","code":""},{"path":"/reference/histogram1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"list numeric vector containing minimum maximum values vector (range) class input vector (class)","code":""},{"path":"/reference/histogram1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/histogram2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes a histogram of the input variable without plotting. — histogram2DS","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"function produces information required plot histogram. done without allowing bins (cells) number counts less pre-specified disclosure control set minimum cell size table. bin less counts threshold counts density replaced 0 value.","code":""},{"path":"/reference/histogram2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"","code":"histogram2DS(x, num.breaks, min, max, method.indicator, k, noise)"},{"path":"/reference/histogram2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"x character string providing name server-side numeric vector histogram desired. num.breaks number breaks range variable divided. min numeric, lower limit distribution. max numeric, upper limit distribution. method.indicator number equal either 1, 2 3 indicating method disclosure control used generation histogram. value equal 1 'smallCellsRule' used. value equal 2 'deterministic' method used. value set 3 'probabilistic' method used. k number nearest neighbours centroid calculated method.indicator equal 2 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 3 (.e. probabilistic method).","code":""},{"path":"/reference/histogram2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"list object class histogram number invalid cells","code":""},{"path":"/reference/histogram2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"Please find details documentation clientside ds.histogram function.","code":""},{"path":"/reference/histogram2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/igb_standardsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"Converts birth measurements INTERGROWTH z-scores/centiles (generic)","code":""},{"path":"/reference/igb_standardsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"","code":"igb_standardsDS( gagebrth = gagebrth, z = z, p = p, val = val, var = var, sex = sex, fun = fun )"},{"path":"/reference/igb_standardsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"gagebrth name \"gestational age birth days\" variable. z z-score(s) convert (must 0 1). Default value 0. value used fun set \"igb_zscore2value\". p centile(s) convert (must 0 100). Default value p=50. value used fun set \"igb_centile2value\". val name anthropometric variable convert. var name measurement convert (\"lencm\", \"wtkg\", \"hcircm\", \"wlr\") sex name sex factor variable. variable coded Male/Female. coded differently (e.g. 0/1), can use ds.recodeValues function recode categories Male/Female use ds.igb_standards fun name function used. can one : \"igb_centile2value\", \"igb_zscore2value\", \"igb_value2zscore\" (default), \"igb_value2centile\".","code":""},{"path":"/reference/igb_standardsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"assigns converted measurement new object server-side","code":""},{"path":"/reference/igb_standardsDS.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"gestational ages 24 33 weeks, INTERGROWTH early preterm standard used.","code":""},{"path":"/reference/igb_standardsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/isNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if a vector is empty — isNaDS","title":"Checks if a vector is empty — isNaDS","text":"function similar R function .na instead vector booleans returns just one boolean tell element missing values.","code":""},{"path":"/reference/isNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if a vector is empty — isNaDS","text":"","code":"isNaDS(x)"},{"path":"/reference/isNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if a vector is empty — isNaDS","text":"x character string, name server-side vector","code":""},{"path":"/reference/isNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if a vector is empty — isNaDS","text":"list two elements: .na (TRUE vector contains NAs, FALSE otherwise) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/isNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if a vector is empty — isNaDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/isValidDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if an input is valid — isValidDS","title":"Checks if an input is valid — isValidDS","text":"Tells object server side valid.","code":""},{"path":"/reference/isValidDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if an input is valid — isValidDS","text":"","code":"isValidDS(x)"},{"path":"/reference/isValidDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if an input is valid — isValidDS","text":"x character string, name vector (numeric, integer, factor, character, logical), data.frame matrix","code":""},{"path":"/reference/isValidDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if an input is valid — isValidDS","text":"list valid, boolean TRUE input valid FALSE , class, class input object client-side consistency checking","code":""},{"path":"/reference/isValidDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Checks if an input is valid — isValidDS","text":"function checks object valid.","code":""},{"path":"/reference/isValidDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if an input is valid — isValidDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/kurtosis1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the kurtosis of a numeric variable — kurtosis1DS","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"function calculates kurtosis numeric variable study separately.","code":""},{"path":"/reference/kurtosis1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"","code":"kurtosis1DS(x, method)"},{"path":"/reference/kurtosis1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"x string character, name numeric variable. method integer 1 3 selecting one algorithms computing kurtosis detailed headers client-side ds.kurtosis function.","code":""},{"path":"/reference/kurtosis1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"list including kurtosis input numeric variable, number valid observations class, class input object client-side consistency checking.","code":""},{"path":"/reference/kurtosis1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"function calculates kurtosis input variable x three different methods. method specified argument method client-side ds.kurtosis function.","code":""},{"path":"/reference/kurtosis1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/kurtosis2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the kurtosis of a numeric variable — kurtosis2DS","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"function calculates summary statistics returned client-side used estimation combined kurtosis numeric variable across studies.","code":""},{"path":"/reference/kurtosis2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"","code":"kurtosis2DS(x, global.mean)"},{"path":"/reference/kurtosis2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"x string character, name numeric variable. global.mean numeric, combined mean input variable across studies.","code":""},{"path":"/reference/kurtosis2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"list including sum quartic differences values x global mean x across studies, sum squared differences values x global mean x across studies, number valid observations (.e. length x excluding missing values), class, class input object client-side consistency checking.","code":""},{"path":"/reference/kurtosis2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"function calculates sum squared differences values x global mean x across studies, sum quatric differences values x global mean x across studies number valid observations input variable x.","code":""},{"path":"/reference/kurtosis2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lengthDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the length of a vector or list — lengthDS","title":"Returns the length of a vector or list — lengthDS","text":"function similar R function length.","code":""},{"path":"/reference/lengthDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the length of a vector or list — lengthDS","text":"","code":"lengthDS(x)"},{"path":"/reference/lengthDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the length of a vector or list — lengthDS","text":"x string character, name vector list","code":""},{"path":"/reference/lengthDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the length of a vector or list — lengthDS","text":"list two elements: length (number elements input vector list) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/lengthDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the length of a vector or list — lengthDS","text":"function returns length input vector list.","code":""},{"path":"/reference/lengthDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the length of a vector or list — lengthDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/levelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the levels of a factor vector — levelsDS","title":"Returns the levels of a factor vector — levelsDS","text":"function similar R function levels.","code":""},{"path":"/reference/levelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the levels of a factor vector — levelsDS","text":"","code":"levelsDS(x)"},{"path":"/reference/levelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the levels of a factor vector — levelsDS","text":"x character string, name factor vector","code":""},{"path":"/reference/levelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the levels of a factor vector — levelsDS","text":"list one element: Levels (factor levels present vector)","code":""},{"path":"/reference/levelsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the levels of a factor vector — levelsDS","text":"function returns levels input vector list.","code":""},{"path":"/reference/levelsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the levels of a factor vector — levelsDS","text":"Alex Westerberg, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"lexis1DS — lexis1DS","title":"lexis1DS — lexis1DS","text":"first server-side function called ds.lexis.","code":""},{"path":"/reference/lexis1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lexis1DS — lexis1DS","text":"","code":"lexis1DS(exitCol = NULL)"},{"path":"/reference/lexis1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lexis1DS — lexis1DS","text":"exitCol character string specifying variable holding time individual censored fails","code":""},{"path":"/reference/lexis1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lexis1DS — lexis1DS","text":"List `max.time`","code":""},{"path":"/reference/lexis1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lexis1DS — lexis1DS","text":"aggregate function. details see extensive header ds.lexis.","code":""},{"path":"/reference/lexis1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lexis1DS — lexis1DS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"lexis2DS — lexis2DS","title":"lexis2DS — lexis2DS","text":"second serverside function called ds.lexis.","code":""},{"path":"/reference/lexis2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lexis2DS — lexis2DS","text":"","code":"lexis2DS( datatext = NULL, intervalWidth, maxmaxtime, idCol, entryCol, exitCol, statusCol, vartext = NULL )"},{"path":"/reference/lexis2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lexis2DS — lexis2DS","text":"datatext clientside provided character string specifying data.frame holding data set expanded intervalWidth clientside generated character string specifying width survival epochs expanded data maxmaxtime clientside generated object specifying maximum follow time sources idCol clientside generated character string specifying variable holding IDs individuals data set expanded entryCol clientside specified character string identifying variable holding time individual starts follow exitCol clientside specified character string identifying variable holding time individual ends follow (censored fails) statusCol clientside specified character string identifying variable holding final censoring status (failed/censored) vartext clientside provided vector character strings denoting column names additional variables include final expanded table. 'variables' argument set (null) 'data' argument set full data.frame expanded carried forward","code":""},{"path":"/reference/lexis2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lexis2DS — lexis2DS","text":"List `expanded.table`","code":""},{"path":"/reference/lexis2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lexis2DS — lexis2DS","text":"assign function actually creates expanded dataframe containing survival data piecewise exponential regression. lexis2DS also carries series disclosure checks arguments data fail tests, creation expanded dataframe blocked appropriate serverside error message stored. details see extensive header ds.lexis.","code":""},{"path":"/reference/lexis2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lexis2DS — lexis2DS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis3DS.html","id":null,"dir":"Reference","previous_headings":"","what":"@title lexis3DS — lexis3DS","title":"@title lexis3DS — lexis3DS","text":"third serverside function called ds.lexis.","code":""},{"path":"/reference/lexis3DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"@title lexis3DS — lexis3DS","text":"","code":"lexis3DS()"},{"path":"/reference/lexis3DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"@title lexis3DS — lexis3DS","text":"Data frame `messageobj` object","code":""},{"path":"/reference/lexis3DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"@title lexis3DS — lexis3DS","text":"assign function simplifies returned output ds.lexis. Specifically, without lexis3DS output consists table within list, lexis3DS converts directly dataframe. details see extensive header ds.lexis.","code":""},{"path":"/reference/listDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce objects into a list — listDS","title":"Coerce objects into a list — listDS","text":"function similar R function 'list'","code":""},{"path":"/reference/listDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce objects into a list — listDS","text":"","code":"listDS(x.names = NULL, eltnames = NULL)"},{"path":"/reference/listDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce objects into a list — listDS","text":"x.names character vector object names coerce list. eltnames character vector, names elements list.","code":""},{"path":"/reference/listDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce objects into a list — listDS","text":"list","code":""},{"path":"/reference/listDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerce objects into a list — listDS","text":"Unlike R function 'list' takes also vector characters, names elements output list.","code":""},{"path":"/reference/listDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerce objects into a list — listDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"listDisclosureSettingsDS — listDisclosureSettingsDS","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"serverside function aggregate function called ds.listDisclosureSettings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"","code":"listDisclosureSettingsDS()"},{"path":"/reference/listDisclosureSettingsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"List DataSHIELD disclosure settings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"details see extensive header ds.listDisclosureSettings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team","code":""},{"path":"/reference/lmerSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"lmerSLMA2DS serverside function fits linear mixed effects model (lme) - .e. can include fixed random effects - data one multiple sources pooling via SLMA (study level meta-analysis)","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"","code":"lmerSLMA2DS( formula, offset, weights, dataName, REML = TRUE, control_type, control_value.transmit, optimizer, verbose = 0 )"},{"path":"/reference/lmerSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"formula see help ds.lmerSLMA offset see help ds.lmerSLMA weights see help ds.lmerSLMA dataName see help ds.lmerSLMA REML see help ds.lmerSLMA control_type see help ds.lmerSLMA control_value.transmit see help argument function ds.lmerSLMA optimizer see help ds.lmerSLMA verbose see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"key model components see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"lmerSLMA2DS serverside function called ds.lmerSLMA clientside. analytic work engine lmer function R sits lme4 package. ds.lmerSLMA fits linear mixed effects model (lme) - can include fixed random effects - data single multiple sources. multiple data sources, lme fitted convergence data source independently estimates standard errors returned client thereby enabling cross-study pooling using study level meta-analysis (SLMA). default SLMA undertaken using metafor package, SLMA occurs clientside , far user concerned just standard R environment, user can choose use approach meta-analysis choose. detailed help aspect lmerSLM2DS please see extensive help ds.lmerSLMA. Additional information fitting lmes using lmer engine can obtained using R help lmer lme4 package","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"Tom Bishop, additions Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"lmerSLMADS.assign lmerSLMA2DS fits linear mixed effects model (lme) per study saves outcomes study","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"","code":"lmerSLMADS.assign( formula, offset, weights, dataName, REML = TRUE, control_type, control_value.transmit, optimizer, verbose = 0 )"},{"path":"/reference/lmerSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"formula see help ds.lmerSLMA offset see help ds.lmerSLMA weights see help ds.lmerSLMA dataName see help ds.lmerSLMA REML see help ds.lmerSLMA control_type see help ds.lmerSLMA control_value.transmit see help argument function ds.lmerSLMA optimizer see help ds.lmerSLMA verbose see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"writes lmerMod object summarising fitted model serverside. detailed information see help ds.lmerSLMA.","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"lmerSLMADS.assign serverside function called ds.lmerSLMA clientside. analytic work engine lmer function R sits lme4 package. lmerSLMADS.assign fits linear mixed effects model (lme) including fixed random effects - data single data source saves regression outcomes serverside.","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"TDemetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/logDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the logarithm values of the input variable — logDS","title":"Computes the logarithm values of the input variable — logDS","text":"function similar R function log.","code":""},{"path":"/reference/logDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the logarithm values of the input variable — logDS","text":"","code":"logDS(x, base = exp(1))"},{"path":"/reference/logDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the logarithm values of the input variable — logDS","text":"x string character, name numeric integer vector base positive number, base logarithms computed. Default exp(1).","code":""},{"path":"/reference/logDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the logarithm values of the input variable — logDS","text":"object specified newobj argument ds.log (default name log.newobj) written serverside. output object class numeric.","code":""},{"path":"/reference/logDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the logarithm values of the input variable — logDS","text":"function computes logarithm values input numeric integer vector. default natural logarithms computed.","code":""},{"path":"/reference/logDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the logarithm values of the input variable — logDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"lists all objects on a serverside environment — lsDS","title":"lists all objects on a serverside environment — lsDS","text":"creates list names objects specified serverside environment","code":""},{"path":"/reference/lsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lists all objects on a serverside environment — lsDS","text":"","code":"lsDS(search.filter = NULL, env.to.search)"},{"path":"/reference/lsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lists all objects on a serverside environment — lsDS","text":"search.filter either NULL character string (potentially including '*' wildcards) specifying required search criteria. argument fully specified corresponding argument clientside function. env..search integer (e.g. format '2' '5L' format) specifying position search path environment explored. argument fully specified corresponding argument clientside function.","code":""},{"path":"/reference/lsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lists all objects on a serverside environment — lsDS","text":"list containing: (1) name/details serverside R environment ds.ls searched; (2) vector character strings giving names objects meeting naming criteria specified argument specified R serverside environment; (3) nature search filter string actually applied","code":""},{"path":"/reference/lsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lists all objects on a serverside environment — lsDS","text":"Serverside aggregate function lsDS called clientside function ds.ls. running analyses one may want know objects already generated. request disclosive returns names objects contents. default, objects current 'active analytic environment' (\".GlobalEnv\") displayed. environment contains objects serverside DataSHIELD using main analysis written serverside process managing undertaking analysis (variables, scalars, matrices, data.frames etc). details see help ds.ls function native R function ls","code":""},{"path":"/reference/lsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lists all objects on a serverside environment — lsDS","text":"Gaye, (2015). Updated extended Paul Burton (2020).","code":""},{"path":"/reference/lsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"function based native R function lspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/lsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"","code":"lsplineDS(x = x, knots = NULL, marginal = FALSE, names = NULL)"},{"path":"/reference/lsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"x name input numeric variable knots numeric vector knot positions marginal logical, parametrize spline, see Details names, character, vector names constructed variables","code":""},{"path":"/reference/lsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"lspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/lsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment.","code":""},{"path":"/reference/lsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDS assign function called by ds.matrix — matrixDS","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Creates matrix serverside","code":""},{"path":"/reference/matrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"","code":"matrixDS(mdata.transmit, from, nrows.transmit, ncols.transmit, byrow, dimnames)"},{"path":"/reference/matrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"mdata.transmit specifies elements matrix created. Fully specified argument ds.matrix character string specifying source nature . Fully specified <> argument ds.matrix nrows.transmit specifies number rows matrix created. Fully specified argument ds.matrix ncols.transmit specifies number columns matrix created. Fully specified argument ds.matrix byrow logical value specifying whether, vector, matrix created filled row row column column. Fully specified argument ds.matrix dimnames dimnames attribute matrix: NULL list length 2 giving row column names respectively. empty list treated NULL, list length one row names . Fully specified argument ds.matrix","code":""},{"path":"/reference/matrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Output matrix written serverside. details see help ds.matrix","code":""},{"path":"/reference/matrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Similar matrix() function native R. Creates matrix dimensions specified arguments assigns values elements based argument","code":""},{"path":"/reference/matrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDet1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Calculates determinant square matrix returns output clientside","code":""},{"path":"/reference/matrixDet1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"","code":"matrixDet1DS(M1.name = NULL, logarithm)"},{"path":"/reference/matrixDet1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"M1.name character string specifying name matrix determinant calculated logarithm logical. Default FALSE, returns determinant , TRUE returns logarithm modulus determinant.","code":""},{"path":"/reference/matrixDet1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Output determinant matrix identified argument returned clientside. details see help ds.matrixDet","code":""},{"path":"/reference/matrixDet1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Calculates determinant square matrix (additional information see help det function native R). operation possible number columns rows .","code":""},{"path":"/reference/matrixDet1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDet2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Calculates determinant square matrix writes output serverside","code":""},{"path":"/reference/matrixDet2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"","code":"matrixDet2DS(M1.name = NULL, logarithm)"},{"path":"/reference/matrixDet2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"M1.name character string specifying name matrix determinant calculated logarithm logical. Default FALSE, returns determinant , TRUE returns logarithm modulus determinant.","code":""},{"path":"/reference/matrixDet2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Output determinant matrix identified argument written serverside. details see help ds.matrixDet","code":""},{"path":"/reference/matrixDet2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Calculates determinant square matrix (additional information see help det function native R). operation possible number columns rows .","code":""},{"path":"/reference/matrixDet2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDiagDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Extracts diagonal vector square matrix creates diagonal matrix based vector scalar value writes output serverside","code":""},{"path":"/reference/matrixDiagDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"","code":"matrixDiagDS(x1.transmit, aim, nrows.transmit)"},{"path":"/reference/matrixDiagDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"x1.transmit identifies input matrix vector. Fully specified argument ds.matrixDiag. details see help ds.matrixDiag. aim character string specifying behaviour required function. Fully specified argument ds.matrixDiag. details see help ds.matrixDiag. nrows.transmit scalar value forcing number rows columns output matrix.Fully specified argument ds.matrixDiag. details see help ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Output matrix vector specified argument (default name diag_) written serverside. details see help ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"details see help function ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDimnamesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Adds dimnames (row names, column names ) matrix serverside.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"","code":"matrixDimnamesDS(M1.name = NULL, dimnames)"},{"path":"/reference/matrixDimnamesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"M1.name Specifies name serverside matrix dimnames added. Fully specified argument function ds.matrixDimnames. details see help ds.matrixDimnames. dimnames dimnames attribute matrix: NULL list length 2 giving row column names respectively. Fully specified argument function ds.matrixDimnames. details see help ds.matrixDimnames.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Output serverside matrix specified argument (default name diag_) specified dimnames (row column names) written serverside.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Adds dimnames (row names, column names ) matrix serverside. Similar dimnames function native R. details see help function ds.matrixDimnames","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixInvertDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Inverts square matrix writes output serverside","code":""},{"path":"/reference/matrixInvertDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"","code":"matrixInvertDS(M1.name = NULL)"},{"path":"/reference/matrixInvertDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"M1.name character string specifying name matrix inverted","code":""},{"path":"/reference/matrixInvertDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Output matrix representing inverse written serverside. details see help ds.matrixInvert","code":""},{"path":"/reference/matrixInvertDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Undertakes standard matrix inversion. operation possible number columns rows matrix non-singular - positive definite (eg row column zeros)","code":""},{"path":"/reference/matrixInvertDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixMultDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Calculates matrix product two matrices writes output serverside","code":""},{"path":"/reference/matrixMultDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"","code":"matrixMultDS(M1.name = NULL, M2.name = NULL)"},{"path":"/reference/matrixMultDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"M1.name character string specifying name first matrix (M1) argument specified M1 argument original call ds.matrixMult M2.name character string specifying name second matrix (M2) argument specified M1 argument original call ds.matrixMult","code":""},{"path":"/reference/matrixMultDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Output matrix representing product M1 M2 written serverside. details see help ds.matrixMult","code":""},{"path":"/reference/matrixMultDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Undertakes standard matrix multiplication input matrices B dimensions : mxn B: nxp output C dimensions mxp element C[,j] value equal dot product row column j B dot product obtained sum([,1]*B[1,j] + [,2]*B[2,j] + .... + [,n]*B[n,j]). calculation valid number columns number rows B","code":""},{"path":"/reference/matrixMultDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixTransposeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Transposes matrix writes output serverside","code":""},{"path":"/reference/matrixTransposeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"","code":"matrixTransposeDS(M1.name = NULL)"},{"path":"/reference/matrixTransposeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"M1.name character string specifying name matrix transposed","code":""},{"path":"/reference/matrixTransposeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Output matrix representing transpose written serverside. details see help ds.matrixTranspose","code":""},{"path":"/reference/matrixTransposeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Undertakes standard matrix transposition. operation converts matrix matrix C element C[,j] matrix C equals element [j,] matrix . Matrix therefore number rows matrix C columns vice versa.","code":""},{"path":"/reference/matrixTransposeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/mdPatternDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Missing data pattern with disclosure control — mdPatternDS","title":"Missing data pattern with disclosure control — mdPatternDS","text":"function serverside aggregate function computes missing data pattern using mice::md.pattern applies disclosure control prevent revealing small cell counts.","code":""},{"path":"/reference/mdPatternDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Missing data pattern with disclosure control — mdPatternDS","text":"","code":"mdPatternDS(x)"},{"path":"/reference/mdPatternDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Missing data pattern with disclosure control — mdPatternDS","text":"x character string specifying name data frame matrix containing data analyze missing patterns.","code":""},{"path":"/reference/mdPatternDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Missing data pattern with disclosure control — mdPatternDS","text":"list containing: pattern missing data pattern matrix disclosure control applied valid Logical indicating patterns meet disclosure requirements message message describing validity status class class input object, client-side consistency checking","code":""},{"path":"/reference/mdPatternDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Missing data pattern with disclosure control — mdPatternDS","text":"function calls mice::md.pattern function generate matrix showing missing data patterns input data. ensure disclosure control, pattern counts threshold (nfilter.tab, default=3) suppressed. Suppression Method: pattern count threshold: - Row name changed \"suppressed()\" N threshold - pattern values row set NA - Summary row also set NA (prevents back-calculation) Output Matrix Structure: - Rows represent different missing data patterns (plus summary row bottom) - Row names contain pattern counts (\"suppressed()\" invalid patterns) - Columns show 1 variable observed, 0 missing - Last column shows total number missing values per pattern - Last row shows total number missing values per variable Note Pooling: function called ds.mdPattern type='combine', suppressed patterns excluded pooling prevent disclosure subtraction. means pooled counts may underestimate true total patterns suppressed studies.","code":""},{"path":"/reference/mdPatternDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Missing data pattern with disclosure control — mdPatternDS","text":"Xavier Escribà montagut DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/meanDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes statistical mean of a vector — meanDS","title":"Computes statistical mean of a vector — meanDS","text":"Calculates mean value.","code":""},{"path":"/reference/meanDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes statistical mean of a vector — meanDS","text":"","code":"meanDS(x)"},{"path":"/reference/meanDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes statistical mean of a vector — meanDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/meanDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes statistical mean of a vector — meanDS","text":"list, estimated mean, number missing values, number valid values, total number values, class, class input object client-side consistency checking","code":""},{"path":"/reference/meanDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes statistical mean of a vector — meanDS","text":"length input vector less set filter missing value returned.","code":""},{"path":"/reference/meanDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes statistical mean of a vector — meanDS","text":"Gaye , Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/meanSdGpDS.html","id":null,"dir":"Reference","previous_headings":"","what":"MeanSdGpDS — meanSdGpDS","title":"MeanSdGpDS — meanSdGpDS","text":"Server-side function called ds.meanSdGp","code":""},{"path":"/reference/meanSdGpDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MeanSdGpDS — meanSdGpDS","text":"","code":"meanSdGpDS(x, index)"},{"path":"/reference/meanSdGpDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MeanSdGpDS — meanSdGpDS","text":"x client-side supplied character string identifying variable means/SDs calculated index client-side supplied character string identifying factor across means/SDs calculated","code":""},{"path":"/reference/meanSdGpDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MeanSdGpDS — meanSdGpDS","text":"List results group statistics","code":""},{"path":"/reference/meanSdGpDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MeanSdGpDS — meanSdGpDS","text":"Computes mean standard deviation across groups defined one factor","code":""},{"path":"/reference/meanSdGpDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MeanSdGpDS — meanSdGpDS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/mergeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"mergeDS (assign function) called by ds.merge — mergeDS","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"merges (links) two data.frames together based common values defined vectors data.frame","code":""},{"path":"/reference/mergeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"","code":"mergeDS( x.name, y.name, by.x.names.transmit, by.y.names.transmit, all.x, all.y, sort, suffixes.transmit, no.dups, incomparables )"},{"path":"/reference/mergeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"x.name, name first data.frame merged specified inverted commas. Specified via argument ds.merge function y.name, name second data.frame merged specified inverted commas. Specified via argument ds.merge function .x.names.transmit name single variable vector names multiple variables (transmittable form) containing IDs data data.frame x merged/linked data.frame y. Specified via argument <.x.names> ds.merge function .y.names.transmit name single variable vector names multiple variables (transmittable form) containing IDs data data.frame y merged/linked data.frame x. Specified via argument <.y.names> ds.merge function .x logical, TRUE, extra rows added output, one row x matching row y. Specified via argument <.x> ds.merge function. Default = FALSE. .y logical, TRUE, extra rows added output, one row y matching row x. Specified via argument <.y> ds.merge function. Default = FALSE. sort logical, TRUE merged result sorted elements .x.names .y.names columns. Specified via argument ds.merge function. Default = TRUE. suffixes.transmit character vector length 2 (transmittable form) specifying suffixes used making unique common column names two input data.frames appear merged data.frame. Specified via argument ds.merge function. Default '.x' '.y'. .dups logical, TRUE suffixes appended cases rigorously avoid duplicated column names merged data.frame. Specified via argument <.dups> ds.merge function. Default TRUE apparently implicitly FALSE R version 3.5.0. incomparables, values intended merging one column matched. See 'match' help Native R merge function. Specified via argument ds.merge","code":""},{"path":"/reference/mergeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"merged data.frame specified argument ds.merge (default 'x.name_y.name' argument NULL) written serverside. addition, two validity messages returned clientside indicating whether created data source whether valid form. form valid least one study may studysideMessage can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message() print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message() return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/mergeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"information see details native R function merge DataSHIELD clientside function ds.merge.","code":""},{"path":"/reference/mergeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/metadataDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the metadata, if any, about the specified variable — metadataDS","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"function returns metadata, , specified variable.","code":""},{"path":"/reference/metadataDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"","code":"metadataDS(x)"},{"path":"/reference/metadataDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"x string character, containing name specified variable","code":""},{"path":"/reference/metadataDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"list containing metadata. elements list depend metadata available.","code":""},{"path":"/reference/metadataDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"function returns metadata, obtained attributes function.","code":""},{"path":"/reference/metadataDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"Stuart Wheater, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/miceDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Aggregate function called by ds.mice — miceDS","title":"Aggregate function called by ds.mice — miceDS","text":"function wrapper function mice mice R package. function creates multiple imputations (replacement values) multivariate missing data. method based Fully Conditional Specification, incomplete variable imputed separate model. MICE algorithm can impute mixes continuous, binary, unordered categorical ordered categorical data. addition, MICE can impute continuous two-level data, maintain consistency imputations means passive imputation.","code":""},{"path":"/reference/miceDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Aggregate function called by ds.mice — miceDS","text":"","code":"miceDS( data = data, m = m, maxit = maxit, method = method, post = post, seed = seed, predictorMatrix = predictorMatrix, ncol.pred.mat = ncol.pred.mat, newobj_mids = newobj_mids, newobj_df = newobj_df )"},{"path":"/reference/miceDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Aggregate function called by ds.mice — miceDS","text":"data data frame matrix containing incomplete data. m Number multiple imputations. default m=5. maximum allowed number DataSHIELD m=20. maxit scalar giving number iterations. default 5. maximum allowed number DataSHIELD maxit=30. method Can either single string, vector strings length ncol(data), specifying imputation method used column data. specified single string, method used blocks. default imputation method (argument specified) depends measurement level target column, regulated defaultMethod argument native R mice function. Columns need imputed empty method \"\". post vector strings length ncol(data) specifying expressions strings. string parsed executed within sampler() function post-process imputed values iterations. default vector empty strings, indicating post-processing. Multivariate (block) imputation methods ignore post parameter. seed either NA (default) \"fixed\". seed set \"fixed\" fixed seed random number generator study-specific used. predictorMatrix numeric matrix ncol(data) rows ncol(data) columns, containing 0/1 data specifying set predictors used target column. row corresponds variable imputed. value 1 means column variable used predictor target variables (rows). default, predictorMatrix square matrix ncol(data) rows columns 1's, except diagonal. ncol.pred.mat number columns predictorMatrix. newobj_mids character string provides name output mids object stored data servers. Default mids_object. newobj_df character string provides name output dataframes stored data servers. Default imputationSet. example, m=5, newobj_df=\"imputationSet\", five imputed dataframes saved servers names imputationSet.1, imputationSet.2, imputationSet.3, imputationSet.4, imputationSet.5.","code":""},{"path":"/reference/miceDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Aggregate function called by ds.mice — miceDS","text":"list three elements: method, predictorMatrix post. function also saves server mids object completed datasets dataframes.","code":""},{"path":"/reference/miceDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Aggregate function called by ds.mice — miceDS","text":"additional details see help header mice function native R mice package.","code":""},{"path":"/reference/miceDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Aggregate function called by ds.mice — miceDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/namesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the names of a list object — namesDS","title":"Return the names of a list object — namesDS","text":"Returns names designated server-side list","code":""},{"path":"/reference/namesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the names of a list object — namesDS","text":"","code":"namesDS(xname.transmit)"},{"path":"/reference/namesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the names of a list object — namesDS","text":"xname.transmit character string specifying name list.","code":""},{"path":"/reference/namesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the names of a list object — namesDS","text":"namesDS returns client-side names list object stored server-side.","code":""},{"path":"/reference/namesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Return the names of a list object — namesDS","text":"namesDS aggregate function called ds.names. function similar native R function names subsume functionality, example, works extract names already exist, create new names objects. function restricted objects type list, includes objects primary class list return TRUE native R function .list. example, includes multi-component object created fitting generalized linear model using ds.glmSLMA. resultant object saved separate server formally double class \"glm\" \"ls\" responds TRUE .list(),","code":""},{"path":"/reference/namesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Return the names of a list object — namesDS","text":"Amadou Gaye, updated Paul Burton 25/06/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/nsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"function based native R function ns splines package. function generate B-spline basis matrix natural cubic spline.","code":""},{"path":"/reference/nsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"","code":"nsDS(x, df, knots, intercept, Boundary.knots)"},{"path":"/reference/nsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"x predictor variable. Missing values allowed. df degrees freedom. One can supply df rather knots; ns() chooses df - 1 - intercept knots suitably chosen quantiles x (ignore missing values). default, df = NULL, sets number inner knots length(knots). knots breakpoints define spline. default knots; together natural boundary conditions results basis linear regression x. Typical values mean median one knot, quantiles knots. See also Boundary.knots. intercept TRUE, intercept included basis; default FALSE. Boundary.knots boundary points impose natural boundary conditions anchor B-spline basis (default range data). knots Boundary.knots supplied, basis parameters depend x. Data can extend beyond Boundary.knots","code":""},{"path":"/reference/nsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"matrix dimension length(x) * df either df supplied knots supplied, df = length(knots) + 1 + intercept. Attributes returned correspond arguments ns, explicitly give knots, Boundary.knots etc use predict.ns(). object assigned serverside.","code":""},{"path":"/reference/nsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"ns native R based function splineDesign. generates basis matrix representing family piecewise-cubic splines specified sequence interior knots, natural boundary conditions. enforce constraint function linear beyond boundary knots, can either supplied default extremes data. primary use modeling formula directly specify natural spline term model.","code":""},{"path":"/reference/nsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/numNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Counts the number of missing values — numNaDS","title":"Counts the number of missing values — numNaDS","text":"function just counts number missing entries vector.","code":""},{"path":"/reference/numNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Counts the number of missing values — numNaDS","text":"","code":"numNaDS(x)"},{"path":"/reference/numNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Counts the number of missing values — numNaDS","text":"x character string, name server-side vector","code":""},{"path":"/reference/numNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Counts the number of missing values — numNaDS","text":"list two elements: numNA (integer, number missing values) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/numNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Counts the number of missing values — numNaDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/qlsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"function based native R function qlspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/qlsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"","code":"qlsplineDS(x = x, q = q, na.rm = TRUE, marginal = FALSE, names = NULL)"},{"path":"/reference/qlsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"x name input numeric variable q numeric, single scalar greater equal 2 number equal-frequency intervals along x vector numbers (0; 1) specifying quantiles explicitly. na.rm logical, whether NA removed calculating quantiles, passed na.rm quantile. Default set TRUE. marginal logical, parametrize spline, see Details names character, vector names constructed variables","code":""},{"path":"/reference/qlsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"qlspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/qlsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment. Function qlspline wraps lspline calculates knot positions quantiles x. q numerical scalar greater equal 2, quantiles computed seq(0, 1, length.= q + 1)[-c(1, q+1)], .e. knots q-tiles distribution x. Alternatively, q can vector values [0; 1] specifying quantile probabilities directly (vector passed argument probs quantile).","code":""},{"path":"/reference/qlsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/quantileMeanDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"probabilities 5 used compute corresponding quantiles.","code":""},{"path":"/reference/quantileMeanDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"","code":"quantileMeanDS(x)"},{"path":"/reference/quantileMeanDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/quantileMeanDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"list, quantiles, numeric vector represents sample quantiles, class, class input object client-side consistency checking","code":""},{"path":"/reference/quantileMeanDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"Burton, P.; Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rBinomDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rBinomDS serverside assign function — rBinomDS","title":"rBinomDS serverside assign function — rBinomDS","text":"primary serverside assign function called ds.rBinom","code":""},{"path":"/reference/rBinomDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rBinomDS serverside assign function — rBinomDS","text":"","code":"rBinomDS(n, size = 1, prob = 0.5)"},{"path":"/reference/rBinomDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rBinomDS serverside assign function — rBinomDS","text":"n length pseudorandom number vector generated specified argument function ds.rBinom size scalar must positive integer. Value set directly argument ds.rBinom - details see help ds.rBinom. May scalar vector allowing size vary observation observation. prob numeric scalar range 0 > prob > 1 specifies probability positive response. Value set directly argument ds.rBinom - details see help ds.rBinom May scalar vector allowing size vary observation observation.","code":""},{"path":"/reference/rBinomDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rBinomDS serverside assign function — rBinomDS","text":"vector pseudorandom numbers binomial distribution, written serverside object named argument ds.rBinom.","code":""},{"path":"/reference/rBinomDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rBinomDS serverside assign function — rBinomDS","text":"Generates vector pseudorandom numbers binomial distribution data source specified arguments ds.rBinom. serverside function effectively function rbinom() native R arguments .","code":""},{"path":"/reference/rBinomDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rBinomDS serverside assign function — rBinomDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rNormDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rNormDS serverside assign function — rNormDS","title":"rNormDS serverside assign function — rNormDS","text":"primary serverside assign function called ds.rNorm","code":""},{"path":"/reference/rNormDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rNormDS serverside assign function — rNormDS","text":"","code":"rNormDS(n, mean = 0, sd = 1, force.output.to.k.decimal.places = 9)"},{"path":"/reference/rNormDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rNormDS serverside assign function — rNormDS","text":"n length pseudorandom number vector generated specified argument function ds.rNorm mean specifies mean pseudorandom number vector generated specified argument function ds.rNorm. May scalar vector allowing mean vary observation observation. sd specifies standard deviation pseudorandom number vector generated specified argument function ds.rNorm May scalar vector allowing sd vary observation observation. force.output..k.decimal.places scalar integer. Forces output random number vector k decimal places. 0 rounds coerces decimal random number output integer, k range 1-8 forces output k decimal places. k = 9, rounding occurs native output. Default=9. Value specified argument ds.rNorm","code":""},{"path":"/reference/rNormDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rNormDS serverside assign function — rNormDS","text":"numeric vector pseudorandom numbers normal distribution, rounded decimal places less 9, written serverside object named argument ds.rNorm.","code":""},{"path":"/reference/rNormDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rNormDS serverside assign function — rNormDS","text":"Generates vector pseudorandom numbers normal distribution data source specified arguments ds.rNorm. serverside function effectively function rnorm() native R arguments .","code":""},{"path":"/reference/rNormDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rNormDS serverside assign function — rNormDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rPoisDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rPoisDS serverside assign function — rPoisDS","title":"rPoisDS serverside assign function — rPoisDS","text":"primary serverside assign function called ds.rPois","code":""},{"path":"/reference/rPoisDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rPoisDS serverside assign function — rPoisDS","text":"","code":"rPoisDS(n, lambda = 1)"},{"path":"/reference/rPoisDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rPoisDS serverside assign function — rPoisDS","text":"n length pseudorandom number vector generated specified argument function ds.rPois lambda numeric scalar specifying expected count Poisson distribution used generate random counts. Specified directly lambda argument ds.rPois. May scalar vector allowing lambda vary observation observation.","code":""},{"path":"/reference/rPoisDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rPoisDS serverside assign function — rPoisDS","text":"vector pseudorandom non-negative integers Poisson distribution, written serverside object named argument ds.rPois.","code":""},{"path":"/reference/rPoisDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rPoisDS serverside assign function — rPoisDS","text":"Generates vector pseudorandom numbers (non-negative integers) Poisson distribution data source specified arguments ds.rPois. serverside function effectively function rpois() native R arguments .","code":""},{"path":"/reference/rPoisDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rPoisDS serverside assign function — rPoisDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rUnifDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rUnifDS serverside assign function — rUnifDS","title":"rUnifDS serverside assign function — rUnifDS","text":"primary serverside assign function called ds.rUnif","code":""},{"path":"/reference/rUnifDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rUnifDS serverside assign function — rUnifDS","text":"","code":"rUnifDS(n, min = 0, max = 1, force.output.to.k.decimal.places = 9)"},{"path":"/reference/rUnifDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rUnifDS serverside assign function — rUnifDS","text":"n length pseudorandom number vector generated specified argument function ds.rUnif min numeric scalar specifying minimum range across random numbers generated source. Specified directly min argument ds.rUnif. May scalar vector allowing min vary observation observation. max numeric scalar specifying maximum range across random numbers generated source. Specified directly max argument ds.rUnif. May scalar vector allowing min vary observation observation. force.output..k.decimal.places scalar integer. Forces output random number vector k decimal places. 0 rounds coerces decimal random number output integer, k range 1-8 forces output k decimal places. k = 9, rounding occurs native output. Default=9. Value specified argument ds.rUnif","code":""},{"path":"/reference/rUnifDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rUnifDS serverside assign function — rUnifDS","text":"numeric vector pseudorandom numbers uniform distribution, rounded decimal places less 9, written serverside object named argument ds.rUnif.","code":""},{"path":"/reference/rUnifDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rUnifDS serverside assign function — rUnifDS","text":"Generates vector pseudorandom numbers uniform distribution data source specified arguments ds.rUnif. serverside function effectively function runif() native R arguments .","code":""},{"path":"/reference/rUnifDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rUnifDS serverside assign function — rUnifDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rangeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"returns the minimum and maximum of a numeric vector — rangeDS","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"function similar R function range instead return real minimum maximum, computed values multiplied small random number.","code":""},{"path":"/reference/rangeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"","code":"rangeDS(x)"},{"path":"/reference/rangeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/rangeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"numeric vector contains minimum maximum values vector","code":""},{"path":"/reference/rangeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rbindDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rbindDS called by ds.rbind — rbindDS","title":"rbindDS called by ds.rbind — rbindDS","text":"serverside assign function takes sequence vector, matrix data-frame arguments combines row produce matrix.","code":""},{"path":"/reference/rbindDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rbindDS called by ds.rbind — rbindDS","text":"","code":"rbindDS(x.names.transmit = NULL, colnames.transmit = NULL)"},{"path":"/reference/rbindDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rbindDS called by ds.rbind — rbindDS","text":"x.names.transmit vector character strings representing names elemental components combined converted transmittable format. argument fully specified argument ds.rbind colnames.transmit NULL vector character strings representing forced column names output object converted transmittable format. argument fully specified argument ds.cbind.","code":""},{"path":"/reference/rbindDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rbindDS called by ds.rbind — rbindDS","text":"object specified argument ds.rbind(default name ) written serverside. well writing output object serverside, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.cbind() also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/rbindDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rbindDS called by ds.rbind — rbindDS","text":"sequence vector, matrix data-frame arguments combined row row produce matrix written serverside. details see help ds.rbind native R function rbind.","code":""},{"path":"/reference/rbindDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rbindDS called by ds.rbind — rbindDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/reShapeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"reShapeDS (assign function) called by ds.reShape — reShapeDS","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"Reshapes data frame containing longitudinal otherwise grouped data 'wide' 'long' format vice-versa","code":""},{"path":"/reference/reShapeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"","code":"reShapeDS( data.name, varying.transmit, v.names.transmit, timevar.name, idvar.name, drop.transmit, direction, sep )"},{"path":"/reference/reShapeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"data.name, name data.frame reshaped. Specified via argument ds.reShape function varying.transmit, names sets variables wide format correspond single variables long format (typically may called 'time-varying' 'time-dependent' variables). Specified via argument ds.reShape function. v.names.transmit, names variables long format correspond multiple variables wide format - example, sbp7, sbp11, sbp15 (measured systolic blood pressure ages 7, 11 15 years). Specified via argument ds.reShape function timevar.name, variable long format differentiates multiple records group individual. Specified via argument ds.reShape function idvar.name, names one variables long format identify multiple records group/individual. /variable(s) may also present wide format. Specified via argument ds.reShape function drop.transmit, vector names variables drop reshaping. Specified via argument ds.reShape function direction, character string, partially matched either \"wide\" reshape long wide format, \"long\" reshape wide long format. Specified via argument ds.reShape function sep, character vector length 1, indicating separating character variable names wide format. Specified via argument ds.reShape function","code":""},{"path":"/reference/reShapeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"reshaped data.frame converted long wide format wide long format written serverside given name provided argument ds.reShape 'newObject' name specified.","code":""},{"path":"/reference/reShapeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"function based native R function reshape. reshapes data frame containing longitudinal otherwise grouped data 'wide' format repeated measurements separate columns record 'long' format repeated measurements separate records. reshaping can either direction","code":""},{"path":"/reference/reShapeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"Demetris Avraam, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/recodeValuesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"function recodes specified values elements vector matched set alternative specified values.","code":""},{"path":"/reference/recodeValuesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"","code":"recodeValuesDS( var.name.text = NULL, values2replace.text = NULL, new.values.text = NULL, missing = NULL )"},{"path":"/reference/recodeValuesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"var.name.text character string providing name vector representing variable recoded. argument generated passed directly recodeValuesDS ds.recodeValues values2replace.text character string specifying values vector specified argument replaced new values specified new.values.vector. argument generated passed directly recodeValuesDS ds.recodeValues. effect, argument ds.recodeValues function converted character string format acceptable DataSHIELD R parser data repository can accepted recodeValuesDS new.values.text character string specifying new values specified values vector converted. argument generated passed directly recodeValuesDS ds.recodeValues. effect, argument ds.recodeValues function converted character string format acceptable DataSHIELD R parser data repository can used call recodeValuesDS. missing supplied, missing values variable referred var.name.text replaced value.","code":""},{"path":"/reference/recodeValuesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"object specified argument (default name '_recoded') initially specified calling ds.recodeValues. output object (required recoded variable called written serverside.","code":""},{"path":"/reference/recodeValuesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"details see help header ds.recodeValues","code":""},{"path":"/reference/recodeValuesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/repDS.html","id":null,"dir":"Reference","previous_headings":"","what":"repDS called by ds.rep — repDS","title":"repDS called by ds.rep — repDS","text":"assign function creates repetitive sequence repeating identified scalar, specified elements vector list. analogous rep function native R. sequence written new object serverside","code":""},{"path":"/reference/repDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"repDS called by ds.rep — repDS","text":"","code":"repDS( x1.transmit, times.transmit, length.out.transmit, each.transmit, x1.includes.characters, source.x1, source.times, source.length.out, source.each )"},{"path":"/reference/repDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"repDS called by ds.rep — repDS","text":"x1.transmit argument determines input scalar, vector list. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. times.transmit argument determines number replications pattern replications input scalar/vector construct output repetitive sequence. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. length..transmit argument fixes length output repetitive sequence vector behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. .transmit argument specifies number replications individual elements rather replications full sequence. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument <> call ds.rep calls repDS. x1.includes.characters Boolean parameter determining whether coerce final output sequence numeric. Defaults FALSE output coerced numeric. detailed behaviour see help ds.rep. parameter usually fully defined argument call ds.rep calls repDS. source.x1 defines source scalar vector defined argument. Four character strings allowed: \"clientside\" \"c\" serverside \"s\". behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. source.times see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS. source.length.see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS. source.see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS.","code":""},{"path":"/reference/repDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"repDS called by ds.rep — repDS","text":"vector containing specified repetitive sequence write output object defined argument (default name seq.vect) written serverside source. addition, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.matrixDiag also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/repDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"repDS called by ds.rep — repDS","text":"details can found help details ds.rep following aspects help function rep native R also apply (explained detail exceptions identified help ds.rep): addition Details R help : default behaviour call rep(x, times = 1, length.= NA, = 1) Normally just one additional arguments specified, '' specified either two, replication performed first, followed replication implied times length.. times consists single integer, result consists whole input repeated many times. times vector length x (replication ), result consists x[1] repeated times[1] times, x[2] repeated times[2] times . ***Note exception 1 . length.may given place times, case x repeated many times necessary create vector length. given, length.takes priority times ignored. ***Note exception 3 . Non-integer values times truncated towards zero. times computed quantity prudent add small fuzz use round. analogously .","code":""},{"path":"/reference/repDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"repDS called by ds.rep — repDS","text":"Paul Burton DataSHIELD Development Team, 14/10/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/replaceNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Replaces the missing values in a vector — replaceNaDS","title":"Replaces the missing values in a vector — replaceNaDS","text":"function identifies missing values replaces value values specified analyst.","code":""},{"path":"/reference/replaceNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replaces the missing values in a vector — replaceNaDS","text":"","code":"replaceNaDS(x, replacements)"},{"path":"/reference/replaceNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replaces the missing values in a vector — replaceNaDS","text":"x character, name vector process. replacements vector contains replacement value(s), vector one values study.","code":""},{"path":"/reference/replaceNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replaces the missing values in a vector — replaceNaDS","text":"new vector without missing values","code":""},{"path":"/reference/replaceNaDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Replaces the missing values in a vector — replaceNaDS","text":"function used analyst prefer requires complete vectors. possible specify one value missing value first returning number missing values using function numNaDS cases might sensible replace missing values one specific value e.g. replace missing values vector mean median value. missing values replaced new vector created.","code":""},{"path":"/reference/replaceNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Replaces the missing values in a vector — replaceNaDS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rmDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rmDS an aggregate function called by ds.rm — rmDS","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"deletes R object serverside","code":""},{"path":"/reference/rmDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"","code":"rmDS(x.names.transmit)"},{"path":"/reference/rmDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"x.names.transmit, names objects deleted converted transmissible form, comma separated list character string. argument specified via argument ds.rm","code":""},{"path":"/reference/rmDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"specified object deleted serverside. successful message \"Object successfully deleted\" returned clientside (x.names names object deleted). objects deleted already absent given source, source return message: \"Object deleted, .e. , exist need deleting\".","code":""},{"path":"/reference/rmDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"serverside function based rm() function native R. aggregate function may surprising modifies object serverside, therefore expected assign function. However, assign function last step running write modified object newobj. fail effect function delete object impossible write anywhere.","code":""},{"path":"/reference/rmDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"Paul Burton DataSHIELD Development Team","code":""},{"path":"/reference/rowColCalcDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"function similar R base functions 'rowSums', 'colSums', 'rowMeans' 'colMeans'.","code":""},{"path":"/reference/rowColCalcDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"","code":"rowColCalcDS(dataset.name, operation)"},{"path":"/reference/rowColCalcDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"dataset.name character string providing name server-side array two dimensions. operation integer indicates operation carry : 1 'rowSums', 2 'colSums', 3 'rowMeans' 4 'colMeans'","code":""},{"path":"/reference/rowColCalcDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"numeric vector","code":""},{"path":"/reference/rowColCalcDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"output returned user number entries output vector greater equal allowed size.","code":""},{"path":"/reference/rowColCalcDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/sampleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"draws pseudorandom sample vector, dataframe matrix serverside - special case - randomly permutes vector, dataframe matrix.","code":""},{"path":"/reference/sampleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"","code":"sampleDS( x.transmit, size.transmit, replace.transmit = NULL, prob.transmit = NULL )"},{"path":"/reference/sampleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"x.transmit Either character string providing name serverside vector, matrix data.frame sampled permuted, integer/numeric scalar (e.g. 923) indicating one create new vector serverside randomly permuted sample vector 1:923. x.transmit fully specified [x] argument ds.sample. details see help ds.sample native R help sample(). size.transmit numeric/integer scalar indicating size sample drawn. size.transmit fully specified [size] argument ds.sample. details see help ds.sample native R help sample(). replace.transmit Boolean indicator (TRUE FALSE) specifying whether sample drawn without replacement. Default FALSE sample drawn without replacement. replace.transmit fully specified [replace] argument ds.sample. details see help ds.sample native R help sample(). prob.transmit character string containing name numeric vector probability weights serverside associated elements vector sampled enabling drawing sample elements given higher probability drawn others. prob.transmit fully specified [prob] argument ds.sample. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"object specified argument (default name 'newobj.sample') written serverside. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"Serverside assign function sampleDS called clientside function ds.sample. Based native R function sample() deals slightly differently data.frames matrices. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"Paul Burton, DataSHIELD Development Team, 15/4/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/scatterPlotDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the coordinates of the data to be plot — scatterPlotDS","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"function uses two disclosure control methods generate non-disclosive coordinates returned client generates non-disclosive scatter plots.","code":""},{"path":"/reference/scatterPlotDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"","code":"scatterPlotDS(x.name, y.name, method.indicator, k, noise)"},{"path":"/reference/scatterPlotDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"x.name character string providing name server-side numeric vector, x-variable. y.name character string providing name server-side numeric vector, y-variable. method.indicator integer either 1 2. user selects deterministic method client side function method.indicator set 1 user selects probabilistic method argument set 2. k number nearest neighbours centroid calculated deterministic method selected. noise percentage initial variance used variance embedded noise probabilistic method selected.","code":""},{"path":"/reference/scatterPlotDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"list x y coordinates data plot, along classes x y inputs (class.x class.y)","code":""},{"path":"/reference/scatterPlotDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"user chooses deterministic approach, function finds k-1 nearest neighbours data point 2-dimensional space. nearest neighbours data points minimum Euclidean distances point interest. point interest k-1 nearest neighbours used calculation coordinates centroid k points. Centroid referred centre mass, .e. x-coordinate centroid average value x-coordinates k nearest neighbours y-coordinate centroid average y-coordinates k nearest neighbours. user chooses probabilistic approach, function adds random noise $x$ $y$ separately. random noise follows normal distribution zero mean variance equal 10 disclosure fix random number generator value specified input variables. Thus function returns always noisy data given pair variables.","code":""},{"path":"/reference/scatterPlotDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/seqDS.html","id":null,"dir":"Reference","previous_headings":"","what":"seqDS a serverside assign function called by ds.seq — seqDS","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"assign function seqDS called ds.seq","code":""},{"path":"/reference/seqDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"","code":"seqDS( FROM.value.char, TO.value.char, BY.value.char, LENGTH.OUT.value.char, ALONG.WITH.name )"},{"path":"/reference/seqDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":".value.char starting value sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. .value.char terminal value sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. .value.char value increment step sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. LENGTH..value.char length sequence point extension stopped, expressed integer real number decimal point character form. Fully specified argument ds.seq. ALONG..name convenience, rather specifying value LENGTH.can often better specify variable name argument. Fully specified argument ds.seq.","code":""},{"path":"/reference/seqDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"object specified argument ds.seq (default name newObj) written serverside. well writing output object serverside, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.seq() also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/seqDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"assign function uses native R function seq() create one flexible range sequence vectors can used help manage analyse data. assign function resultant vector written new object specified data source servers. Please see \"details\" ds.seq information allowable combinations arguments etc.","code":""},{"path":"/reference/seqDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"Paul Burton DataSHIELD Development Team, 17/9/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/setSeedDS.html","id":null,"dir":"Reference","previous_headings":"","what":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"aggregate serverside function primes pseudorandom number generator data source","code":""},{"path":"/reference/setSeedDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"","code":"setSeedDS(seedtext = NULL, kind = NULL, normal.kind = NULL)"},{"path":"/reference/setSeedDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"seedtext simply value argument ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois ds.rBinom coerced character format. done clientside functions require DataSHIELD user anything. Please see help clientside functions, particular, information argument details. kind see help set.seed() function native R normal.kind see help set.seed() function native R","code":""},{"path":"/reference/setSeedDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"Sets values vector integers length 626 known .Random.seed data source true current state random seed source.","code":""},{"path":"/reference/setSeedDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"setSeedDS effectively equivalent native R function set.seed() help function can provide many additional details. minor difference first argument setSeedDS, takes integer priming seed character format. However, user integer still specified directly integer argument one clientside functions ds.setSeed, ds.rNorm ..... clientside functions coerces integer character format calls setSeedDS first active line code setSeedDS converts character string back integer treats first argument native R function set.seed(). two arguments set.seed() native R, defaulted specifying NULL. defaulting hard wired setSeedDS function changed analyst means setSeedDS much less flexible native R's set.seed() function. DataSHIELD user requires aspect flexibility returned development team can approached, unless actually theoretical work random number generators likely ","code":""},{"path":"/reference/setSeedDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/skewness1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the skewness of a numeric variable — skewness1DS","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"function calculates skewness numeric variable study separately.","code":""},{"path":"/reference/skewness1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"","code":"skewness1DS(x, method)"},{"path":"/reference/skewness1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"x string character, name numeric variable. method integer 1 3 selecting one algorithms computing skewness detailed headers client-side ds.skewness function.","code":""},{"path":"/reference/skewness1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"list including skewness input numeric variable, number valid observations class, class input object client-side consistency checking.","code":""},{"path":"/reference/skewness1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"function calculates skewness input variable x three different methods. method specified argument method client-side ds.skewness function.","code":""},{"path":"/reference/skewness1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/skewness2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the skewness of a numeric variable — skewness2DS","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"function calculates summary statistics returned client-side used estimation combined skewness numeric variable across studies.","code":""},{"path":"/reference/skewness2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"","code":"skewness2DS(x, global.mean)"},{"path":"/reference/skewness2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"x string character, name numeric variable. global.mean numeric, combined mean input variable across studies.","code":""},{"path":"/reference/skewness2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"list including sum cubed differences values x global mean x across studies, sum squared differences values x global mean x across studies, number valid observations (.e. length x excluding missing values), class, class input object client-side consistency checking.","code":""},{"path":"/reference/skewness2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"function calculates sum squared differences values x global mean x across studies, sum cubed differences values x global mean x across studies number valid observations input variable x.","code":""},{"path":"/reference/skewness2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/sqrtDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the square root values of the input variable — sqrtDS","title":"Computes the square root values of the input variable — sqrtDS","text":"function similar R function sqrt.","code":""},{"path":"/reference/sqrtDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the square root values of the input variable — sqrtDS","text":"","code":"sqrtDS(x)"},{"path":"/reference/sqrtDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the square root values of the input variable — sqrtDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/sqrtDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the square root values of the input variable — sqrtDS","text":"object specified newobj argument ds.sqrt (default name sqrt.newobj) written server-side. output object class numeric integer.","code":""},{"path":"/reference/sqrtDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the square root values of the input variable — sqrtDS","text":"function computes square root values input numeric integer vector.","code":""},{"path":"/reference/sqrtDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the square root values of the input variable — sqrtDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/table1DDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates 1-dimensional contingency tables — table1DDS","title":"Creates 1-dimensional contingency tables — table1DDS","text":"function generates 1-dimensional table potentially disclosive cells. (based set threshold) replaced missing value ('NA').","code":""},{"path":"/reference/table1DDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates 1-dimensional contingency tables — table1DDS","text":"","code":"table1DDS(xvect)"},{"path":"/reference/table1DDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates 1-dimensional contingency tables — table1DDS","text":"xvect numerical vector discrete values - usually factor.","code":""},{"path":"/reference/table1DDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates 1-dimensional contingency tables — table1DDS","text":"list contains two elements: 'table', 1-dimensional table 'message' message informs validity table.","code":""},{"path":"/reference/table1DDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates 1-dimensional contingency tables — table1DDS","text":"generates 1-dimensional tables valid (non-disclosive) 1-dimensional tables defined data sources table cells counts 1 set threshold. output table invalid cells total count replaced missing values. total count visible table returned client side. message also returned 1-dimensional; message says \"invalid table - invalid counts present\" table invalid 'valid table' otherwise.","code":""},{"path":"/reference/table1DDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Creates 1-dimensional contingency tables — table1DDS","text":"Gaye .","code":""},{"path":"/reference/table2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"Helps creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/table2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"","code":"table2DS(newobj, rvar.transmit, cvar.transmit, stvar.transmit)"},{"path":"/reference/table2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"newobj character string providing name output table object written serverside TRUE. explicit name table object specified, nevertheless TRUE, name serverside table object defaults 'newObj'. Fully specified argument ds.table. information see help ds.table rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table","code":""},{"path":"/reference/table2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"information see help ds.table","code":""},{"path":"/reference/table2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":" argument ds.table set TRUE, aggregate function returns non-disclosive information table object written serverside tableDS.assign. information see help ds.table, tableDS.assign tableDS DataSHIELD table function native R.","code":""},{"path":"/reference/table2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tableDS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"helps creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/tableDS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"","code":"tableDS.assign( rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, cvar.all.unique.levels.transmit, stvar.all.unique.levels.transmit, exclude.transmit, useNA.transmit )"},{"path":"/reference/tableDS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table rvar..unique.levels.transmit character string containing unique level rvar, across studies, separated ','. cvar..unique.levels.transmit character string containing unique level cvar, across studies, separated ','. stvar..unique.levels.transmit character string containing unique level stvar, across studies, separated ','. exclude.transmit information see help argument ds.table. Fully specified argument ds.table useNA.transmit information see help argument ds.table. Fully specified argument ds.table","code":""},{"path":"/reference/tableDS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"information see help ds.table","code":""},{"path":"/reference/tableDS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":" argument ds.table set TRUE, assign function writes table requested format specified ds.table function object named argument ds.table. information see help ds.table DataSHIELD table function native R.","code":""},{"path":"/reference/tableDS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tableDS.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/tableDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"","code":"tableDS( rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, cvar.all.unique.levels.transmit, stvar.all.unique.levels.transmit, exclude.transmit, useNA.transmit, force.nfilter.transmit )"},{"path":"/reference/tableDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table rvar..unique.levels.transmit character string containing unique level rvar, across studies, separated ','. cvar..unique.levels.transmit character string containing unique level cvar, across studies, separated ','. stvar..unique.levels.transmit character string containing unique level stvar, across studies, separated ','. exclude.transmit information see help argument ds.table. Fully specified argument ds.table useNA.transmit information see help argument ds.table. Fully specified argument ds.table force.nfilter.transmit information see help argument ds.table. Fully specified argument ds.table","code":""},{"path":"/reference/tableDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"information see help ds.table","code":""},{"path":"/reference/tableDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"serverside function workhorse ds.table - creating table requested format specified ds.table. information see help ds.table DataSHIELD table function native R.","code":""},{"path":"/reference/tableDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tapplyDS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"Apply one selected range functions summarize outcome variable one indexing factors write resultant summary newobj serverside","code":""},{"path":"/reference/tapplyDS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"","code":"tapplyDS.assign(X.name, INDEX.names.transmit, FUN.name)"},{"path":"/reference/tapplyDS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"X.name, name variable summarized. Specified via argument ds.tapply.assign function INDEX.names.transmit, name single factor vector names factors index variable summarized. Specified via argument ds.tapply.assign function FUN.name, name one allowable summarizing functions applied. Specified via argument ds.tapply.assign function.","code":""},{"path":"/reference/tapplyDS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"array summarized values created tapplyDS.assign function. array written newobj serverside. number dimensions INDEX.","code":""},{"path":"/reference/tapplyDS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"see details ds.tapply.assign function","code":""},{"path":"/reference/tapplyDS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tapplyDS.html","id":null,"dir":"Reference","previous_headings":"","what":"tapplyDS called by ds.tapply — tapplyDS","title":"tapplyDS called by ds.tapply — tapplyDS","text":"Apply one selected range functions summarize outcome variable one indexing factors write resultant summary clientside","code":""},{"path":"/reference/tapplyDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tapplyDS called by ds.tapply — tapplyDS","text":"","code":"tapplyDS(X.name, INDEX.names.transmit, FUN.name)"},{"path":"/reference/tapplyDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tapplyDS called by ds.tapply — tapplyDS","text":"X.name, name variable summarized. Specified via argument ds.tapply function INDEX.names.transmit, name single factor vector names factors index variable summarized. Specified via argument ds.tapply function FUN.name, name one allowable summarizing functions applied. Specified via argument ds.tapply function.","code":""},{"path":"/reference/tapplyDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tapplyDS called by ds.tapply — tapplyDS","text":"array summarized values created tapplyDS function. array returned clientside. number dimensions INDEX.","code":""},{"path":"/reference/tapplyDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tapplyDS called by ds.tapply — tapplyDS","text":"see details ds.tapply function","code":""},{"path":"/reference/tapplyDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tapplyDS called by ds.tapply — tapplyDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/unListDS.html","id":null,"dir":"Reference","previous_headings":"","what":"unListDS a serverside assign function called by ds.unList — unListDS","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"function based native R function unlist coerces object list class back class coerced list","code":""},{"path":"/reference/unListDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"","code":"unListDS(x.name)"},{"path":"/reference/unListDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"x.name name input object unlisted. must specified inverted commas e.g. x.name=\"input.object.name\". Fully specified x.name argument ds.unList","code":""},{"path":"/reference/unListDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"object specified newobj argument ds.unList function (default \"unlist.newobj\" newobj argument NULL). written serverside. well writing output object newobj serverside, two validity messages returned indicating whether newobj created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.seq also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating newobj studysideMessage saved. outcome object ds.unList typically list object names, errors creating message returned ds.message(\"\") study read \"Outcome object list without names. studysideMessage may hidden. Please check output OK\". suggests - case specific function - one check far one can nature output call ds.unList - e.g. ds.class, ds.length etc","code":""},{"path":"/reference/unListDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"See details native R function unlist. function represents substantive restructuring earlier version created Amadou Gaye. details working please see 'details' help ds.unList.","code":""},{"path":"/reference/unListDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"Amadou Gaye (2016), Paul Burton (19/09/2019) DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/uniqueDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Applies the unique method to a server-side variable. — uniqueDS","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"function similar R function unique.","code":""},{"path":"/reference/uniqueDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"","code":"uniqueDS(x.name.transmit = NULL)"},{"path":"/reference/uniqueDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"x.name.transmit name variable upon unique method applied","code":""},{"path":"/reference/uniqueDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"object specified newobj argument written server-side.","code":""},{"path":"/reference/uniqueDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"function computes uniques values variable.","code":""},{"path":"/reference/uniqueDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"Stuart Wheater DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/varDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the variance of vector — varDS","title":"Computes the variance of vector — varDS","text":"Calculates variance.","code":""},{"path":"/reference/varDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the variance of vector — varDS","text":"","code":"varDS(x)"},{"path":"/reference/varDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the variance of vector — varDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/varDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the variance of vector — varDS","text":"list, sum input variable, sum squares input variable, number missing values, number valid values, number total length variable, class, class input object client-side consistency checking","code":""},{"path":"/reference/varDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the variance of vector — varDS","text":"length input vector less set filter missing value returned.","code":""},{"path":"/reference/varDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the variance of vector — varDS","text":"Amadou Gaye, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/vectorDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates a vector on the server-side. — vectorDS","title":"Creates a vector on the server-side. — vectorDS","text":"function similar R function c.","code":""},{"path":"/reference/vectorDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates a vector on the server-side. — vectorDS","text":"","code":"vectorDS(...)"},{"path":"/reference/vectorDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates a vector on the server-side. — vectorDS","text":"... parameter used form vector.","code":""},{"path":"/reference/vectorDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates a vector on the server-side. — vectorDS","text":"object specified newobj argument written server-side.","code":""},{"path":"/reference/vectorDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates a vector on the server-side. — vectorDS","text":"function computes vectors values.","code":""},{"path":"/reference/vectorDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Creates a vector on the server-side. — vectorDS","text":"Stuart Wheater DataSHIELD Development Team","code":""}] +[{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Paul Burton. Author. Rebecca Wilson. Author. Olly Butters. Author. Patricia Ryser-Welch. Author. Alex Westerberg. Author. Leire Abarrategui. Author. Roberto Villegas-Diaz. Author. Demetris Avraam. Author. Yannick Marcon. Author. Tom Bishop. Author. Amadou Gaye. Author. Xavier Escribà-Montagut. Author. Stuart Wheater. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg , Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye , Escribà-Montagut X, Wheater S (????). dsBase: 'DataSHIELD' Server Side Base Functions. R package version 7.0.0.9000. Gaye , Marcon Y, Isaeva J, LaFlamme P, Turner , Jones E, Minion J, Boyd , Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir , Doiron D, Giepmans L, Wallace S, Budin-Ljøsne , Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry , Peters , Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier , Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking analysis data, data analysis.” International Journal Epidemiology, 43(6), 1929–1944. doi:10.1093/ije/dyu188. Wilson R, Butters O, Avraam D, Baker J, Tedds J, Turner , Murtagh M, Burton P (2017). “DataSHIELD – New Directions Dimensions.” Data Science Journal, 16(21), 1–21. doi:10.5334/dsj-2017-021. Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan , Murtagh M, Nestor M, Nybo Andersen , Parker S, Pinot de Moira , Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1–21. doi:10.1093/bioadv/vbaf046.","code":"@Manual{, title = {dsBase: 'DataSHIELD' Server Side Base Functions}, author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater}, note = {R package version 7.0.0.9000}, } @Article{, title = {{DataSHIELD: taking the analysis to the data, not the data to the analysis}}, author = {Amadou Gaye and Yannick Marcon and Julia Isaeva and Philippe {LaFlamme} and Andrew Turner and Elinor M Jones and Joel Minion and Andrew W Boyd and Christopher J Newby and Marja-Liisa Nuotio and Rebecca Wilson and Oliver Butters and Barnaby Murtagh and Ipek Demir and Dany Doiron and Lisette Giepmans and Susan E Wallace and Isabelle Budin-Lj{\\o}sne and Carsten O. Schmidt and Paolo Boffetta and Mathieu Boniol and Maria Bota and Kim W Carter and Nick {deKlerk} and Chris Dibben and Richard W Francis and Tero Hiekkalinna and Kristian Hveem and Kirsti Kval{\\o}y and Sean Millar and Ivan J Perry and Annette Peters and Catherine M Phillips and Frank Popham and Gillian Raab and Eva Reischl and Nuala Sheehan and Melanie Waldenberger and Markus Perola and Edwin {{van den Heuvel}} and John Macleod and Bartha M Knoppers and Ronald P Stolk and Isabel Fortier and Jennifer R Harris and Bruce H R Woffenbuttel and Madeleine J Murtagh and Vincent Ferretti and Paul R Burton}, journal = {International Journal of Epidemiology}, year = {2014}, volume = {43}, number = {6}, pages = {1929--1944}, doi = {10.1093/ije/dyu188}, } @Article{, title = {{DataSHIELD – New Directions and Dimensions}}, author = {Rebecca C. Wilson and Oliver W. Butters and Demetris Avraam and James Baker and Jonathan A. Tedds and Andrew Turner and Madeleine Murtagh and Paul R. Burton}, journal = {Data Science Journal}, year = {2017}, volume = {16}, number = {21}, pages = {1--21}, doi = {10.5334/dsj-2017-021}, } @Article{, title = {{DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform}}, author = {Demetris Avraam and Rebecca C Wilson and Noemi {{Aguirre Chan}} and Soumya Banerjee and Tom R P Bishop and Olly Butters and Tim Cadman and Luise Cederkvist and Liesbeth Duijts and Xavier {{Escrib{\\a`a} Montagut}} and Hugh Garner and Gon{\\c c}alo {Gon{\\c c}alves} and Juan R Gonz{\\a'a}lez and Sido Haakma and Mette Hartlev and Jan Hasenauer and Manuel Huth and Eleanor Hyde and Vincent W V Jaddoe and Yannick Marcon and Michaela Th Mayrhofer and Fruzsina Molnar-Gabor and Andrei Scott Morgan and Madeleine Murtagh and Marc Nestor and Anne-Marie {{Nybo Andersen}} and Simon Parker and Angela {{Pinot de Moira}} and Florian Schwarz and Katrine Strandberg-Larsen and Morris A Swertz and Marieke Welten and Stuart Wheater and Paul R Burton}, journal = {Bioinformatics Advances}, year = {2024}, volume = {5}, number = {1}, pages = {1--21}, doi = {10.1093/bioadv/vbaf046}, editor = {Thomas Lengauer}, publisher = {Oxford University Press (OUP)}, }"},{"path":[]},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"DataSHIELD Server Side Base Functions","text":"can install released version dsBase CRAN : development version GitHub : full list development branches, checkout https://github.com/datashield/dsBase/branches","code":"install.packages(\"dsBase\") install.packages(\"remotes\") remotes::install_github(\"datashield/dsBase\", \"\") # Install v6.3.6 with the following remotes::install_github(\"datashield/dsBase\", \"6.3.6\")"},{"path":"/index.html","id":"about","dir":"","previous_headings":"","what":"About","title":"DataSHIELD Server Side Base Functions","text":"DataSHIELD software package allows non-disclosive federated analysis sensitive data. website (https://www.datashield.org) depth descriptions , works install . key point highlight DataSHIELD client-server infrastructure, dsBase package (https://github.com/datashield/dsBase) needs used conjunction dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying use one without makes sense. Detailed instructions install DataSHIELD https://wiki.datashield.org/. code organised :","code":""},{"path":"/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"DataSHIELD Server Side Base Functions","text":"[1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg , Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye , Escribà Montagut X, Wheater S (2025). dsBase: ‘DataSHIELD’ Server Side Base Functions. R package version 6.3.4. https://doi.org/10.32614/CRAN.package.dsBase. [2] Gaye , Marcon Y, Isaeva J, LaFlamme P, Turner , Jones E, Minion J, Boyd , Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir , Doiron D, Giepmans L, Wallace S, Budin-Ljøsne , Oliver Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry , Peters , Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier , Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking analysis data, data analysis.” International Journal Epidemiology, 43(6), 1929-1944. https://doi.org/10.1093/ije/dyu188. [3] Wilson R, W. Butters O, Avraam D, Baker J, Tedds J, Turner , Murtagh M, R. Burton P (2017). “DataSHIELD – New Directions Dimensions.” Data Science Journal, 16(21), 1-21. https://doi.org/10.5334/dsj-2017-021. [4] Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan , Murtagh M, Nestor M, Nybo Andersen , Parker S, Pinot de Moira , Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1-21. https://doi.org/10.1093/bioadv/vbaf046. Note: Apple Mx architecture users, please aware numerical limitations platform, leads unexpected results using base R packages, like stats​. x <- c(0, 3, 7) 1 - cor(x, x)​ result value zero. Also See: details see https://cran.r-project.org/doc/FAQ/R-FAQ.html#-doesn_0027t-R-think--numbers--equal_003f bug report: https://bugs.r-project.org/show_bug.cgi?id=18941","code":""},{"path":"/reference/BooleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"BooleDS — BooleDS","title":"BooleDS — BooleDS","text":"Converts individual elements vector object Boolean indicators.","code":""},{"path":"/reference/BooleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BooleDS — BooleDS","text":"","code":"BooleDS( V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, na.assign.text, numeric.output = TRUE )"},{"path":"/reference/BooleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BooleDS — BooleDS","text":"V1.name character string specifying name vector Boolean operator applied V2.name character string specifying name vector scalar compared. Boolean.operator.n integer value (1 6) providing numeric coding character string specifying one six possible Boolean operators: '==', '!=', '>', '>=','<', '<=' legally passed client server via DataSHIELD parser na.assign.text character string taking values 'NA', '1' '0'. 'NA' NA values input vector remain NAs output vector. '1' '0' NA values input vector converted 1 0 respectively. numeric.output TRUE/FALSE indicator defaulting TRUE determining whether final output variable class numeric (1/0) class logical (TRUE/FALSE).","code":""},{"path":"/reference/BooleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"BooleDS — BooleDS","text":"levels input variable.","code":""},{"path":"/reference/BooleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"BooleDS — BooleDS","text":"function converts input vector Boolean indicators.","code":""},{"path":"/reference/BooleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"BooleDS — BooleDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/absDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the absolute values of the input variable — absDS","title":"Computes the absolute values of the input variable — absDS","text":"function similar R function abs.","code":""},{"path":"/reference/absDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the absolute values of the input variable — absDS","text":"","code":"absDS(x)"},{"path":"/reference/absDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the absolute values of the input variable — absDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/absDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the absolute values of the input variable — absDS","text":"object specified newobj argument ds.abs (default name abs.newobj) written serverside. output object class numeric integer.","code":""},{"path":"/reference/absDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the absolute values of the input variable — absDS","text":"function computes absolute values input numeric integer vector.","code":""},{"path":"/reference/absDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the absolute values of the input variable — absDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asCharacterDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class character — asCharacterDS","title":"Coerces an R object into class character — asCharacterDS","text":"function based native R function .character","code":""},{"path":"/reference/asCharacterDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class character — asCharacterDS","text":"","code":"asCharacterDS(x.name)"},{"path":"/reference/asCharacterDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class character — asCharacterDS","text":"x.name name input object coerced class character. Must specified inverted commas. argument usually specified directly x.name argument clientside function ds.asCharacter","code":""},{"path":"/reference/asCharacterDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class character — asCharacterDS","text":"object specified newobj argument (default name \"ascharacter.newobj\") written serverside. details see help clientside function ds.asCharacter","code":""},{"path":"/reference/asCharacterDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class character — asCharacterDS","text":"See help function .character native R","code":""},{"path":"/reference/asCharacterDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class character — asCharacterDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asDataMatrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"Coerces R object matrix maintaining original class columns data.frames.","code":""},{"path":"/reference/asDataMatrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"","code":"asDataMatrixDS(x.name)"},{"path":"/reference/asDataMatrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"x.name name input object coerced class data.matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asDataMatrix","code":""},{"path":"/reference/asDataMatrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"object specified argument (default name \"asdatamatrix.newobj\") written serverside. details see help clientside function ds.asDataMatrix","code":""},{"path":"/reference/asDataMatrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"assign function based native R function data.matrix applied data.frame, native R function .matrix converts columns character class. contrast, applied data.frame native R function data.matrix converts data.frame matrix maintains data columns original class","code":""},{"path":"/reference/asDataMatrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactor1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Determines the levels of the input variable in each single study — asFactor1DS","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"function aggregate DataSHIELD function returns levels input variable single study client-side function.","code":""},{"path":"/reference/asFactor1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"","code":"asFactor1DS(input.var.name = NULL)"},{"path":"/reference/asFactor1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"input.var.name name variable converted factor.","code":""},{"path":"/reference/asFactor1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"levels input variable.","code":""},{"path":"/reference/asFactor1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"function encodes input vector factor returns levels ascending order levels numerical alphabetical order levels type character.","code":""},{"path":"/reference/asFactor1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactor2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts a numeric vector into a factor — asFactor2DS","title":"Converts a numeric vector into a factor — asFactor2DS","text":"function assign DataSHIELD function converts numeric vector factor type presented vector matrix dummy variables.","code":""},{"path":"/reference/asFactor2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts a numeric vector into a factor — asFactor2DS","text":"","code":"asFactor2DS( input.var.name = NULL, all.unique.levels.transmit = NULL, fixed.dummy.vars = NULL, baseline.level = NULL )"},{"path":"/reference/asFactor2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts a numeric vector into a factor — asFactor2DS","text":"input.var.name name variable converted factor. .unique.levels.transmit levels variable transmitted . fixed.dummy.vars boolean determines whether new object represented vector matrix dummy variables indicating factor level data point. argument set FALSE (default) input variable converted factor assigned vector. set TRUE input variable converted factor assigned matrix dummy variables. baseline.level number indicating baseline level used creation matrix dummy variables.","code":""},{"path":"/reference/asFactor2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts a numeric vector into a factor — asFactor2DS","text":"object class factor","code":""},{"path":"/reference/asFactor2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Converts a numeric vector into a factor — asFactor2DS","text":"functions converts input variable factor presented vector fixed.dummy.vars set FALSE matrix dummy variables fixed.dummy.vars set TRUE (see help file ds.asFactor.b details).","code":""},{"path":"/reference/asFactor2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts a numeric vector into a factor — asFactor2DS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactorSimpleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts a numeric vector into a factor — asFactorSimpleDS","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"function assign DataSHIELD function coerces numeric character vector factor","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"","code":"asFactorSimpleDS(input.var.name = NULL)"},{"path":"/reference/asFactorSimpleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"input.var.name name variable converted factor.","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"object class factor","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"functions converts input variable factor. Unlike ds.asFactor serverside functions, ds.asFactorSimple coerce class variable factor study. check enforce consistency factor levels across sources allow force arbitrary set levels unless levels actually exist sources. addition, allow create array binary dummy variables equivalent factor. need things use ds.asFactor function.","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asIntegerDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class integer — asIntegerDS","title":"Coerces an R object into class integer — asIntegerDS","text":"function based native R function .integer.","code":""},{"path":"/reference/asIntegerDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class integer — asIntegerDS","text":"","code":"asIntegerDS(x.name)"},{"path":"/reference/asIntegerDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class integer — asIntegerDS","text":"x.name name input object coerced class integer. Must specified inverted commas. argument usually specified directly argument clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class integer — asIntegerDS","text":"object specified argument (default name \"asinteger.newobj\") written serverside. details see help clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class integer — asIntegerDS","text":"See help function .integer native R, details section help file clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class integer — asIntegerDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asListDS.html","id":null,"dir":"Reference","previous_headings":"","what":"asListDS a serverside assign function called by ds.asList — asListDS","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"Coerces R object list","code":""},{"path":"/reference/asListDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"","code":"asListDS(x.name)"},{"path":"/reference/asListDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"x.name name input object coerced class data.matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asList","code":""},{"path":"/reference/asListDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"input object coerced list, ds.asList writes serverside. way .list coerces objects list depends class object","code":""},{"path":"/reference/asListDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"assign function based native R function .list additional information can found help .list","code":""},{"path":"/reference/asListDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asLogicalDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class logical — asLogicalDS","title":"Coerces an R object into class logical — asLogicalDS","text":"function based native R function .logical","code":""},{"path":"/reference/asLogicalDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class logical — asLogicalDS","text":"","code":"asLogicalDS(x.name)"},{"path":"/reference/asLogicalDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class logical — asLogicalDS","text":"x.name name input object coerced class logical. Must specified inverted commas. argument usually specified directly argument clientside function ds.asLogical","code":""},{"path":"/reference/asLogicalDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class logical — asLogicalDS","text":"object specified argument (default name .logic) written serverside. details see help clientside function ds.asLogical","code":""},{"path":"/reference/asLogicalDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class logical — asLogicalDS","text":"See help function .logical native R","code":""},{"path":"/reference/asLogicalDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class logical — asLogicalDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asMatrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into a matrix — asMatrixDS","title":"Coerces an R object into a matrix — asMatrixDS","text":"function based native R function .matrix","code":""},{"path":"/reference/asMatrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into a matrix — asMatrixDS","text":"","code":"asMatrixDS(x.name)"},{"path":"/reference/asMatrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into a matrix — asMatrixDS","text":"x.name name input object coerced class matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asMatrix","code":""},{"path":"/reference/asMatrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into a matrix — asMatrixDS","text":"object specified argument (default name .mat) written serverside. details see help clientside function ds.asMatrix","code":""},{"path":"/reference/asMatrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into a matrix — asMatrixDS","text":"See help function .matrix native R","code":""},{"path":"/reference/asMatrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into a matrix — asMatrixDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asNumericDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class numeric — asNumericDS","title":"Coerces an R object into class numeric — asNumericDS","text":"function based native R function .numeric.","code":""},{"path":"/reference/asNumericDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class numeric — asNumericDS","text":"","code":"asNumericDS(x.name)"},{"path":"/reference/asNumericDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class numeric — asNumericDS","text":"x.name name input object coerced class numeric. Must specified inverted commas. argument usually specified directly argument clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class numeric — asNumericDS","text":"object specified argument (default name .num) written serverside. details see help clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class numeric — asNumericDS","text":"See help function .numeric native R, details section help file clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class numeric — asNumericDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/aucDS.html","id":null,"dir":"Reference","previous_headings":"","what":"aucDS an aggregate function called by ds.auc — aucDS","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"function calculates C-statistic AUC logistic regression models.","code":""},{"path":"/reference/aucDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"","code":"aucDS(pred = pred, y = y)"},{"path":"/reference/aucDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"pred name vector predicted values y name outcome variable. Note variable include complete cases used regression model.","code":""},{"path":"/reference/aucDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"returns AUC standard error","code":""},{"path":"/reference/aucDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"AUC determines discriminative ability model.","code":""},{"path":"/reference/aucDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/booleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"booleDS — booleDS","title":"booleDS — booleDS","text":"Converts individual elements vector object Boolean indicators.","code":""},{"path":"/reference/booleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"booleDS — booleDS","text":"","code":"booleDS( V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, na.assign.text, numeric.output = TRUE )"},{"path":"/reference/booleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"booleDS — booleDS","text":"V1.name character string specifying name vector Boolean operator applied V2.name character string specifying name vector scalar compared. Boolean.operator.n integer value (1 6) providing numeric coding character string specifying one six possible Boolean operators: '==', '!=', '>', '>=','<', '<=' legally passed client server via DataSHIELD parser na.assign.text character string taking values 'NA', '1' '0'. 'NA' NA values input vector remain NAs output vector. '1' '0' NA values input vector converted 1 0 respectively. numeric.output TRUE/FALSE indicator defaulting TRUE determining whether final output variable class numeric (1/0) class logical (TRUE/FALSE).","code":""},{"path":"/reference/booleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"booleDS — booleDS","text":"levels input variable.","code":""},{"path":"/reference/booleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"booleDS — booleDS","text":"function converts input vector Boolean indicators.","code":""},{"path":"/reference/booleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"booleDS — booleDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGGDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"order create non disclosive box plot, data passed client purely geometrical aspects plot, ggplot object contains data inside, graphical parameters passed. three different cases depending grouping variables. outliers also removed graphical parameters.","code":""},{"path":"/reference/boxPlotGGDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"","code":"boxPlotGGDS(data_table.name, group = NULL, group2 = NULL)"},{"path":"/reference/boxPlotGGDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"data_table.name character Name server-side data frame holds information plotted, arranged : Column 'x': Names X axis boxplot, aka variables plot Column 'value': Values variable (raw data columns rbinded) Column 'group': (Optional) Values grouping variable Column 'group2': (Optional) Values second grouping variable group character (default NULL) Name first grouping variable. group2 character (default NULL) Name second grouping variable.","code":""},{"path":"/reference/boxPlotGGDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"list : -data frame Geometrical parameters (identity stats ggplot) -character Type plot (single_group, double_group no_group)","code":""},{"path":"/reference/boxPlotGGDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"Arrange data frame pass boxplot function","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"","code":"boxPlotGG_data_TreatmentDS(table.name, variables, group = NULL, group2 = NULL)"},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"table.name character Name server-side data frame holds information plotted later variables character vector Name column(s) data frame include boxplot group character (default NULL) Name first grouping variable. group2 character (default NULL) Name second grouping variable.","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"data frame following structure: Column 'x': Names X axis boxplot, aka variables plot Column 'value': Values variable (raw data columns rbinded) Column 'group': (Optional) Values grouping variable Column 'group2': (Optional) Values second grouping variable","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"Arrange vector pass boxplot function","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"","code":"boxPlotGG_data_Treatment_numericDS(vector.name)"},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"vector.name character Name server-side numeric vector arrange plotted later","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"data frame following structure: Column 'x': Names X axis boxplot, aka name vector (vector.name argument) Column 'value': Values variable","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/bp_standardsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates Blood pressure z-scores — bp_standardsDS","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"function calculates blood pressure z-scores two steps: Step 1. Calculates z-score height according CDC growth chart (growth chart!). Step 2. Calculates z-score BP according fourth report BP management, USA","code":""},{"path":"/reference/bp_standardsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"","code":"bp_standardsDS( sex = sex, age = age, height = height, bp = bp, systolic = systolic )"},{"path":"/reference/bp_standardsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"sex name sex variable. variable coded 1 males 2 females. coded differently (e.g. 0/1), can use ds.recodeValues function recode categories 1/2 use ds.bp_standards age name age variable years. height name height variable cm bp name blood pressure variable. systolic logical. TRUE (default) function assumes conversion systolic blood pressure. FALSE function assumes conversion diastolic blood pressure.","code":""},{"path":"/reference/bp_standardsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"assigns new object server-side. assigned object list two elements: 'Zbp' zscores blood pressure 'perc' percentiles BP zscores.","code":""},{"path":"/reference/bp_standardsDS.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"z-scores height based CDC growth charts calculated sds function childsds R package.","code":""},{"path":"/reference/bp_standardsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/cDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenates objects into a vector or list — cDS","title":"Concatenates objects into a vector or list — cDS","text":"function similar R base function 'c'.","code":""},{"path":"/reference/cDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenates objects into a vector or list — cDS","text":"","code":"cDS(x.names)"},{"path":"/reference/cDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenates objects into a vector or list — cDS","text":"x.names character vector object names concatenate.","code":""},{"path":"/reference/cDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenates objects into a vector or list — cDS","text":"vector list","code":""},{"path":"/reference/cDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Concatenates objects into a vector or list — cDS","text":"Unlike R base function 'c' vector list certain length allowed output","code":""},{"path":"/reference/cDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Concatenates objects into a vector or list — cDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/cbindDS.html","id":null,"dir":"Reference","previous_headings":"","what":"cbindDS called by ds.cbind — cbindDS","title":"cbindDS called by ds.cbind — cbindDS","text":"serverside assign function takes sequence vector, matrix data-frame arguments combines column produce data-frame.","code":""},{"path":"/reference/cbindDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cbindDS called by ds.cbind — cbindDS","text":"","code":"cbindDS(x.names.transmit = NULL, colnames.transmit = NULL)"},{"path":"/reference/cbindDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"cbindDS called by ds.cbind — cbindDS","text":"x.names.transmit vector character strings representing names elemental components combined converted transmittable format. argument fully specified x argument client-side ds.cbind function. colnames.transmit vector character strings representing column names output object converted transmittable format.","code":""},{"path":"/reference/cbindDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"cbindDS called by ds.cbind — cbindDS","text":"object specified newobj argument ds.cbind (default name cbind.newobj) written serverside. output object class data.frame.","code":""},{"path":"/reference/cbindDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"cbindDS called by ds.cbind — cbindDS","text":"sequence vector, matrix data-frame arguments combined column column produce data-frame written serverside. critical requirement length component variables, number rows component data.frames matrices must . output data.frame number rows. details see help ds.cbind native R function cbind.","code":""},{"path":"/reference/cbindDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"cbindDS called by ds.cbind — cbindDS","text":"Paul Burton Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/changeRefGroupDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Changes a reference level of a factor — changeRefGroupDS","title":"Changes a reference level of a factor — changeRefGroupDS","text":"function similar R function relevel,","code":""},{"path":"/reference/changeRefGroupDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Changes a reference level of a factor — changeRefGroupDS","text":"","code":"changeRefGroupDS(x, ref = NULL, reorderByRef = NULL)"},{"path":"/reference/changeRefGroupDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Changes a reference level of a factor — changeRefGroupDS","text":"x character string, name factor vector. ref character, reference level reorderByRef boolean tells whether new vector ordered reference group.","code":""},{"path":"/reference/changeRefGroupDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Changes a reference level of a factor — changeRefGroupDS","text":"factor length input vector","code":""},{"path":"/reference/changeRefGroupDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Changes a reference level of a factor — changeRefGroupDS","text":"addition R function , function allows user re-order vector, putting reference group first. user chooses re-order warning issued can introduce mismatch values vector put back table reordered way. mismatch can render results operations table invalid.","code":""},{"path":"/reference/changeRefGroupDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Changes a reference level of a factor — changeRefGroupDS","text":"Isaeva, J., Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/checkNegValueDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if a numeric variable has negative values — checkNegValueDS","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"function called client function ds.glm.","code":""},{"path":"/reference/checkNegValueDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"","code":"checkNegValueDS(weights)"},{"path":"/reference/checkNegValueDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"weights numeric vector","code":""},{"path":"/reference/checkNegValueDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"boolean; TRUE vector one negative values FALSE otherwise","code":""},{"path":"/reference/checkNegValueDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"user sets parameter 'weights' client side function ds.glm server side function called verify 'weights' vector negative values negative allowed weights.","code":""},{"path":"/reference/checkNegValueDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"Gaye, .","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":null,"dir":"Reference","previous_headings":"","what":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"server-side function check server running \"permissive\" privacy control level.","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"","code":"checkPermissivePrivacyControlLevel(privacyControlLevels)"},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"privacyControlLevels vector strings contains privacy control level names permitted calling method.","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"return value, called side effects","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"Tests whether R option \"datashield.privacyControlLevel\" set \"permissive\", cause call stop() message \"BLOCKED: server running 'non-permissive' mode caused method blocked\".","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"Wheater, Dr SM., DataSHIELD Development Team.","code":""},{"path":"/reference/classDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the class of an object — classDS","title":"Returns the class of an object — classDS","text":"function similar R function class.","code":""},{"path":"/reference/classDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the class of an object — classDS","text":"","code":"classDS(x)"},{"path":"/reference/classDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the class of an object — classDS","text":"x string character, name object","code":""},{"path":"/reference/classDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the class of an object — classDS","text":"class input object","code":""},{"path":"/reference/classDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the class of an object — classDS","text":"function returns class object","code":""},{"path":"/reference/classDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the class of an object — classDS","text":"Stuart Wheater, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/colnamesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the column names of a data frame or matrix — colnamesDS","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"function similar R function colnames.","code":""},{"path":"/reference/colnamesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"","code":"colnamesDS(x)"},{"path":"/reference/colnamesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"x string character, name dataframe matrix","code":""},{"path":"/reference/colnamesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"column names input object","code":""},{"path":"/reference/colnamesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"function returns column names input dataframe matrix","code":""},{"path":"/reference/colnamesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"Demetris Avraam, DataSHIELD Development Team","code":""},{"path":"/reference/completeCasesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"Identifies strips rows data.frame, matrix vector contain NAs.","code":""},{"path":"/reference/completeCasesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"","code":"completeCasesDS(x1.transmit)"},{"path":"/reference/completeCasesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"x1.transmit argument determines input data.frame, matrix vector rows NAs stripped. argument fully specified argument ds.completeCases function.","code":""},{"path":"/reference/completeCasesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"modified data.frame, matrix vector rows containing least one NA deleted. modified object written serverside source. addition, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.completeCases also returns studysideMessages can help explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/completeCasesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"case data.frame matrix, completeCasesDS identifies rows containing one NAs deletes rows altogether. one variable NA given row lead deletion whole row. case vector, completeCasesDS acts equivalent manner equivalent 'row' simply strips observations recorded NA. ds.completeCASES analogous complete.cases function native R. Limited additional information can therefore found help(\"complete.cases\") native R.","code":""},{"path":"/reference/completeCasesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/corDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"function computes sum vector variable sum products two variables (.e. scalar product two vectors).","code":""},{"path":"/reference/corDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"","code":"corDS(x = NULL, y = NULL)"},{"path":"/reference/corDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"x character, name vector, matrix dataframe variables(s) correlation(s) () going calculated . y NULL (default) name vector, matrix dataframe compatible dimensions x.","code":""},{"path":"/reference/corDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"list includes matrix elements sum products two variables, matrix elements sum values variable, matrix elements number complete cases pair variables, list number missing values variable separately (columnwise) number missing values casewise, vector elements sum squares variable. first disclosure control checks number variables bigger percentage individual-level records (allowed percentage pre-specified 'nfilter.glm'). second disclosure control checks none dichotomous level fewer counts pre-specified 'nfilter.tab' threshold. list also includes class, class input object client-side consistency checking.","code":""},{"path":"/reference/corDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"computes sum vector variable sum products two variables","code":""},{"path":"/reference/corDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/corTestDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests for correlation between paired samples — corTestDS","title":"Tests for correlation between paired samples — corTestDS","text":"function similar R function cor.test.","code":""},{"path":"/reference/corTestDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests for correlation between paired samples — corTestDS","text":"","code":"corTestDS(x, y, method, exact, conf.level)"},{"path":"/reference/corTestDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests for correlation between paired samples — corTestDS","text":"x character string providing name numerical vector. y character string providing name numerical vector. method character string indicating correlation coefficient used test. One \"pearson\", \"kendall\", \"spearman\", can abbreviated. exact logical indicating whether exact p-value computed. Used Kendall's tau Spearman's rho. conf.level confidence level returned confidence interval. Currently used Pearson product moment correlation coefficient least 4 complete pairs observations.","code":""},{"path":"/reference/corTestDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tests for correlation between paired samples — corTestDS","text":"list results correlation test class, class input object client-side consistency checking.","code":""},{"path":"/reference/corTestDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tests for correlation between paired samples — corTestDS","text":"function runs two-sided correlation test","code":""},{"path":"/reference/corTestDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Tests for correlation between paired samples — corTestDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/covDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"function computes sum vector variable sum products two variables (.e. scalar product two vectors).","code":""},{"path":"/reference/covDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"","code":"covDS(x = NULL, y = NULL, use = NULL)"},{"path":"/reference/covDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"x character, name vector, matrix dataframe variable(s) covariance(s) correlation(s) () going calculated . y NULL (default) name vector, matrix dataframe compatible dimensions x. use character string giving method computing covariances presence missing values. must one strings \"casewise.complete\" \"pairwise.complete\". use set 'casewise.complete' rows missing values omitted vector, matrix dataframe calculations sums. use set 'pairwise.complete' (default case set client-side), sums products computed two variables using complete pairs observations two variables.","code":""},{"path":"/reference/covDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"list includes matrix elements sum products two variables, matrix elements sum values variable, matrix elements number complete cases pair variables, list number missing values variable separately (columnwise) number missing values casewise pairwise depending argument use, error message indicates whether input variables pass disclosure controls. first disclosure control checks number variables bigger percentage individual-level records (allowed percentage pre-specified 'nfilter.glm'). second disclosure control checks none dichotomous level fewer counts pre-specified 'nfilter.tab' threshold. input variables pass disclosure controls output values replaced NAs. list also includes class, class input object client-side consistency checking.","code":""},{"path":"/reference/covDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"computes sum vector variable sum products two variables","code":""},{"path":"/reference/covDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameDS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameDS called by ds.dataFrame — dataFrameDS","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"serverside function creates data frame elemental components. : pre-existing data frames; single variables; /matrices","code":""},{"path":"/reference/dataFrameDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"","code":"dataFrameDS( vectors = NULL, r.names = NULL, ch.rows = FALSE, ch.names = TRUE, clnames = NULL, strAsFactors = TRUE, completeCases = FALSE )"},{"path":"/reference/dataFrameDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"vectors list contains elemental components combine. correspond vector character strings specified argument x clientside function ds.dataFrame() r.names NULL character vector specifying names rows. Default NULL. ch.rows logical, TRUE rows checked consistency length names. Default FALSE. ch.names logical, TRUE names variables data frame checked ensure syntactically valid variable names duplicated. Default TRUE. fact, clientside function ensures duplicated names can presented dataFrameDS argument kept check forms syntactic validity. clnames list characters, column names output data frame. generated clientside function names vectors, column names data.frames matrices combined producing output data.frame strAsFactors logical, TRUE determines whether character vectors automatically converted factors? Default TRUE. completeCases logical. TRUE indicates complete cases included: rows missing values component excluded. Default FALSE.","code":""},{"path":"/reference/dataFrameDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"dataframe composed specified elemental components created serverside named according argument clientside function ds.dataFrame()","code":""},{"path":"/reference/dataFrameDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"data frame list variables number rows unique row names, class 'data.frame'. ds.dataFrame create data frame combining series elemental components may pre-existing data.frames, matrices variables. critical requirement length component variables, number rows component data.frames matrices must . output data.frame number rows. serverside function dataFrameDS() calls native R function data.frame() several arguments precisely data.frame(). consequence, additional information can sought help() data.frame().","code":""},{"path":"/reference/dataFrameDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSortDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Sorts data frame using specified alphanumeric numeric sort key","code":""},{"path":"/reference/dataFrameSortDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"","code":"dataFrameSortDS( df.name = NULL, sort.key.name = NULL, sort.descending, sort.method )"},{"path":"/reference/dataFrameSortDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"df.name character string providing name serverside data.frame sorted. parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.key.name character string providing name sort key. serverside vector may sit inside data frame sorted independently serverside analysis environment. , sits outside data frame must length data frame. parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.descending logical, TRUE data.frame sorted sort key descending order. Default = FALSE (sort order ascending). parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.method character string taking one values: \"default\", \"d\", \"alphabetic\", \"\", \"numeric\", \"n\", NULL. Default value \"default\". parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\").","code":""},{"path":"/reference/dataFrameSortDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"appropriately re-sorted data.frame written serverside R environment data.frame named according argument(default name 'dataframesort.newobj') name specified","code":""},{"path":"/reference/dataFrameSortDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Serverside assign function dataFrameSortDS called clientside function ds.dataFrameSort. vector matrix can added , coerced , data frame (using function [ds.dataFrame]) means can sorted/reordered using ds.dataFrameSort. Fundamentally, function [ds.dataFrameSort] sort specified data frame serverside using sort key also serverside. details see help clientside function: [ds.dataFrameShort]","code":""},{"path":"/reference/dataFrameSortDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Paul Burton, critical error identification Leire Abarrategui-Martinez, DataSHIELD Development Team, 2/4/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"First serverside function subsetting data frame row column.","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"","code":"dataFrameSubset1DS( df.name = NULL, V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, keep.cols = NULL, rm.cols = NULL, keep.NAs = NULL )"},{"path":"/reference/dataFrameSubset1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"df.name character string providing name data.frame sorted. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset V1.name character string specifying name subsetting vector Boolean operator applied define subset created. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset V2.name character string specifying name vector scalar values vector specified argument compared. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset Boolean.operator.n character string specifying one six possible Boolean operators: '==', '!=', '>', '>=', '<', '<=' argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset keep.cols numeric vector specifying numbers columns kept final subset subsetting column. example: keep.cols=c(2:5,7,12) keep columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset rm.cols numeric vector specifying numbers columns removed creating final subset subsetting column. example: rm.cols=c(2:5,7,12) remove columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset keep.NAs logical, TRUE NAs vector holding final Boolean vector indicating whether given row included subset converted 1s included subset. NAs caused NAs either . FALSE NULL NAs final Boolean vector converted 0s corresponding row therefore excluded subset. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"first serverside function called ds.dataFrameSubset provides first level traps comprehensive series disclosure risks can returned directly clientside dataFrameSubset1DS aggregate function. second serverside function called ds.dataFrameSubset (dataFrameSubset2DS) carries disclosure tests, assign function writes subsetted data.frame serverside. consequence, records error messages studysideMessages can retrieved using ds.message","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"data frame list variables number rows, class 'data.frame'. details see help header ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"Second serverside function subsetting data frame row column.","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"","code":"dataFrameSubset2DS( df.name = NULL, V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, keep.cols = NULL, rm.cols = NULL, keep.NAs = NULL )"},{"path":"/reference/dataFrameSubset2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"df.name character string providing name data.frame sorted. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset V1.name character string specifying name subsetting vector Boolean operator applied define subset created. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset V2.name character string specifying name vector scalar values vector specified argument compared. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset Boolean.operator.n character string specifying one six possible Boolean operators: '==', '!=', '>', '>=', '<', '<=' argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset keep.cols numeric vector specifying numbers columns kept final subset subsetting column. example: keep.cols=c(2:5,7,12) keep columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset rm.cols numeric vector specifying numbers columns removed creating final subset subsetting column. example: rm.cols=c(2:5,7,12) remove columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset keep.NAs logical, TRUE NAs vector holding final Boolean vector indicating whether given row included subset converted 1s included subset. NAs caused NAs either . FALSE NULL NAs final Boolean vector converted 0s corresponding row therefore excluded subset. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"object specified argument (default name '_subset') initially specified calling ds.dataFrameSubset. output object (required subsetted data.frame called written serverside. addition, two validity messages returned via ds.dataFrameSubset indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - dataFrameSubset2DS (via ds.dataFrame()) also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"data frame list variables number rows, class 'data.frame'. details see help header ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/densityGridDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates a density grid with or without a priori defined limits — densityGridDS","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Generates density grid can used heatmap contour plots.","code":""},{"path":"/reference/densityGridDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"","code":"densityGridDS( x, y, limits = FALSE, x.min = NULL, x.max = NULL, y.min = NULL, y.max = NULL, numints = 20 )"},{"path":"/reference/densityGridDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"x character string providing name server-side numerical vector y character string providing name server-side numerical vector limits logical expression whether limits density grid defined user. limits set \"FALSE\", min max x y used range. limits set \"TRUE\", limits defined x.min, x.max, y.min y.max used. x.min minimum value x axis grid density object, needed x.max maximum value x axis grid density object, needed y.min minimum value y axis grid density object, needed y.max maximum value y axis grid density object, needed numints number intervals grid density object, default 20","code":""},{"path":"/reference/densityGridDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"list grid density matrix (grid) classes x y inputs (class.x class.y)","code":""},{"path":"/reference/densityGridDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Invalid cells (cells count < set filter value minimum allowed counts table cells) turn 0.","code":""},{"path":"/reference/densityGridDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Julia Isaeva, Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dimDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the dimension of a data frame or matrix — dimDS","title":"Returns the dimension of a data frame or matrix — dimDS","text":"function similar R function dim.","code":""},{"path":"/reference/dimDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the dimension of a data frame or matrix — dimDS","text":"","code":"dimDS(x)"},{"path":"/reference/dimDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the dimension of a data frame or matrix — dimDS","text":"x string character, name dataframe matrix","code":""},{"path":"/reference/dimDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the dimension of a data frame or matrix — dimDS","text":"list two elements: dim (dimension input object) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/dimDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the dimension of a data frame or matrix — dimDS","text":"function returns dimension input dataframe matrix","code":""},{"path":"/reference/dimDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the dimension of a data frame or matrix — dimDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dmtC2SDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"Creates data.frame, matrix tibble serverside equivalent data.frame, matrix tibble (DMT) clientside.","code":""},{"path":"/reference/dmtC2SDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"","code":"dmtC2SDS( dfdata.mat.transmit, inout.object.transmit, from, nrows.transmit, ncols.transmit, colnames.transmit, colclass.transmit, byrow )"},{"path":"/reference/dmtC2SDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"dfdata.mat.transmit character string format can pass DataSHIELD R parser specifies name DMT copied clientside serverside. Value fully specified argument ds.dmtC2S. inout.object.transmit character string taking values \"DF\", \"MAT\" \"TBL\". value argument automatically set ds.dmtC2S depending whether clientside DMT data.frame, matrix tibble. Correspondingly, value determines whether object created serverside data.frame, matrix tibble. unlikely always work (class misspecifications may occur) works test cases. character string specifying source . Fixed clientside function \"clientside.matdftbl\". nrows.transmit specifies number rows matrix created. Fixed clientside function equal number rows clientside DMT transferred. ncols.transmit specifies number columns matrix created. Fixed clientside function equal number columns clientside DMT transferred. colnames.transmit parser-transmissible vector specifying name column DMT transferred clientside serverside. Generated automatically clientside function colnames clientside DMT. colclass.transmit parser-transmissible vector specifying class vector representing individual column DMT transferred. Generated automatically clientside function. allows transmission DMTs containing columns different classes.something going go wrong class misspecification (see inout.object.transmit) DMT complex combination data/column types likely cause. suggests always check class serverside DMT individual columns (latter important). situation arises class columns crucial function needed please contact DataSHIELD forum can try remedy problem. byrow logical value specifying whether DMT created serverside filled row row column column. fixed clientside function FALSE (fill column column).","code":""},{"path":"/reference/dmtC2SDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"object specified argument (default name \"matdftbl.copied.C2S\") written data.frame, matrix tibble serverside.","code":""},{"path":"/reference/dmtC2SDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"dmtC2SDS serverside assign function called ds.dmtC2S. information works see help ds.dmtC2S","code":""},{"path":"/reference/dmtC2SDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"Paul Burton DataSHIELD Development Team - 3rd June, 2021","code":""},{"path":"/reference/dsBase-package.html","id":null,"dir":"Reference","previous_headings":"","what":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","title":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","text":"Base 'DataSHIELD' functions server side. 'DataSHIELD' software package allows non-disclosive federated analysis sensitive data. 'DataSHIELD' analytic functions designed share non disclosive summary statistics, built automated output checking based statistical disclosure control. data sites setting threshold values automated output checks. details, see 'citation(\"dsBase\")'.","code":""},{"path":"/reference/dsBase-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","text":"Maintainer: Stuart Wheater stuart.wheater@arjuna.com (ORCID) Authors: Stuart Wheater stuart.wheater@arjuna.com (ORCID) Paul Burton (ORCID) Rebecca Wilson (ORCID) Olly Butters (ORCID) Patricia Ryser-Welch (ORCID) Alex Westerberg Leire Abarrategui Roberto Villegas-Diaz (ORCID) Demetris Avraam (ORCID) Yannick Marcon yannick.marcon@obiba.org (ORCID) Tom Bishop Amadou Gaye (ORCID) Xavier Escribà-Montagut (ORCID)","code":""},{"path":"/reference/elsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"function based native R function elspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/elsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"","code":"elsplineDS(x = x, n = n, marginal = FALSE, names = NULL)"},{"path":"/reference/elsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"x name input numeric variable n integer greater 2, knots computed cut n equally-spaced intervals along range x marginal logical, parametrize spline, see Details names character, vector names constructed variables","code":""},{"path":"/reference/elsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"elspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/elsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment. Function elspline wraps lspline computes knot positions cut range x n equal-width intervals.","code":""},{"path":"/reference/elsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/expDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the exponential values of the input variable — expDS","title":"Computes the exponential values of the input variable — expDS","text":"function similar R function exp.","code":""},{"path":"/reference/expDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the exponential values of the input variable — expDS","text":"","code":"expDS(x)"},{"path":"/reference/expDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the exponential values of the input variable — expDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/expDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the exponential values of the input variable — expDS","text":"object specified newobj argument ds.exp (default name exp.newobj) written serverside. output object class numeric.","code":""},{"path":"/reference/expDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the exponential values of the input variable — expDS","text":"function computes exponential values input numeric integer vector.","code":""},{"path":"/reference/expDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the exponential values of the input variable — expDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/fixClassDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Change Class of Target Variables in a Data Frame — fixClassDS","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"Change Class Target Variables Data Frame","code":""},{"path":"/reference/fixClassDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"","code":"fixClassDS(df.name, target_vars, target_class)"},{"path":"/reference/fixClassDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"df.name string representing name data frame. target_vars character vector specifying columns modified. target_class character vector specifying new classes column (1 = factor, 2 = integer, 3 = numeric, 4 = character, 5 = logical).","code":""},{"path":"/reference/fixClassDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"modified data frame specified columns converted target classes.","code":""},{"path":"/reference/fixColsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Missing Columns with NA Values — fixColsDS","title":"Add Missing Columns with NA Values — fixColsDS","text":"Add Missing Columns NA Values","code":""},{"path":"/reference/fixColsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Missing Columns with NA Values — fixColsDS","text":"","code":"fixColsDS(.data, cols)"},{"path":"/reference/fixColsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Missing Columns with NA Values — fixColsDS","text":".data string representing name data frame. cols character vector specifying columns added missing.","code":""},{"path":"/reference/fixColsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Missing Columns with NA Values — fixColsDS","text":"modified data frame missing columns added filled NA.","code":""},{"path":"/reference/fixLevelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"Set Factor Levels Specific Columns Data Frame","code":""},{"path":"/reference/fixLevelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"","code":"fixLevelsDS(df.name, vars, levels)"},{"path":"/reference/fixLevelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"df.name string representing name data frame modify. vars character vector specifying columns modified. levels named list element contains levels corresponding factor variable.","code":""},{"path":"/reference/fixLevelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"modified data frame specified columns converted factors provided levels.","code":""},{"path":"/reference/gamlssDS.html","id":null,"dir":"Reference","previous_headings":"","what":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"function calls gamlssDS wrapper function gamlss R package. function returns object class \"gamlss\", generalized additive model location, scale shape (GAMLSS). function also saves residuals object server-side name specified newobj argument. addition, argument centiles set TRUE, function calls centiles function gamlss package returns sample percentages centile curve.","code":""},{"path":"/reference/gamlssDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"","code":"gamlssDS( formula = formula, sigma.formula = sigma.formula, nu.formula = nu.formula, tau.formula = tau.formula, family = family, data = data, method = method, mu.fix = mu.fix, sigma.fix = sigma.fix, nu.fix = nu.fix, tau.fix = tau.fix, control = control, i.control = i.control, centiles = centiles, xvar = xvar, newobj = newobj )"},{"path":"/reference/gamlssDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"formula formula object, response left ~ operator, terms, separated + operators, right. Nonparametric smoothing terms indicated pb() penalised beta splines, cs smoothing splines, lo loess smooth terms random ra random terms, e.g. y~cs(x,df=5)+x1+x2*x3. sigma.formula formula object fitting model sigma parameter, formula , e.g. sigma.formula=~cs(x,df=5). nu.formula formula object fitting model nu parameter, e.g. nu.formula=~x tau.formula formula object fitting model tau parameter, e.g. tau.formula=~cs(x,df=2) family gamlss.family object, used define distribution link functions various parameters. distribution families supported gamlss() can found gamlss.family. Functions BI() (binomial) produce family object. Also can given without parentheses .e. BI. Family functions can take arguments, BI(mu.link=probit). data data frame containing variables occurring formula. missing, variables parent environment. method character indicating algorithm GAMLSS. Can either 'RS', 'CG' 'mixed'. method='RS' function use Rigby Stasinopoulos algorithm, method='CG' function use Cole Green algorithm, method='mixed' function use RS algorithm twice switching Cole Green algorithm 10 extra iterations. mu.fix logical, indicate whether mu parameter kept fixed fitting processes. sigma.fix logical, indicate whether sigma parameter kept fixed fitting processes. nu.fix logical, indicate whether nu parameter kept fixed fitting processes. tau.fix logical, indicate whether tau parameter kept fixed fitting processes. control sets control parameters outer iterations algorithm using gamlss.control function. vector 7 numeric values: () c.crit (convergence criterion algorithm), (ii) n.cyc (number cycles algorithm), (iii) mu.step (step length parameter mu), (iv) sigma.step (step length parameter sigma), (v) nu.step (step length parameter nu), (vi) tau.step (step length parameter tau), (vii) gd.tol (global deviance tolerance level). default values 7 parameters set c(0.001, 20, 1, 1, 1, 1, Inf). .control sets control parameters inner iterations RS algorithm using glim.control function. vector 4 numeric values: () cc (convergence criterion algorithm), (ii) cyc (number cycles algorithm), (iii) bf.cyc (number cycles backfitting algorithm), (iv) bf.tol (convergence criterion (tolerance level) backfitting algorithm). default values 4 parameters set c(0.001, 50, 30, 0.001). centiles logical, indicating whether function centiles() used tabulate sample percentages centile curve. Default set FALSE. xvar unique explanatory variable used centiles() function. variable used centiles argument set TRUE. restriction centiles function applies models one explanatory variable . newobj character string provides name output object stored data servers. Default gamlss_residuals.","code":""},{"path":"/reference/gamlssDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"gamlss object components native R gamlss function. Individual-level information like components y (response response) residuals (normalised quantile residuals model) disclosed client-side.","code":""},{"path":"/reference/gamlssDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"additional details see help header gamlss centiles functions native R gamlss package.","code":""},{"path":"/reference/gamlssDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/getAllLevelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"Retrieve Factor Levels Specific Columns","code":""},{"path":"/reference/getAllLevelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"","code":"getAllLevelsDS(df.name, factor_vars)"},{"path":"/reference/getAllLevelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"df.name string representing name data frame. factor_vars character vector specifying factor columns.","code":""},{"path":"/reference/getAllLevelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"list factor levels specified columns.","code":""},{"path":"/reference/getClassAllColsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"Get Class Columns Data Frame","code":""},{"path":"/reference/getClassAllColsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"","code":"getClassAllColsDS(df.name)"},{"path":"/reference/getClassAllColsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"df.name string representing name data frame.","code":""},{"path":"/reference/getClassAllColsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"tibble class column data frame.","code":""},{"path":"/reference/getWGSRDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"Calculate Growth Reference z-score given anthropometric measurement function similar R function getWGSR zscorer package.","code":""},{"path":"/reference/getWGSRDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"","code":"getWGSRDS(sex, firstPart, secondPart, index, standing = NA, thirdPart = NA)"},{"path":"/reference/getWGSRDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"sex name binary variable indicates sex subject. must coded 1 = male 2 = female. project variable sex different levels, recode levels 1 males 2 females using ds.recodeValues DataSHIELD function use ds.getWGSR. firstPart Name variable specifying: Weight (kg) BMI/, W/, W/H, W/L Head circumference (cm) HC/Height (cm) H/Length (cm) L/MUAC (cm) MUAC/Sub-scapular skinfold (mm) SSF/Triceps skinfold (mm) TSF/Give quoted variable name (e.g.) \"weight\". careful units (weight kg; height, length, head circumference, MUAC cm, skinfolds mm). secondPart Name variable specifying: Age (days) H/, HC/, L/, MUAC/, SSF/, TSF/Height (cm) BMI/, W/H Length (cm) W/L Give quoted variable name (e.g.) \"age\". careful units (age days; height length cm). index index calculated added data. One : bfa BMI age hca Head circumference age hfa Height age lfa Length age mfa MUAC age ssa Sub-scapular skinfold age tsa Triceps skinfold age wfa Weight age wfh Weight height wfl Weight length Give quoted index name (e.g.) \"wfh\". standing Variable specifying stature measured. NA (default) age (\"hfa\" \"lfa\") height rules (\"wfh\" \"wfl\") applied. must coded 1 = Standing; 2 = Supine; 3 = Unknown. Missing values recoded 3 = Unknown. Give single value (e.g.\"1\"). value specified height age rules applied. thirdPart Name variable specifying age (days) BMI/. Give quoted variable name (e.g.) \"age\". careful units (age days).","code":""},{"path":"/reference/getWGSRDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"ds.getWGSR assigns numeric vector includes z-scores specified index.","code":""},{"path":"/reference/getWGSRDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"function computes Growth Reference z-scores anthropometric data weight, height length, MUAC, head circumference, sub-scapular skinfold triceps skinfold. Note function might fail return NAs variables outside ranges given WGS (Child Growth Standards) reference (.e. 45 120 cm height 0 60 months age). user check ranges units data.","code":""},{"path":"/reference/getWGSRDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glm1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"glm1DS called by ds.glm — glm1DS","title":"glm1DS called by ds.glm — glm1DS","text":"first server-side aggregate function called ds.glm","code":""},{"path":"/reference/glm1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"glm1DS called by ds.glm — glm1DS","text":"","code":"glm1DS(formula, family, weights, offset, data)"},{"path":"/reference/glm1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"glm1DS called by ds.glm — glm1DS","text":"formula glm() formula consistent R syntax eg U~x+y+Z regress variables U x,y Z family glm() family consistent R syntax eg \"gaussian\", \"poisson\", \"binomial\" weights optional variable providing regression weights offset offset data optional character string specifying data.frame object holding data analysed specified model","code":""},{"path":"/reference/glm1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"glm1DS called by ds.glm — glm1DS","text":"List values GLM model.","code":""},{"path":"/reference/glm1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"glm1DS called by ds.glm — glm1DS","text":"aggregation function sets model structure creates starting beta.vector feeds, via ds.glm, glm2DS enable iterative fitting generalized linear model specified. details please see extensive header ds.glm.","code":""},{"path":"/reference/glm1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"glm1DS called by ds.glm — glm1DS","text":"Burton PR DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glm2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"glm2DS called by ds.glm — glm2DS","title":"glm2DS called by ds.glm — glm2DS","text":"second server-side aggregate function called ds.glm.","code":""},{"path":"/reference/glm2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"glm2DS called by ds.glm — glm2DS","text":"","code":"glm2DS(formula, family, beta.vect, offset, weights, dataName)"},{"path":"/reference/glm2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"glm2DS called by ds.glm — glm2DS","text":"formula glm() formula consistent R syntax eg U~x+y+Z regress variables U x, y Z family glm() family consistent R syntax eg \"gaussian\", \"poisson\", \"binomial\" beta.vect numeric vector created clientside function specifying vector regression coefficients current iteration offset optional variable providing regression offset weights optional variable providing regression weights dataName optional character string specifying data.frame object holding data analysed specified model ","code":""},{"path":"/reference/glm2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"glm2DS called by ds.glm — glm2DS","text":"List values GLM model","code":""},{"path":"/reference/glm2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"glm2DS called by ds.glm — glm2DS","text":"aggregate function uses model structure starting beta.vector constructed glm1DS iteratively fit generalized linear model specified. function glm2DS also carries series disclosure checks arguments data fail tests, model construction blocked appropriate serverside error message created returned ds.glm clientside. details please see extensive header ds.glm.","code":""},{"path":"/reference/glm2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"glm2DS called by ds.glm — glm2DS","text":"Paul Burton, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmPredictDS.ag.html","id":null,"dir":"Reference","previous_headings":"","what":"predict regression responses from a glm object — glmPredictDS.ag","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"identify return key components/summaries serverside glm_predict object can safely returned clientside without disclosure risk","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"","code":"glmPredictDS.ag( glmname.transmit, newdataname.transmit, output.type, se.fit, dispersion, terms.transmit, na.action )"},{"path":"/reference/glmPredictDS.ag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"glmname.transmit character string specifying name glm object serverside used prediction. Fully specified glmname argument ds.glmPredict newdataname.transmit character string specifying (optional) dataframe serverside look (potentially) new covariate values base predictions. Fully specified newdataname argument ds.glmPredict. output.type character string taking values 'response', 'link' 'terms'. Fully specified corresponding argument ds.glmPredict. se.fit logical standard errors fitted predictions required. Fully specified corresponding argument ds.glmPredict. dispersion numeric value specifying dispersion GLM fit assumed computing standard errors. Fully specified corresponding argument ds.glmPredict. terms.transmit character vector specifying subset terms return prediction. Fully specified 'terms' argument ds.glmPredict. na.action character string determining done missing values data.frame identified . Fully specified na.action argument ds.glmPredict.","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"components/summarising statistics serverside predict_glm object can safely transmitted clientside without risk disclosure. details see DataSHIELD help ds.glmPredict glmPredict.help native R predict.glm predict.glm native R","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"Serverside aggregate function called ds.glmPredict. called immediately assign function glmPredict.created predict_glm object serverside applying equivalent predict.glm() native R glm object serverside. aggregate function, glmPredict.ag, identifies returns components predict_glm object can safely returned clientside without risk disclosure. details see DataSHIELD help ds.glmPredict glmPredict.help native R predict.glm","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmPredictDS.as.html","id":null,"dir":"Reference","previous_headings":"","what":"predict regression responses from a glm object — glmPredictDS.as","title":"predict regression responses from a glm object — glmPredictDS.as","text":"create predict_glm object serverside applying equivalent predict.glm() native R glm object serverside. Identify return components predict_glm object can safely sent clientside without risk disclosure","code":""},{"path":"/reference/glmPredictDS.as.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"predict regression responses from a glm object — glmPredictDS.as","text":"","code":"glmPredictDS.as( glmname.transmit, newdataname.transmit, output.type, se.fit, dispersion, terms.transmit, na.action )"},{"path":"/reference/glmPredictDS.as.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"predict regression responses from a glm object — glmPredictDS.as","text":"glmname.transmit character string specifying name glm object serverside used prediction. Fully specified glmname argument ds.glmPredict newdataname.transmit character string specifying (optional) dataframe serverside look (potentially) new covariate values base predictions. Fully specified newdataname argument ds.glmPredict. output.type character string taking values 'response', 'link' 'terms'. Fully specified corresponding argument ds.glmPredict. se.fit logical standard errors fitted predictions required. Fully specified corresponding argument ds.glmPredict. dispersion numeric value specifying dispersion GLM fit assumed computing standard errors. Fully specified corresponding argument ds.glmPredict. terms.transmit character vector specifying subset terms return prediction. Fully specified 'terms' argument ds.glmPredict. na.action character string determining done missing values data.frame identified . Fully specified na.action argument ds.glmPredict.","code":""},{"path":"/reference/glmPredictDS.as.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"predict regression responses from a glm object — glmPredictDS.as","text":"glmPredict.writes new object serverside containing output precisely equivalent output predict.glm native R. details see DataSHIELD help ds.glmPredict help predict.glm native R","code":""},{"path":"/reference/glmPredictDS.as.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"predict regression responses from a glm object — glmPredictDS.as","text":"Serverside assign function called ds.glmPredict makes predictions regression responses based serverside glm object already created serverside ds.glmSLMA writes predict_glm object serverside. details see help ds.glmPredict help native R predict.glm","code":""},{"path":"/reference/glmPredictDS.as.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"predict regression responses from a glm object — glmPredictDS.as","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMA11DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMA11DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"","code":"glmSLMA11DS(formula, family, weights, offset, data)"},{"path":"/reference/glmSLMA11DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA weights character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. offset character string specifying variable used offset. Specified call ds.glmSLMA. data character string specifying name data.frame holding data model. Specified dataName call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"assesses returns information failure pass disclosure traps test model complexity (saturation). detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"glmSLMADS.assign aggregate function called clientside function ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS assign function glmSLMADS.assign detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"Paul Burton DataSHIELD Development Team (14/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"","code":"glmSLMA2DS(formula, family, offset, weights, newobj, dataName)"},{"path":"/reference/glmSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA offset character string specifying variable used offset. Specified call ds.glmSLMA. weights character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. newobj character string specifying name glm object written serverside glmSLMADS.assign. either name specified newobj argument ds.glmSLMA newobj unspecified NULL called new.glm.obj. dataName character string specifying name data.frame holding data model. Specified call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"quantitative, Boolean, character objects required enable SLMA pooling separate glm models fitted study - particular including study-specific regression coefficients corresponding standard errors.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"glmSLMADS.assign aggregate function called clientside function ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS assign function glmSLMADS.assign detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"Paul Burton DataSHIELD Development Team (14/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"","code":"glmSLMADS.assign(formula, family, offsetName, weightsName, dataName)"},{"path":"/reference/glmSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA offsetName character string specifying variable used offset. Specified call ds.glmSLMA. weightsName character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. dataName character string specifying name data.frame holding data model. Specified call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"writes glm object summarising fitted model serverside. detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"glmSLMADS.assign assign function called clientside function ds.glmSLMA. ds.glmSLMA also calls two aggregate functions glmSLMA1DS glmSLMA2DS. detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"Paul Burton DataSHIELD Development Team (14/7/20)","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize a glm object on the serverside — glmSummaryDS.ag","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"returns non-disclosive elements clientside glm object corresponding object holding output summary(glm object) serverside.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"","code":"glmSummaryDS.ag(x.transmit)"},{"path":"/reference/glmSummaryDS.ag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"x.transmit character string specifying name glm object serverside summarised. specified x.name argument ds.glmSummary","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"returns clientside non-disclosive elements (non-disclosive elements) specified serverside glm corresponding summary_glm object.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"Serverside aggregate function called ds.glmSummary. ds.glmSummary first calls glmSummaryDS.ag create glm_summary object serverside based applying native R's summary.glm() serverside glm object previously created ds.glmSLMA. calls glmSummaryDS.ag return clientside non-disclosive elements (non-disclosive elements) serverside glm corresponding summary_glm object.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSummaryDS.as.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize a glm object on the serverside — glmSummaryDS.as","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"summarize glm object serverside create summary_glm object. Also identify return components glm object summary_glm object can safely sent clientside without risk disclosure","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"","code":"glmSummaryDS.as(x.transmit)"},{"path":"/reference/glmSummaryDS.as.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"x.transmit character string specifying name glm object serverside summarised. specified x.name argument ds.glmSummary","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"writes object serverside precisely equivalent summary(glm object) native R","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"Serverside assign function called ds.glmSummary summarises glm object already created serverside fitting ds.glmSLMA writes summary_glm object serverside. details see help ds.glmSLMA help native R glm() summary.glm","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmerSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"glmerSLMA2DS fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data one multiple sources pooling via SLMA (study level meta-analysis)","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"","code":"glmerSLMA2DS( formula, offset, weights, dataName, family, control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL )"},{"path":"/reference/glmerSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"formula see help ds.glmerSLMA offset see help ds.glmerSLMA weights see help ds.glmerSLMA dataName see help ds.glmerSLMA family see help ds.glmerSLMA control_type see help ds.glmerSLMA control_value.transmit see help argument function ds.glmerSLMA nAGQ integer scalar, defaulting 1L. PRACTICE, MAY NECESSARY SET nAGQ 0L model appears converge perfectly well (e.g. verbose=2 demonstrates good initial convergence log-likelihood regression coefficients) formal convergence get declared - output produced - despite running model many iterations. nAGQ argument set nAGQ argument ds.glmerSLMA details can found help(ds.glmerSLMA) native R help glmer() verbose see help ds.glmerSLMA theta see help argument function ds.glmerSLMA fixef see help argument function ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"key model components see help ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"glmerSLMA2DS serverside function called ds.glmerSLMA clientside. analytic work engine glmer function R sits lme4 package. ds.glmerSLMA fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data single multiple sources. multiple data sources, glme fitted convergence data source independently estimates standard errors returned client thereby enabling cross-study pooling using study level meta-analysis (SLMA). default SLMA undertaken using metafor package, SLMA occurs clientside , far user concerned just standard R environment, user can choose use approach meta-analysis choose. Additional information fitting glmes using glmer engine can obtained using R help glmer lme4 package","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"Tom Bishop, additions Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"glmerSLMADS.assign glmerSLMA2DS fits generalized linear mixed effects model (glme) per study saves outcomes study","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"","code":"glmerSLMADS.assign( formula, offset, weights, dataName, family, control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL )"},{"path":"/reference/glmerSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"formula see help ds.glmerSLMA offset see help ds.glmerSLMA weights see help ds.glmerSLMA dataName see help ds.glmerSLMA family see help ds.glmerSLMA control_type see help ds.glmerSLMA control_value.transmit see help argument function ds.glmerSLMA nAGQ integer scalar, defaulting 1L. PRACTICE, MAY NECESSARY SET nAGQ 0L model appears converge perfectly well (e.g. verbose=2 demonstrates good initial convergence log-likelihood regression coefficients) formal convergence get declared - output produced - despite running model many iterations. nAGQ argument set nAGQ argument ds.glmerSLMA details can found help(ds.glmerSLMA) native R help glmer() verbose see help ds.glmerSLMA theta see help argument function ds.glmerSLMA fixef see help argument function ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"writes glmerMod object summarising fitted model serverside. detailed information see help ds.glmerSLMA.","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"glmerSLMADS.assign serverside function called ds.glmerSLMA clientside. analytic work engine glmer function R sits lme4 package. glmerSLMADS.assign fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data single data source saves regression outcomes serverside.","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/heatmapPlotDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"function calculates coordinates centroids n nearest neighbours.","code":""},{"path":"/reference/heatmapPlotDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"","code":"heatmapPlotDS(x.name, y.name, k, noise, method.indicator)"},{"path":"/reference/heatmapPlotDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"x.name character string providing name server-side numeric vector, x-variable. y.name character string providing name server-side numeric vector, y-variable. k number nearest neighbours centroid calculated method.indicator equal 1 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 2 (.e. probabilistic method). method.indicator number equal either 1 2. value equal 1 'deterministic' method used. value set 2 'probabilistic' method used.","code":""},{"path":"/reference/heatmapPlotDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"list x y coordinates centroids deterministic method used x y coordinated noisy data probabilistic method used, along classes x y inputs (class.x class.y)","code":""},{"path":"/reference/heatmapPlotDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"function finds n-1 nearest neighbours data point 2-dimensional space. nearest neighbours data points minimum Euclidean distances point interest. point interest n-1 nearest neighbours used calculation coordinates centroid n points. Centroid referred centre mass, .e. x-coordinate centroid average value x-coordinates n nearest neighbours y-coordinate centroid average y-coordinates n nearest neighbours. coordinates centroids return client side function can used plot non-disclosive graphs (e.g. scatter plots, heatmap plots, contour plots, etc).","code":""},{"path":"/reference/heatmapPlotDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/hetcorDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Heterogeneous Correlation Matrix — hetcorDS","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"function based hetcor function R package polycor.","code":""},{"path":"/reference/hetcorDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"","code":"hetcorDS(data, ML, std.err, bins, pd, use)"},{"path":"/reference/hetcorDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"data name data frame consisting factors, ordered factors, logical variables, character variables, /numeric variables, first several variables. ML TRUE, compute maximum-likelihood estimates; FALSE (default), compute quick two-step estimates. std.err TRUE (default), compute standard errors. bins number bins use continuous variables testing bivariate normality; default 4. pd TRUE (default) correlation matrix positive-definite, attempt made adjust positive-definite matrix, using nearPD function Matrix package. Note default arguments nearPD used (except corr=TRUE); control call nearPD directly. use \"complete.obs\", remove observations missing data; \"pairwise.complete.obs\", compute correlation using observations valid data pair variables.","code":""},{"path":"/reference/hetcorDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Returns object class \"hetcor\" following components: correlation matrix; type correlation: \"Pearson\", \"Polychoric\", \"Polyserial\"; standard errors correlations, requested; number (numbers) observations correlations based; p-values tests bivariate normality pair variables; method missing data handled: \"complete.obs\" \"pairwise.complete.obs\"; TRUE ML estimates, FALSE two-step estimates.","code":""},{"path":"/reference/hetcorDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Computes heterogeneous correlation matrix, consisting Pearson product-moment correlations numeric variables, polyserial correlations numeric ordinal variables, polychoric correlations ordinal variables.","code":""},{"path":"/reference/hetcorDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/histogram1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"returns the minimum and the maximum of the input numeric vector — histogram1DS","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"function returns minimum maximum input numeric vector depends argument method.indicator. method.indicator set 1 (.e. 'smallCellsRule' used) computed minimum maximum values multiplied small random number. method.indicator set 2 (.e. 'deterministic' method used) function returns minimum maximum values vector scaled centroids. method.indicator set 3 (.e. 'probabilistic' method used) function returns minimum maximum values generated 'noisy' vector.","code":""},{"path":"/reference/histogram1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"","code":"histogram1DS(x, method.indicator, k, noise)"},{"path":"/reference/histogram1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"x character string providing name server-side numeric vector histogram desired. method.indicator number equal either 1, 2 3 indicating method disclosure control used generation histogram. value equal 1 'smallCellsRule' used. value equal 2 'deterministic' method used. value set 3 'probabilistic' method used. k number nearest neighbours centroid calculated method.indicator equal 2 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 3 (.e. probabilistic method).","code":""},{"path":"/reference/histogram1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"list numeric vector containing minimum maximum values vector (range) class input vector (class)","code":""},{"path":"/reference/histogram1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/histogram2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes a histogram of the input variable without plotting. — histogram2DS","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"function produces information required plot histogram. done without allowing bins (cells) number counts less pre-specified disclosure control set minimum cell size table. bin less counts threshold counts density replaced 0 value.","code":""},{"path":"/reference/histogram2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"","code":"histogram2DS(x, num.breaks, min, max, method.indicator, k, noise)"},{"path":"/reference/histogram2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"x character string providing name server-side numeric vector histogram desired. num.breaks number breaks range variable divided. min numeric, lower limit distribution. max numeric, upper limit distribution. method.indicator number equal either 1, 2 3 indicating method disclosure control used generation histogram. value equal 1 'smallCellsRule' used. value equal 2 'deterministic' method used. value set 3 'probabilistic' method used. k number nearest neighbours centroid calculated method.indicator equal 2 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 3 (.e. probabilistic method).","code":""},{"path":"/reference/histogram2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"list object class histogram number invalid cells","code":""},{"path":"/reference/histogram2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"Please find details documentation clientside ds.histogram function.","code":""},{"path":"/reference/histogram2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/igb_standardsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"Converts birth measurements INTERGROWTH z-scores/centiles (generic)","code":""},{"path":"/reference/igb_standardsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"","code":"igb_standardsDS( gagebrth = gagebrth, z = z, p = p, val = val, var = var, sex = sex, fun = fun )"},{"path":"/reference/igb_standardsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"gagebrth name \"gestational age birth days\" variable. z z-score(s) convert (must 0 1). Default value 0. value used fun set \"igb_zscore2value\". p centile(s) convert (must 0 100). Default value p=50. value used fun set \"igb_centile2value\". val name anthropometric variable convert. var name measurement convert (\"lencm\", \"wtkg\", \"hcircm\", \"wlr\") sex name sex factor variable. variable coded Male/Female. coded differently (e.g. 0/1), can use ds.recodeValues function recode categories Male/Female use ds.igb_standards fun name function used. can one : \"igb_centile2value\", \"igb_zscore2value\", \"igb_value2zscore\" (default), \"igb_value2centile\".","code":""},{"path":"/reference/igb_standardsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"assigns converted measurement new object server-side","code":""},{"path":"/reference/igb_standardsDS.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"gestational ages 24 33 weeks, INTERGROWTH early preterm standard used.","code":""},{"path":"/reference/igb_standardsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/isNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if a vector is empty — isNaDS","title":"Checks if a vector is empty — isNaDS","text":"function similar R function .na instead vector booleans returns just one boolean tell element missing values.","code":""},{"path":"/reference/isNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if a vector is empty — isNaDS","text":"","code":"isNaDS(x)"},{"path":"/reference/isNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if a vector is empty — isNaDS","text":"x character string, name server-side vector","code":""},{"path":"/reference/isNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if a vector is empty — isNaDS","text":"list two elements: .na (TRUE vector contains NAs, FALSE otherwise) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/isNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if a vector is empty — isNaDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/isValidDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if an input is valid — isValidDS","title":"Checks if an input is valid — isValidDS","text":"Tells object server side valid.","code":""},{"path":"/reference/isValidDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if an input is valid — isValidDS","text":"","code":"isValidDS(x)"},{"path":"/reference/isValidDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if an input is valid — isValidDS","text":"x character string, name vector (numeric, integer, factor, character, logical), data.frame matrix","code":""},{"path":"/reference/isValidDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if an input is valid — isValidDS","text":"list valid, boolean TRUE input valid FALSE , class, class input object client-side consistency checking","code":""},{"path":"/reference/isValidDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Checks if an input is valid — isValidDS","text":"function checks object valid.","code":""},{"path":"/reference/isValidDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if an input is valid — isValidDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/kurtosis1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the kurtosis of a numeric variable — kurtosis1DS","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"function calculates kurtosis numeric variable study separately.","code":""},{"path":"/reference/kurtosis1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"","code":"kurtosis1DS(x, method)"},{"path":"/reference/kurtosis1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"x string character, name numeric variable. method integer 1 3 selecting one algorithms computing kurtosis detailed headers client-side ds.kurtosis function.","code":""},{"path":"/reference/kurtosis1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"list including kurtosis input numeric variable, number valid observations class, class input object client-side consistency checking.","code":""},{"path":"/reference/kurtosis1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"function calculates kurtosis input variable x three different methods. method specified argument method client-side ds.kurtosis function.","code":""},{"path":"/reference/kurtosis1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/kurtosis2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the kurtosis of a numeric variable — kurtosis2DS","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"function calculates summary statistics returned client-side used estimation combined kurtosis numeric variable across studies.","code":""},{"path":"/reference/kurtosis2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"","code":"kurtosis2DS(x, global.mean)"},{"path":"/reference/kurtosis2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"x string character, name numeric variable. global.mean numeric, combined mean input variable across studies.","code":""},{"path":"/reference/kurtosis2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"list including sum quartic differences values x global mean x across studies, sum squared differences values x global mean x across studies, number valid observations (.e. length x excluding missing values), class, class input object client-side consistency checking.","code":""},{"path":"/reference/kurtosis2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"function calculates sum squared differences values x global mean x across studies, sum quatric differences values x global mean x across studies number valid observations input variable x.","code":""},{"path":"/reference/kurtosis2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lengthDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the length of a vector or list — lengthDS","title":"Returns the length of a vector or list — lengthDS","text":"function similar R function length.","code":""},{"path":"/reference/lengthDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the length of a vector or list — lengthDS","text":"","code":"lengthDS(x)"},{"path":"/reference/lengthDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the length of a vector or list — lengthDS","text":"x string character, name vector list","code":""},{"path":"/reference/lengthDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the length of a vector or list — lengthDS","text":"list two elements: length (number elements input vector list) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/lengthDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the length of a vector or list — lengthDS","text":"function returns length input vector list.","code":""},{"path":"/reference/lengthDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the length of a vector or list — lengthDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/levelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the levels of a factor vector — levelsDS","title":"Returns the levels of a factor vector — levelsDS","text":"function similar R function levels.","code":""},{"path":"/reference/levelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the levels of a factor vector — levelsDS","text":"","code":"levelsDS(x)"},{"path":"/reference/levelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the levels of a factor vector — levelsDS","text":"x character string, name factor vector","code":""},{"path":"/reference/levelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the levels of a factor vector — levelsDS","text":"list one element: Levels (factor levels present vector)","code":""},{"path":"/reference/levelsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the levels of a factor vector — levelsDS","text":"function returns levels input vector list.","code":""},{"path":"/reference/levelsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the levels of a factor vector — levelsDS","text":"Alex Westerberg, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"lexis1DS — lexis1DS","title":"lexis1DS — lexis1DS","text":"first server-side function called ds.lexis.","code":""},{"path":"/reference/lexis1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lexis1DS — lexis1DS","text":"","code":"lexis1DS(exitCol = NULL)"},{"path":"/reference/lexis1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lexis1DS — lexis1DS","text":"exitCol character string specifying variable holding time individual censored fails","code":""},{"path":"/reference/lexis1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lexis1DS — lexis1DS","text":"List `max.time`","code":""},{"path":"/reference/lexis1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lexis1DS — lexis1DS","text":"aggregate function. details see extensive header ds.lexis.","code":""},{"path":"/reference/lexis1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lexis1DS — lexis1DS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"lexis2DS — lexis2DS","title":"lexis2DS — lexis2DS","text":"second serverside function called ds.lexis.","code":""},{"path":"/reference/lexis2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lexis2DS — lexis2DS","text":"","code":"lexis2DS( datatext = NULL, intervalWidth, maxmaxtime, idCol, entryCol, exitCol, statusCol, vartext = NULL )"},{"path":"/reference/lexis2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lexis2DS — lexis2DS","text":"datatext clientside provided character string specifying data.frame holding data set expanded intervalWidth clientside generated character string specifying width survival epochs expanded data maxmaxtime clientside generated object specifying maximum follow time sources idCol clientside generated character string specifying variable holding IDs individuals data set expanded entryCol clientside specified character string identifying variable holding time individual starts follow exitCol clientside specified character string identifying variable holding time individual ends follow (censored fails) statusCol clientside specified character string identifying variable holding final censoring status (failed/censored) vartext clientside provided vector character strings denoting column names additional variables include final expanded table. 'variables' argument set (null) 'data' argument set full data.frame expanded carried forward","code":""},{"path":"/reference/lexis2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lexis2DS — lexis2DS","text":"List `expanded.table`","code":""},{"path":"/reference/lexis2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lexis2DS — lexis2DS","text":"assign function actually creates expanded dataframe containing survival data piecewise exponential regression. lexis2DS also carries series disclosure checks arguments data fail tests, creation expanded dataframe blocked appropriate serverside error message stored. details see extensive header ds.lexis.","code":""},{"path":"/reference/lexis2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lexis2DS — lexis2DS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis3DS.html","id":null,"dir":"Reference","previous_headings":"","what":"@title lexis3DS — lexis3DS","title":"@title lexis3DS — lexis3DS","text":"third serverside function called ds.lexis.","code":""},{"path":"/reference/lexis3DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"@title lexis3DS — lexis3DS","text":"","code":"lexis3DS()"},{"path":"/reference/lexis3DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"@title lexis3DS — lexis3DS","text":"Data frame `messageobj` object","code":""},{"path":"/reference/lexis3DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"@title lexis3DS — lexis3DS","text":"assign function simplifies returned output ds.lexis. Specifically, without lexis3DS output consists table within list, lexis3DS converts directly dataframe. details see extensive header ds.lexis.","code":""},{"path":"/reference/listDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce objects into a list — listDS","title":"Coerce objects into a list — listDS","text":"function similar R function 'list'","code":""},{"path":"/reference/listDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce objects into a list — listDS","text":"","code":"listDS(x.names = NULL, eltnames = NULL)"},{"path":"/reference/listDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce objects into a list — listDS","text":"x.names character vector object names coerce list. eltnames character vector, names elements list.","code":""},{"path":"/reference/listDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce objects into a list — listDS","text":"list","code":""},{"path":"/reference/listDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerce objects into a list — listDS","text":"Unlike R function 'list' takes also vector characters, names elements output list.","code":""},{"path":"/reference/listDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerce objects into a list — listDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"listDisclosureSettingsDS — listDisclosureSettingsDS","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"serverside function aggregate function called ds.listDisclosureSettings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"","code":"listDisclosureSettingsDS()"},{"path":"/reference/listDisclosureSettingsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"List DataSHIELD disclosure settings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"details see extensive header ds.listDisclosureSettings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team","code":""},{"path":"/reference/lmerSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"lmerSLMA2DS serverside function fits linear mixed effects model (lme) - .e. can include fixed random effects - data one multiple sources pooling via SLMA (study level meta-analysis)","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"","code":"lmerSLMA2DS( formula, offset, weights, dataName, REML = TRUE, control_type, control_value.transmit, optimizer, verbose = 0 )"},{"path":"/reference/lmerSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"formula see help ds.lmerSLMA offset see help ds.lmerSLMA weights see help ds.lmerSLMA dataName see help ds.lmerSLMA REML see help ds.lmerSLMA control_type see help ds.lmerSLMA control_value.transmit see help argument function ds.lmerSLMA optimizer see help ds.lmerSLMA verbose see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"key model components see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"lmerSLMA2DS serverside function called ds.lmerSLMA clientside. analytic work engine lmer function R sits lme4 package. ds.lmerSLMA fits linear mixed effects model (lme) - can include fixed random effects - data single multiple sources. multiple data sources, lme fitted convergence data source independently estimates standard errors returned client thereby enabling cross-study pooling using study level meta-analysis (SLMA). default SLMA undertaken using metafor package, SLMA occurs clientside , far user concerned just standard R environment, user can choose use approach meta-analysis choose. detailed help aspect lmerSLM2DS please see extensive help ds.lmerSLMA. Additional information fitting lmes using lmer engine can obtained using R help lmer lme4 package","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"Tom Bishop, additions Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"lmerSLMADS.assign lmerSLMA2DS fits linear mixed effects model (lme) per study saves outcomes study","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"","code":"lmerSLMADS.assign( formula, offset, weights, dataName, REML = TRUE, control_type, control_value.transmit, optimizer, verbose = 0 )"},{"path":"/reference/lmerSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"formula see help ds.lmerSLMA offset see help ds.lmerSLMA weights see help ds.lmerSLMA dataName see help ds.lmerSLMA REML see help ds.lmerSLMA control_type see help ds.lmerSLMA control_value.transmit see help argument function ds.lmerSLMA optimizer see help ds.lmerSLMA verbose see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"writes lmerMod object summarising fitted model serverside. detailed information see help ds.lmerSLMA.","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"lmerSLMADS.assign serverside function called ds.lmerSLMA clientside. analytic work engine lmer function R sits lme4 package. lmerSLMADS.assign fits linear mixed effects model (lme) including fixed random effects - data single data source saves regression outcomes serverside.","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"TDemetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/logDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the logarithm values of the input variable — logDS","title":"Computes the logarithm values of the input variable — logDS","text":"function similar R function log.","code":""},{"path":"/reference/logDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the logarithm values of the input variable — logDS","text":"","code":"logDS(x, base = exp(1))"},{"path":"/reference/logDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the logarithm values of the input variable — logDS","text":"x string character, name numeric integer vector base positive number, base logarithms computed. Default exp(1).","code":""},{"path":"/reference/logDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the logarithm values of the input variable — logDS","text":"object specified newobj argument ds.log (default name log.newobj) written serverside. output object class numeric.","code":""},{"path":"/reference/logDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the logarithm values of the input variable — logDS","text":"function computes logarithm values input numeric integer vector. default natural logarithms computed.","code":""},{"path":"/reference/logDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the logarithm values of the input variable — logDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"lists all objects on a serverside environment — lsDS","title":"lists all objects on a serverside environment — lsDS","text":"creates list names objects specified serverside environment","code":""},{"path":"/reference/lsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lists all objects on a serverside environment — lsDS","text":"","code":"lsDS(search.filter = NULL, env.to.search)"},{"path":"/reference/lsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lists all objects on a serverside environment — lsDS","text":"search.filter either NULL character string (potentially including '*' wildcards) specifying required search criteria. argument fully specified corresponding argument clientside function. env..search integer (e.g. format '2' '5L' format) specifying position search path environment explored. argument fully specified corresponding argument clientside function.","code":""},{"path":"/reference/lsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lists all objects on a serverside environment — lsDS","text":"list containing: (1) name/details serverside R environment ds.ls searched; (2) vector character strings giving names objects meeting naming criteria specified argument specified R serverside environment; (3) nature search filter string actually applied","code":""},{"path":"/reference/lsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lists all objects on a serverside environment — lsDS","text":"Serverside aggregate function lsDS called clientside function ds.ls. running analyses one may want know objects already generated. request disclosive returns names objects contents. default, objects current 'active analytic environment' (\".GlobalEnv\") displayed. environment contains objects serverside DataSHIELD using main analysis written serverside process managing undertaking analysis (variables, scalars, matrices, data.frames etc). details see help ds.ls function native R function ls","code":""},{"path":"/reference/lsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lists all objects on a serverside environment — lsDS","text":"Gaye, (2015). Updated extended Paul Burton (2020).","code":""},{"path":"/reference/lsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"function based native R function lspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/lsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"","code":"lsplineDS(x = x, knots = NULL, marginal = FALSE, names = NULL)"},{"path":"/reference/lsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"x name input numeric variable knots numeric vector knot positions marginal logical, parametrize spline, see Details names, character, vector names constructed variables","code":""},{"path":"/reference/lsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"lspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/lsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment.","code":""},{"path":"/reference/lsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDS assign function called by ds.matrix — matrixDS","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Creates matrix serverside","code":""},{"path":"/reference/matrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"","code":"matrixDS(mdata.transmit, from, nrows.transmit, ncols.transmit, byrow, dimnames)"},{"path":"/reference/matrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"mdata.transmit specifies elements matrix created. Fully specified argument ds.matrix character string specifying source nature . Fully specified <> argument ds.matrix nrows.transmit specifies number rows matrix created. Fully specified argument ds.matrix ncols.transmit specifies number columns matrix created. Fully specified argument ds.matrix byrow logical value specifying whether, vector, matrix created filled row row column column. Fully specified argument ds.matrix dimnames dimnames attribute matrix: NULL list length 2 giving row column names respectively. empty list treated NULL, list length one row names . Fully specified argument ds.matrix","code":""},{"path":"/reference/matrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Output matrix written serverside. details see help ds.matrix","code":""},{"path":"/reference/matrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Similar matrix() function native R. Creates matrix dimensions specified arguments assigns values elements based argument","code":""},{"path":"/reference/matrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDet1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Calculates determinant square matrix returns output clientside","code":""},{"path":"/reference/matrixDet1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"","code":"matrixDet1DS(M1.name = NULL, logarithm)"},{"path":"/reference/matrixDet1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"M1.name character string specifying name matrix determinant calculated logarithm logical. Default FALSE, returns determinant , TRUE returns logarithm modulus determinant.","code":""},{"path":"/reference/matrixDet1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Output determinant matrix identified argument returned clientside. details see help ds.matrixDet","code":""},{"path":"/reference/matrixDet1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Calculates determinant square matrix (additional information see help det function native R). operation possible number columns rows .","code":""},{"path":"/reference/matrixDet1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDet2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Calculates determinant square matrix writes output serverside","code":""},{"path":"/reference/matrixDet2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"","code":"matrixDet2DS(M1.name = NULL, logarithm)"},{"path":"/reference/matrixDet2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"M1.name character string specifying name matrix determinant calculated logarithm logical. Default FALSE, returns determinant , TRUE returns logarithm modulus determinant.","code":""},{"path":"/reference/matrixDet2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Output determinant matrix identified argument written serverside. details see help ds.matrixDet","code":""},{"path":"/reference/matrixDet2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Calculates determinant square matrix (additional information see help det function native R). operation possible number columns rows .","code":""},{"path":"/reference/matrixDet2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDiagDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Extracts diagonal vector square matrix creates diagonal matrix based vector scalar value writes output serverside","code":""},{"path":"/reference/matrixDiagDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"","code":"matrixDiagDS(x1.transmit, aim, nrows.transmit)"},{"path":"/reference/matrixDiagDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"x1.transmit identifies input matrix vector. Fully specified argument ds.matrixDiag. details see help ds.matrixDiag. aim character string specifying behaviour required function. Fully specified argument ds.matrixDiag. details see help ds.matrixDiag. nrows.transmit scalar value forcing number rows columns output matrix.Fully specified argument ds.matrixDiag. details see help ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Output matrix vector specified argument (default name diag_) written serverside. details see help ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"details see help function ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDimnamesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Adds dimnames (row names, column names ) matrix serverside.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"","code":"matrixDimnamesDS(M1.name = NULL, dimnames)"},{"path":"/reference/matrixDimnamesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"M1.name Specifies name serverside matrix dimnames added. Fully specified argument function ds.matrixDimnames. details see help ds.matrixDimnames. dimnames dimnames attribute matrix: NULL list length 2 giving row column names respectively. Fully specified argument function ds.matrixDimnames. details see help ds.matrixDimnames.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Output serverside matrix specified argument (default name diag_) specified dimnames (row column names) written serverside.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Adds dimnames (row names, column names ) matrix serverside. Similar dimnames function native R. details see help function ds.matrixDimnames","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixInvertDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Inverts square matrix writes output serverside","code":""},{"path":"/reference/matrixInvertDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"","code":"matrixInvertDS(M1.name = NULL)"},{"path":"/reference/matrixInvertDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"M1.name character string specifying name matrix inverted","code":""},{"path":"/reference/matrixInvertDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Output matrix representing inverse written serverside. details see help ds.matrixInvert","code":""},{"path":"/reference/matrixInvertDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Undertakes standard matrix inversion. operation possible number columns rows matrix non-singular - positive definite (eg row column zeros)","code":""},{"path":"/reference/matrixInvertDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixMultDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Calculates matrix product two matrices writes output serverside","code":""},{"path":"/reference/matrixMultDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"","code":"matrixMultDS(M1.name = NULL, M2.name = NULL)"},{"path":"/reference/matrixMultDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"M1.name character string specifying name first matrix (M1) argument specified M1 argument original call ds.matrixMult M2.name character string specifying name second matrix (M2) argument specified M1 argument original call ds.matrixMult","code":""},{"path":"/reference/matrixMultDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Output matrix representing product M1 M2 written serverside. details see help ds.matrixMult","code":""},{"path":"/reference/matrixMultDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Undertakes standard matrix multiplication input matrices B dimensions : mxn B: nxp output C dimensions mxp element C[,j] value equal dot product row column j B dot product obtained sum([,1]*B[1,j] + [,2]*B[2,j] + .... + [,n]*B[n,j]). calculation valid number columns number rows B","code":""},{"path":"/reference/matrixMultDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixTransposeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Transposes matrix writes output serverside","code":""},{"path":"/reference/matrixTransposeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"","code":"matrixTransposeDS(M1.name = NULL)"},{"path":"/reference/matrixTransposeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"M1.name character string specifying name matrix transposed","code":""},{"path":"/reference/matrixTransposeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Output matrix representing transpose written serverside. details see help ds.matrixTranspose","code":""},{"path":"/reference/matrixTransposeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Undertakes standard matrix transposition. operation converts matrix matrix C element C[,j] matrix C equals element [j,] matrix . Matrix therefore number rows matrix C columns vice versa.","code":""},{"path":"/reference/matrixTransposeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/mdPatternDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Missing data pattern with disclosure control — mdPatternDS","title":"Missing data pattern with disclosure control — mdPatternDS","text":"function serverside aggregate function computes missing data pattern using mice::md.pattern applies disclosure control prevent revealing small cell counts.","code":""},{"path":"/reference/mdPatternDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Missing data pattern with disclosure control — mdPatternDS","text":"","code":"mdPatternDS(x)"},{"path":"/reference/mdPatternDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Missing data pattern with disclosure control — mdPatternDS","text":"x character string specifying name data frame matrix containing data analyze missing patterns.","code":""},{"path":"/reference/mdPatternDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Missing data pattern with disclosure control — mdPatternDS","text":"list containing: pattern missing data pattern matrix disclosure control applied valid Logical indicating patterns meet disclosure requirements message message describing validity status class class input object, client-side consistency checking","code":""},{"path":"/reference/mdPatternDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Missing data pattern with disclosure control — mdPatternDS","text":"function calls mice::md.pattern function generate matrix showing missing data patterns input data. ensure disclosure control, pattern counts threshold (nfilter.tab, default=3) suppressed. Suppression Method: pattern count threshold: - Row name changed \"suppressed()\" N threshold - pattern values row set NA - Summary row also set NA (prevents back-calculation) Output Matrix Structure: - Rows represent different missing data patterns (plus summary row bottom) - Row names contain pattern counts (\"suppressed()\" invalid patterns) - Columns show 1 variable observed, 0 missing - Last column shows total number missing values per pattern - Last row shows total number missing values per variable Note Pooling: function called ds.mdPattern type='combine', suppressed patterns excluded pooling prevent disclosure subtraction. means pooled counts may underestimate true total patterns suppressed studies.","code":""},{"path":"/reference/mdPatternDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Missing data pattern with disclosure control — mdPatternDS","text":"Xavier Escribà montagut DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/meanDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes statistical mean of a vector — meanDS","title":"Computes statistical mean of a vector — meanDS","text":"Calculates mean value.","code":""},{"path":"/reference/meanDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes statistical mean of a vector — meanDS","text":"","code":"meanDS(x)"},{"path":"/reference/meanDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes statistical mean of a vector — meanDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/meanDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes statistical mean of a vector — meanDS","text":"list, estimated mean, number missing values, number valid values, total number values, class, class input object client-side consistency checking","code":""},{"path":"/reference/meanDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes statistical mean of a vector — meanDS","text":"length input vector less set filter missing value returned.","code":""},{"path":"/reference/meanDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes statistical mean of a vector — meanDS","text":"Gaye , Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/meanSdGpDS.html","id":null,"dir":"Reference","previous_headings":"","what":"MeanSdGpDS — meanSdGpDS","title":"MeanSdGpDS — meanSdGpDS","text":"Server-side function called ds.meanSdGp","code":""},{"path":"/reference/meanSdGpDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MeanSdGpDS — meanSdGpDS","text":"","code":"meanSdGpDS(x, index)"},{"path":"/reference/meanSdGpDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MeanSdGpDS — meanSdGpDS","text":"x client-side supplied character string identifying variable means/SDs calculated index client-side supplied character string identifying factor across means/SDs calculated","code":""},{"path":"/reference/meanSdGpDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MeanSdGpDS — meanSdGpDS","text":"List results group statistics","code":""},{"path":"/reference/meanSdGpDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MeanSdGpDS — meanSdGpDS","text":"Computes mean standard deviation across groups defined one factor","code":""},{"path":"/reference/meanSdGpDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MeanSdGpDS — meanSdGpDS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/mergeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"mergeDS (assign function) called by ds.merge — mergeDS","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"merges (links) two data.frames together based common values defined vectors data.frame","code":""},{"path":"/reference/mergeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"","code":"mergeDS( x.name, y.name, by.x.names.transmit, by.y.names.transmit, all.x, all.y, sort, suffixes.transmit, no.dups, incomparables )"},{"path":"/reference/mergeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"x.name, name first data.frame merged specified inverted commas. Specified via argument ds.merge function y.name, name second data.frame merged specified inverted commas. Specified via argument ds.merge function .x.names.transmit name single variable vector names multiple variables (transmittable form) containing IDs data data.frame x merged/linked data.frame y. Specified via argument <.x.names> ds.merge function .y.names.transmit name single variable vector names multiple variables (transmittable form) containing IDs data data.frame y merged/linked data.frame x. Specified via argument <.y.names> ds.merge function .x logical, TRUE, extra rows added output, one row x matching row y. Specified via argument <.x> ds.merge function. Default = FALSE. .y logical, TRUE, extra rows added output, one row y matching row x. Specified via argument <.y> ds.merge function. Default = FALSE. sort logical, TRUE merged result sorted elements .x.names .y.names columns. Specified via argument ds.merge function. Default = TRUE. suffixes.transmit character vector length 2 (transmittable form) specifying suffixes used making unique common column names two input data.frames appear merged data.frame. Specified via argument ds.merge function. Default '.x' '.y'. .dups logical, TRUE suffixes appended cases rigorously avoid duplicated column names merged data.frame. Specified via argument <.dups> ds.merge function. Default TRUE apparently implicitly FALSE R version 3.5.0. incomparables, values intended merging one column matched. See 'match' help Native R merge function. Specified via argument ds.merge","code":""},{"path":"/reference/mergeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"merged data.frame specified argument ds.merge (default 'x.name_y.name' argument NULL) written serverside. addition, two validity messages returned clientside indicating whether created data source whether valid form. form valid least one study may studysideMessage can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message() print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message() return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/mergeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"information see details native R function merge DataSHIELD clientside function ds.merge.","code":""},{"path":"/reference/mergeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/metadataDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the metadata, if any, about the specified variable — metadataDS","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"function returns metadata, , specified variable.","code":""},{"path":"/reference/metadataDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"","code":"metadataDS(x)"},{"path":"/reference/metadataDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"x string character, containing name specified variable","code":""},{"path":"/reference/metadataDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"list containing metadata. elements list depend metadata available.","code":""},{"path":"/reference/metadataDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"function returns metadata, obtained attributes function.","code":""},{"path":"/reference/metadataDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"Stuart Wheater, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/miceDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Aggregate function called by ds.mice — miceDS","title":"Aggregate function called by ds.mice — miceDS","text":"function wrapper function mice mice R package. function creates multiple imputations (replacement values) multivariate missing data. method based Fully Conditional Specification, incomplete variable imputed separate model. MICE algorithm can impute mixes continuous, binary, unordered categorical ordered categorical data. addition, MICE can impute continuous two-level data, maintain consistency imputations means passive imputation.","code":""},{"path":"/reference/miceDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Aggregate function called by ds.mice — miceDS","text":"","code":"miceDS( data = data, m = m, maxit = maxit, method = method, post = post, seed = seed, predictorMatrix = predictorMatrix, ncol.pred.mat = ncol.pred.mat, newobj_mids = newobj_mids, newobj_df = newobj_df )"},{"path":"/reference/miceDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Aggregate function called by ds.mice — miceDS","text":"data data frame matrix containing incomplete data. m Number multiple imputations. default m=5. maximum allowed number DataSHIELD m=20. maxit scalar giving number iterations. default 5. maximum allowed number DataSHIELD maxit=30. method Can either single string, vector strings length ncol(data), specifying imputation method used column data. specified single string, method used blocks. default imputation method (argument specified) depends measurement level target column, regulated defaultMethod argument native R mice function. Columns need imputed empty method \"\". post vector strings length ncol(data) specifying expressions strings. string parsed executed within sampler() function post-process imputed values iterations. default vector empty strings, indicating post-processing. Multivariate (block) imputation methods ignore post parameter. seed either NA (default) \"fixed\". seed set \"fixed\" fixed seed random number generator study-specific used. predictorMatrix numeric matrix ncol(data) rows ncol(data) columns, containing 0/1 data specifying set predictors used target column. row corresponds variable imputed. value 1 means column variable used predictor target variables (rows). default, predictorMatrix square matrix ncol(data) rows columns 1's, except diagonal. ncol.pred.mat number columns predictorMatrix. newobj_mids character string provides name output mids object stored data servers. Default mids_object. newobj_df character string provides name output dataframes stored data servers. Default imputationSet. example, m=5, newobj_df=\"imputationSet\", five imputed dataframes saved servers names imputationSet.1, imputationSet.2, imputationSet.3, imputationSet.4, imputationSet.5.","code":""},{"path":"/reference/miceDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Aggregate function called by ds.mice — miceDS","text":"list three elements: method, predictorMatrix post. function also saves server mids object completed datasets dataframes.","code":""},{"path":"/reference/miceDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Aggregate function called by ds.mice — miceDS","text":"additional details see help header mice function native R mice package.","code":""},{"path":"/reference/miceDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Aggregate function called by ds.mice — miceDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/namesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the names of a list object — namesDS","title":"Return the names of a list object — namesDS","text":"Returns names designated server-side list","code":""},{"path":"/reference/namesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the names of a list object — namesDS","text":"","code":"namesDS(xname.transmit)"},{"path":"/reference/namesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the names of a list object — namesDS","text":"xname.transmit character string specifying name list.","code":""},{"path":"/reference/namesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the names of a list object — namesDS","text":"namesDS returns client-side names list object stored server-side.","code":""},{"path":"/reference/namesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Return the names of a list object — namesDS","text":"namesDS aggregate function called ds.names. function similar native R function names subsume functionality, example, works extract names already exist, create new names objects. function restricted objects type list, includes objects primary class list return TRUE native R function .list. example, includes multi-component object created fitting generalized linear model using ds.glmSLMA. resultant object saved separate server formally double class \"glm\" \"ls\" responds TRUE .list(),","code":""},{"path":"/reference/namesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Return the names of a list object — namesDS","text":"Amadou Gaye, updated Paul Burton 25/06/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/nsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"function based native R function ns splines package. function generate B-spline basis matrix natural cubic spline.","code":""},{"path":"/reference/nsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"","code":"nsDS(x, df, knots, intercept, Boundary.knots)"},{"path":"/reference/nsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"x predictor variable. Missing values allowed. df degrees freedom. One can supply df rather knots; ns() chooses df - 1 - intercept knots suitably chosen quantiles x (ignore missing values). default, df = NULL, sets number inner knots length(knots). knots breakpoints define spline. default knots; together natural boundary conditions results basis linear regression x. Typical values mean median one knot, quantiles knots. See also Boundary.knots. intercept TRUE, intercept included basis; default FALSE. Boundary.knots boundary points impose natural boundary conditions anchor B-spline basis (default range data). knots Boundary.knots supplied, basis parameters depend x. Data can extend beyond Boundary.knots","code":""},{"path":"/reference/nsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"matrix dimension length(x) * df either df supplied knots supplied, df = length(knots) + 1 + intercept. Attributes returned correspond arguments ns, explicitly give knots, Boundary.knots etc use predict.ns(). object assigned serverside.","code":""},{"path":"/reference/nsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"ns native R based function splineDesign. generates basis matrix representing family piecewise-cubic splines specified sequence interior knots, natural boundary conditions. enforce constraint function linear beyond boundary knots, can either supplied default extremes data. primary use modeling formula directly specify natural spline term model.","code":""},{"path":"/reference/nsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/numNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Counts the number of missing values — numNaDS","title":"Counts the number of missing values — numNaDS","text":"function just counts number missing entries vector.","code":""},{"path":"/reference/numNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Counts the number of missing values — numNaDS","text":"","code":"numNaDS(x)"},{"path":"/reference/numNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Counts the number of missing values — numNaDS","text":"x character string, name server-side vector","code":""},{"path":"/reference/numNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Counts the number of missing values — numNaDS","text":"list two elements: numNA (integer, number missing values) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/numNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Counts the number of missing values — numNaDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/qlsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"function based native R function qlspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/qlsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"","code":"qlsplineDS(x = x, q = q, na.rm = TRUE, marginal = FALSE, names = NULL)"},{"path":"/reference/qlsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"x name input numeric variable q numeric, single scalar greater equal 2 number equal-frequency intervals along x vector numbers (0; 1) specifying quantiles explicitly. na.rm logical, whether NA removed calculating quantiles, passed na.rm quantile. Default set TRUE. marginal logical, parametrize spline, see Details names character, vector names constructed variables","code":""},{"path":"/reference/qlsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"qlspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/qlsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment. Function qlspline wraps lspline calculates knot positions quantiles x. q numerical scalar greater equal 2, quantiles computed seq(0, 1, length.= q + 1)[-c(1, q+1)], .e. knots q-tiles distribution x. Alternatively, q can vector values [0; 1] specifying quantile probabilities directly (vector passed argument probs quantile).","code":""},{"path":"/reference/qlsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/quantileMeanDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"probabilities 5 used compute corresponding quantiles.","code":""},{"path":"/reference/quantileMeanDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"","code":"quantileMeanDS(x)"},{"path":"/reference/quantileMeanDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/quantileMeanDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"list, quantiles, numeric vector represents sample quantiles, class, class input object client-side consistency checking","code":""},{"path":"/reference/quantileMeanDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"Burton, P.; Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rBinomDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rBinomDS serverside assign function — rBinomDS","title":"rBinomDS serverside assign function — rBinomDS","text":"primary serverside assign function called ds.rBinom","code":""},{"path":"/reference/rBinomDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rBinomDS serverside assign function — rBinomDS","text":"","code":"rBinomDS(n, size = 1, prob = 0.5)"},{"path":"/reference/rBinomDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rBinomDS serverside assign function — rBinomDS","text":"n length pseudorandom number vector generated specified argument function ds.rBinom size scalar must positive integer. Value set directly argument ds.rBinom - details see help ds.rBinom. May scalar vector allowing size vary observation observation. prob numeric scalar range 0 > prob > 1 specifies probability positive response. Value set directly argument ds.rBinom - details see help ds.rBinom May scalar vector allowing size vary observation observation.","code":""},{"path":"/reference/rBinomDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rBinomDS serverside assign function — rBinomDS","text":"vector pseudorandom numbers binomial distribution, written serverside object named argument ds.rBinom.","code":""},{"path":"/reference/rBinomDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rBinomDS serverside assign function — rBinomDS","text":"Generates vector pseudorandom numbers binomial distribution data source specified arguments ds.rBinom. serverside function effectively function rbinom() native R arguments .","code":""},{"path":"/reference/rBinomDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rBinomDS serverside assign function — rBinomDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rNormDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rNormDS serverside assign function — rNormDS","title":"rNormDS serverside assign function — rNormDS","text":"primary serverside assign function called ds.rNorm","code":""},{"path":"/reference/rNormDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rNormDS serverside assign function — rNormDS","text":"","code":"rNormDS(n, mean = 0, sd = 1, force.output.to.k.decimal.places = 9)"},{"path":"/reference/rNormDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rNormDS serverside assign function — rNormDS","text":"n length pseudorandom number vector generated specified argument function ds.rNorm mean specifies mean pseudorandom number vector generated specified argument function ds.rNorm. May scalar vector allowing mean vary observation observation. sd specifies standard deviation pseudorandom number vector generated specified argument function ds.rNorm May scalar vector allowing sd vary observation observation. force.output..k.decimal.places scalar integer. Forces output random number vector k decimal places. 0 rounds coerces decimal random number output integer, k range 1-8 forces output k decimal places. k = 9, rounding occurs native output. Default=9. Value specified argument ds.rNorm","code":""},{"path":"/reference/rNormDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rNormDS serverside assign function — rNormDS","text":"numeric vector pseudorandom numbers normal distribution, rounded decimal places less 9, written serverside object named argument ds.rNorm.","code":""},{"path":"/reference/rNormDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rNormDS serverside assign function — rNormDS","text":"Generates vector pseudorandom numbers normal distribution data source specified arguments ds.rNorm. serverside function effectively function rnorm() native R arguments .","code":""},{"path":"/reference/rNormDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rNormDS serverside assign function — rNormDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rPoisDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rPoisDS serverside assign function — rPoisDS","title":"rPoisDS serverside assign function — rPoisDS","text":"primary serverside assign function called ds.rPois","code":""},{"path":"/reference/rPoisDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rPoisDS serverside assign function — rPoisDS","text":"","code":"rPoisDS(n, lambda = 1)"},{"path":"/reference/rPoisDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rPoisDS serverside assign function — rPoisDS","text":"n length pseudorandom number vector generated specified argument function ds.rPois lambda numeric scalar specifying expected count Poisson distribution used generate random counts. Specified directly lambda argument ds.rPois. May scalar vector allowing lambda vary observation observation.","code":""},{"path":"/reference/rPoisDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rPoisDS serverside assign function — rPoisDS","text":"vector pseudorandom non-negative integers Poisson distribution, written serverside object named argument ds.rPois.","code":""},{"path":"/reference/rPoisDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rPoisDS serverside assign function — rPoisDS","text":"Generates vector pseudorandom numbers (non-negative integers) Poisson distribution data source specified arguments ds.rPois. serverside function effectively function rpois() native R arguments .","code":""},{"path":"/reference/rPoisDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rPoisDS serverside assign function — rPoisDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rUnifDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rUnifDS serverside assign function — rUnifDS","title":"rUnifDS serverside assign function — rUnifDS","text":"primary serverside assign function called ds.rUnif","code":""},{"path":"/reference/rUnifDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rUnifDS serverside assign function — rUnifDS","text":"","code":"rUnifDS(n, min = 0, max = 1, force.output.to.k.decimal.places = 9)"},{"path":"/reference/rUnifDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rUnifDS serverside assign function — rUnifDS","text":"n length pseudorandom number vector generated specified argument function ds.rUnif min numeric scalar specifying minimum range across random numbers generated source. Specified directly min argument ds.rUnif. May scalar vector allowing min vary observation observation. max numeric scalar specifying maximum range across random numbers generated source. Specified directly max argument ds.rUnif. May scalar vector allowing min vary observation observation. force.output..k.decimal.places scalar integer. Forces output random number vector k decimal places. 0 rounds coerces decimal random number output integer, k range 1-8 forces output k decimal places. k = 9, rounding occurs native output. Default=9. Value specified argument ds.rUnif","code":""},{"path":"/reference/rUnifDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rUnifDS serverside assign function — rUnifDS","text":"numeric vector pseudorandom numbers uniform distribution, rounded decimal places less 9, written serverside object named argument ds.rUnif.","code":""},{"path":"/reference/rUnifDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rUnifDS serverside assign function — rUnifDS","text":"Generates vector pseudorandom numbers uniform distribution data source specified arguments ds.rUnif. serverside function effectively function runif() native R arguments .","code":""},{"path":"/reference/rUnifDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rUnifDS serverside assign function — rUnifDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rangeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"returns the minimum and maximum of a numeric vector — rangeDS","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"function similar R function range instead return real minimum maximum, computed values multiplied small random number.","code":""},{"path":"/reference/rangeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"","code":"rangeDS(x)"},{"path":"/reference/rangeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/rangeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"numeric vector contains minimum maximum values vector","code":""},{"path":"/reference/rangeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rbindDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rbindDS called by ds.rbind — rbindDS","title":"rbindDS called by ds.rbind — rbindDS","text":"serverside assign function takes sequence vector, matrix data-frame arguments combines row produce matrix.","code":""},{"path":"/reference/rbindDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rbindDS called by ds.rbind — rbindDS","text":"","code":"rbindDS(x.names.transmit = NULL, colnames.transmit = NULL)"},{"path":"/reference/rbindDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rbindDS called by ds.rbind — rbindDS","text":"x.names.transmit vector character strings representing names elemental components combined converted transmittable format. argument fully specified argument ds.rbind colnames.transmit NULL vector character strings representing forced column names output object converted transmittable format. argument fully specified argument ds.cbind.","code":""},{"path":"/reference/rbindDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rbindDS called by ds.rbind — rbindDS","text":"object specified argument ds.rbind(default name ) written serverside. well writing output object serverside, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.cbind() also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/rbindDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rbindDS called by ds.rbind — rbindDS","text":"sequence vector, matrix data-frame arguments combined row row produce matrix written serverside. details see help ds.rbind native R function rbind.","code":""},{"path":"/reference/rbindDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rbindDS called by ds.rbind — rbindDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/reShapeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"reShapeDS (assign function) called by ds.reShape — reShapeDS","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"Reshapes data frame containing longitudinal otherwise grouped data 'wide' 'long' format vice-versa","code":""},{"path":"/reference/reShapeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"","code":"reShapeDS( data.name, varying.transmit, v.names.transmit, timevar.name, idvar.name, drop.transmit, direction, sep )"},{"path":"/reference/reShapeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"data.name, name data.frame reshaped. Specified via argument ds.reShape function varying.transmit, names sets variables wide format correspond single variables long format (typically may called 'time-varying' 'time-dependent' variables). Specified via argument ds.reShape function. v.names.transmit, names variables long format correspond multiple variables wide format - example, sbp7, sbp11, sbp15 (measured systolic blood pressure ages 7, 11 15 years). Specified via argument ds.reShape function timevar.name, variable long format differentiates multiple records group individual. Specified via argument ds.reShape function idvar.name, names one variables long format identify multiple records group/individual. /variable(s) may also present wide format. Specified via argument ds.reShape function drop.transmit, vector names variables drop reshaping. Specified via argument ds.reShape function direction, character string, partially matched either \"wide\" reshape long wide format, \"long\" reshape wide long format. Specified via argument ds.reShape function sep, character vector length 1, indicating separating character variable names wide format. Specified via argument ds.reShape function","code":""},{"path":"/reference/reShapeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"reshaped data.frame converted long wide format wide long format written serverside given name provided argument ds.reShape 'newObject' name specified.","code":""},{"path":"/reference/reShapeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"function based native R function reshape. reshapes data frame containing longitudinal otherwise grouped data 'wide' format repeated measurements separate columns record 'long' format repeated measurements separate records. reshaping can either direction","code":""},{"path":"/reference/reShapeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"Demetris Avraam, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/recodeValuesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"function recodes specified values elements vector matched set alternative specified values.","code":""},{"path":"/reference/recodeValuesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"","code":"recodeValuesDS( var.name.text = NULL, values2replace.text = NULL, new.values.text = NULL, missing = NULL )"},{"path":"/reference/recodeValuesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"var.name.text character string providing name vector representing variable recoded. argument generated passed directly recodeValuesDS ds.recodeValues values2replace.text character string specifying values vector specified argument replaced new values specified new.values.vector. argument generated passed directly recodeValuesDS ds.recodeValues. effect, argument ds.recodeValues function converted character string format acceptable DataSHIELD R parser data repository can accepted recodeValuesDS new.values.text character string specifying new values specified values vector converted. argument generated passed directly recodeValuesDS ds.recodeValues. effect, argument ds.recodeValues function converted character string format acceptable DataSHIELD R parser data repository can used call recodeValuesDS. missing supplied, missing values variable referred var.name.text replaced value.","code":""},{"path":"/reference/recodeValuesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"object specified argument (default name '_recoded') initially specified calling ds.recodeValues. output object (required recoded variable called written serverside.","code":""},{"path":"/reference/recodeValuesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"details see help header ds.recodeValues","code":""},{"path":"/reference/recodeValuesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/repDS.html","id":null,"dir":"Reference","previous_headings":"","what":"repDS called by ds.rep — repDS","title":"repDS called by ds.rep — repDS","text":"assign function creates repetitive sequence repeating identified scalar, specified elements vector list. analogous rep function native R. sequence written new object serverside","code":""},{"path":"/reference/repDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"repDS called by ds.rep — repDS","text":"","code":"repDS( x1.transmit, times.transmit, length.out.transmit, each.transmit, x1.includes.characters, source.x1, source.times, source.length.out, source.each )"},{"path":"/reference/repDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"repDS called by ds.rep — repDS","text":"x1.transmit argument determines input scalar, vector list. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. times.transmit argument determines number replications pattern replications input scalar/vector construct output repetitive sequence. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. length..transmit argument fixes length output repetitive sequence vector behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. .transmit argument specifies number replications individual elements rather replications full sequence. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument <> call ds.rep calls repDS. x1.includes.characters Boolean parameter determining whether coerce final output sequence numeric. Defaults FALSE output coerced numeric. detailed behaviour see help ds.rep. parameter usually fully defined argument call ds.rep calls repDS. source.x1 defines source scalar vector defined argument. Four character strings allowed: \"clientside\" \"c\" serverside \"s\". behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. source.times see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS. source.length.see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS. source.see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS.","code":""},{"path":"/reference/repDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"repDS called by ds.rep — repDS","text":"vector containing specified repetitive sequence write output object defined argument (default name seq.vect) written serverside source. addition, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.matrixDiag also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/repDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"repDS called by ds.rep — repDS","text":"details can found help details ds.rep following aspects help function rep native R also apply (explained detail exceptions identified help ds.rep): addition Details R help : default behaviour call rep(x, times = 1, length.= NA, = 1) Normally just one additional arguments specified, '' specified either two, replication performed first, followed replication implied times length.. times consists single integer, result consists whole input repeated many times. times vector length x (replication ), result consists x[1] repeated times[1] times, x[2] repeated times[2] times . ***Note exception 1 . length.may given place times, case x repeated many times necessary create vector length. given, length.takes priority times ignored. ***Note exception 3 . Non-integer values times truncated towards zero. times computed quantity prudent add small fuzz use round. analogously .","code":""},{"path":"/reference/repDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"repDS called by ds.rep — repDS","text":"Paul Burton DataSHIELD Development Team, 14/10/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/replaceNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Replaces the missing values in a vector — replaceNaDS","title":"Replaces the missing values in a vector — replaceNaDS","text":"function identifies missing values replaces value values specified analyst.","code":""},{"path":"/reference/replaceNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replaces the missing values in a vector — replaceNaDS","text":"","code":"replaceNaDS(x, replacements)"},{"path":"/reference/replaceNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replaces the missing values in a vector — replaceNaDS","text":"x character, name vector process. replacements vector contains replacement value(s), vector one values study.","code":""},{"path":"/reference/replaceNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replaces the missing values in a vector — replaceNaDS","text":"new vector without missing values","code":""},{"path":"/reference/replaceNaDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Replaces the missing values in a vector — replaceNaDS","text":"function used analyst prefer requires complete vectors. possible specify one value missing value first returning number missing values using function numNaDS cases might sensible replace missing values one specific value e.g. replace missing values vector mean median value. missing values replaced new vector created.","code":""},{"path":"/reference/replaceNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Replaces the missing values in a vector — replaceNaDS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rmDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rmDS an aggregate function called by ds.rm — rmDS","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"deletes R object serverside","code":""},{"path":"/reference/rmDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"","code":"rmDS(x.names.transmit)"},{"path":"/reference/rmDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"x.names.transmit, names objects deleted converted transmissible form, comma separated list character string. argument specified via argument ds.rm","code":""},{"path":"/reference/rmDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"specified object deleted serverside. successful message \"Object successfully deleted\" returned clientside (x.names names object deleted). objects deleted already absent given source, source return message: \"Object deleted, .e. , exist need deleting\".","code":""},{"path":"/reference/rmDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"serverside function based rm() function native R. aggregate function may surprising modifies object serverside, therefore expected assign function. However, assign function last step running write modified object newobj. fail effect function delete object impossible write anywhere.","code":""},{"path":"/reference/rmDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"Paul Burton DataSHIELD Development Team","code":""},{"path":"/reference/rowColCalcDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"function similar R base functions 'rowSums', 'colSums', 'rowMeans' 'colMeans'.","code":""},{"path":"/reference/rowColCalcDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"","code":"rowColCalcDS(dataset.name, operation)"},{"path":"/reference/rowColCalcDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"dataset.name character string providing name server-side array two dimensions. operation integer indicates operation carry : 1 'rowSums', 2 'colSums', 3 'rowMeans' 4 'colMeans'","code":""},{"path":"/reference/rowColCalcDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"numeric vector","code":""},{"path":"/reference/rowColCalcDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"output returned user number entries output vector greater equal allowed size.","code":""},{"path":"/reference/rowColCalcDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/sampleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"draws pseudorandom sample vector, dataframe matrix serverside - special case - randomly permutes vector, dataframe matrix.","code":""},{"path":"/reference/sampleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"","code":"sampleDS( x.transmit, size.transmit, replace.transmit = NULL, prob.transmit = NULL )"},{"path":"/reference/sampleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"x.transmit Either character string providing name serverside vector, matrix data.frame sampled permuted, integer/numeric scalar (e.g. 923) indicating one create new vector serverside randomly permuted sample vector 1:923. x.transmit fully specified [x] argument ds.sample. details see help ds.sample native R help sample(). size.transmit numeric/integer scalar indicating size sample drawn. size.transmit fully specified [size] argument ds.sample. details see help ds.sample native R help sample(). replace.transmit Boolean indicator (TRUE FALSE) specifying whether sample drawn without replacement. Default FALSE sample drawn without replacement. replace.transmit fully specified [replace] argument ds.sample. details see help ds.sample native R help sample(). prob.transmit character string containing name numeric vector probability weights serverside associated elements vector sampled enabling drawing sample elements given higher probability drawn others. prob.transmit fully specified [prob] argument ds.sample. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"object specified argument (default name 'newobj.sample') written serverside. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"Serverside assign function sampleDS called clientside function ds.sample. Based native R function sample() deals slightly differently data.frames matrices. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"Paul Burton, DataSHIELD Development Team, 15/4/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/scatterPlotDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the coordinates of the data to be plot — scatterPlotDS","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"function uses two disclosure control methods generate non-disclosive coordinates returned client generates non-disclosive scatter plots.","code":""},{"path":"/reference/scatterPlotDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"","code":"scatterPlotDS(x.name, y.name, method.indicator, k, noise)"},{"path":"/reference/scatterPlotDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"x.name character string providing name server-side numeric vector, x-variable. y.name character string providing name server-side numeric vector, y-variable. method.indicator integer either 1 2. user selects deterministic method client side function method.indicator set 1 user selects probabilistic method argument set 2. k number nearest neighbours centroid calculated deterministic method selected. noise percentage initial variance used variance embedded noise probabilistic method selected.","code":""},{"path":"/reference/scatterPlotDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"list x y coordinates data plot, along classes x y inputs (class.x class.y)","code":""},{"path":"/reference/scatterPlotDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"user chooses deterministic approach, function finds k-1 nearest neighbours data point 2-dimensional space. nearest neighbours data points minimum Euclidean distances point interest. point interest k-1 nearest neighbours used calculation coordinates centroid k points. Centroid referred centre mass, .e. x-coordinate centroid average value x-coordinates k nearest neighbours y-coordinate centroid average y-coordinates k nearest neighbours. user chooses probabilistic approach, function adds random noise $x$ $y$ separately. random noise follows normal distribution zero mean variance equal 10 disclosure fix random number generator value specified input variables. Thus function returns always noisy data given pair variables.","code":""},{"path":"/reference/scatterPlotDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/seqDS.html","id":null,"dir":"Reference","previous_headings":"","what":"seqDS a serverside assign function called by ds.seq — seqDS","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"assign function seqDS called ds.seq","code":""},{"path":"/reference/seqDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"","code":"seqDS( FROM.value.char, TO.value.char, BY.value.char, LENGTH.OUT.value.char, ALONG.WITH.name )"},{"path":"/reference/seqDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":".value.char starting value sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. .value.char terminal value sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. .value.char value increment step sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. LENGTH..value.char length sequence point extension stopped, expressed integer real number decimal point character form. Fully specified argument ds.seq. ALONG..name convenience, rather specifying value LENGTH.can often better specify variable name argument. Fully specified argument ds.seq.","code":""},{"path":"/reference/seqDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"object specified argument ds.seq (default name newObj) written serverside. well writing output object serverside, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.seq() also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/seqDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"assign function uses native R function seq() create one flexible range sequence vectors can used help manage analyse data. assign function resultant vector written new object specified data source servers. Please see \"details\" ds.seq information allowable combinations arguments etc.","code":""},{"path":"/reference/seqDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"Paul Burton DataSHIELD Development Team, 17/9/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/setSeedDS.html","id":null,"dir":"Reference","previous_headings":"","what":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"aggregate serverside function primes pseudorandom number generator data source","code":""},{"path":"/reference/setSeedDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"","code":"setSeedDS(seedtext = NULL, kind = NULL, normal.kind = NULL)"},{"path":"/reference/setSeedDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"seedtext simply value argument ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois ds.rBinom coerced character format. done clientside functions require DataSHIELD user anything. Please see help clientside functions, particular, information argument details. kind see help set.seed() function native R normal.kind see help set.seed() function native R","code":""},{"path":"/reference/setSeedDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"Sets values vector integers length 626 known .Random.seed data source true current state random seed source.","code":""},{"path":"/reference/setSeedDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"setSeedDS effectively equivalent native R function set.seed() help function can provide many additional details. minor difference first argument setSeedDS, takes integer priming seed character format. However, user integer still specified directly integer argument one clientside functions ds.setSeed, ds.rNorm ..... clientside functions coerces integer character format calls setSeedDS first active line code setSeedDS converts character string back integer treats first argument native R function set.seed(). two arguments set.seed() native R, defaulted specifying NULL. defaulting hard wired setSeedDS function changed analyst means setSeedDS much less flexible native R's set.seed() function. DataSHIELD user requires aspect flexibility returned development team can approached, unless actually theoretical work random number generators likely ","code":""},{"path":"/reference/setSeedDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/skewness1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the skewness of a numeric variable — skewness1DS","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"function calculates skewness numeric variable study separately.","code":""},{"path":"/reference/skewness1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"","code":"skewness1DS(x, method)"},{"path":"/reference/skewness1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"x string character, name numeric variable. method integer 1 3 selecting one algorithms computing skewness detailed headers client-side ds.skewness function.","code":""},{"path":"/reference/skewness1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"list including skewness input numeric variable, number valid observations class, class input object client-side consistency checking.","code":""},{"path":"/reference/skewness1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"function calculates skewness input variable x three different methods. method specified argument method client-side ds.skewness function.","code":""},{"path":"/reference/skewness1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/skewness2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the skewness of a numeric variable — skewness2DS","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"function calculates summary statistics returned client-side used estimation combined skewness numeric variable across studies.","code":""},{"path":"/reference/skewness2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"","code":"skewness2DS(x, global.mean)"},{"path":"/reference/skewness2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"x string character, name numeric variable. global.mean numeric, combined mean input variable across studies.","code":""},{"path":"/reference/skewness2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"list including sum cubed differences values x global mean x across studies, sum squared differences values x global mean x across studies, number valid observations (.e. length x excluding missing values), class, class input object client-side consistency checking.","code":""},{"path":"/reference/skewness2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"function calculates sum squared differences values x global mean x across studies, sum cubed differences values x global mean x across studies number valid observations input variable x.","code":""},{"path":"/reference/skewness2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/sqrtDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the square root values of the input variable — sqrtDS","title":"Computes the square root values of the input variable — sqrtDS","text":"function similar R function sqrt.","code":""},{"path":"/reference/sqrtDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the square root values of the input variable — sqrtDS","text":"","code":"sqrtDS(x)"},{"path":"/reference/sqrtDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the square root values of the input variable — sqrtDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/sqrtDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the square root values of the input variable — sqrtDS","text":"object specified newobj argument ds.sqrt (default name sqrt.newobj) written server-side. output object class numeric integer.","code":""},{"path":"/reference/sqrtDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the square root values of the input variable — sqrtDS","text":"function computes square root values input numeric integer vector.","code":""},{"path":"/reference/sqrtDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the square root values of the input variable — sqrtDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/table1DDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates 1-dimensional contingency tables — table1DDS","title":"Creates 1-dimensional contingency tables — table1DDS","text":"function generates 1-dimensional table potentially disclosive cells. (based set threshold) replaced missing value ('NA').","code":""},{"path":"/reference/table1DDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates 1-dimensional contingency tables — table1DDS","text":"","code":"table1DDS(xvect)"},{"path":"/reference/table1DDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates 1-dimensional contingency tables — table1DDS","text":"xvect numerical vector discrete values - usually factor.","code":""},{"path":"/reference/table1DDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates 1-dimensional contingency tables — table1DDS","text":"list contains two elements: 'table', 1-dimensional table 'message' message informs validity table.","code":""},{"path":"/reference/table1DDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates 1-dimensional contingency tables — table1DDS","text":"generates 1-dimensional tables valid (non-disclosive) 1-dimensional tables defined data sources table cells counts 1 set threshold. output table invalid cells total count replaced missing values. total count visible table returned client side. message also returned 1-dimensional; message says \"invalid table - invalid counts present\" table invalid 'valid table' otherwise.","code":""},{"path":"/reference/table1DDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Creates 1-dimensional contingency tables — table1DDS","text":"Gaye .","code":""},{"path":"/reference/table2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"Helps creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/table2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"","code":"table2DS(newobj, rvar.transmit, cvar.transmit, stvar.transmit)"},{"path":"/reference/table2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"newobj character string providing name output table object written serverside TRUE. explicit name table object specified, nevertheless TRUE, name serverside table object defaults 'newObj'. Fully specified argument ds.table. information see help ds.table rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table","code":""},{"path":"/reference/table2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"information see help ds.table","code":""},{"path":"/reference/table2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":" argument ds.table set TRUE, aggregate function returns non-disclosive information table object written serverside tableDS.assign. information see help ds.table, tableDS.assign tableDS DataSHIELD table function native R.","code":""},{"path":"/reference/table2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tableDS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"helps creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/tableDS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"","code":"tableDS.assign( rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, cvar.all.unique.levels.transmit, stvar.all.unique.levels.transmit, exclude.transmit, useNA.transmit )"},{"path":"/reference/tableDS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table rvar..unique.levels.transmit character string containing unique level rvar, across studies, separated ','. cvar..unique.levels.transmit character string containing unique level cvar, across studies, separated ','. stvar..unique.levels.transmit character string containing unique level stvar, across studies, separated ','. exclude.transmit information see help argument ds.table. Fully specified argument ds.table useNA.transmit information see help argument ds.table. Fully specified argument ds.table","code":""},{"path":"/reference/tableDS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"information see help ds.table","code":""},{"path":"/reference/tableDS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":" argument ds.table set TRUE, assign function writes table requested format specified ds.table function object named argument ds.table. information see help ds.table DataSHIELD table function native R.","code":""},{"path":"/reference/tableDS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tableDS.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/tableDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"","code":"tableDS( rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, cvar.all.unique.levels.transmit, stvar.all.unique.levels.transmit, exclude.transmit, useNA.transmit, force.nfilter.transmit )"},{"path":"/reference/tableDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table rvar..unique.levels.transmit character string containing unique level rvar, across studies, separated ','. cvar..unique.levels.transmit character string containing unique level cvar, across studies, separated ','. stvar..unique.levels.transmit character string containing unique level stvar, across studies, separated ','. exclude.transmit information see help argument ds.table. Fully specified argument ds.table useNA.transmit information see help argument ds.table. Fully specified argument ds.table force.nfilter.transmit information see help argument ds.table. Fully specified argument ds.table","code":""},{"path":"/reference/tableDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"information see help ds.table","code":""},{"path":"/reference/tableDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"serverside function workhorse ds.table - creating table requested format specified ds.table. information see help ds.table DataSHIELD table function native R.","code":""},{"path":"/reference/tableDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tapplyDS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"Apply one selected range functions summarize outcome variable one indexing factors write resultant summary newobj serverside","code":""},{"path":"/reference/tapplyDS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"","code":"tapplyDS.assign(X.name, INDEX.names.transmit, FUN.name)"},{"path":"/reference/tapplyDS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"X.name, name variable summarized. Specified via argument ds.tapply.assign function INDEX.names.transmit, name single factor vector names factors index variable summarized. Specified via argument ds.tapply.assign function FUN.name, name one allowable summarizing functions applied. Specified via argument ds.tapply.assign function.","code":""},{"path":"/reference/tapplyDS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"array summarized values created tapplyDS.assign function. array written newobj serverside. number dimensions INDEX.","code":""},{"path":"/reference/tapplyDS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"see details ds.tapply.assign function","code":""},{"path":"/reference/tapplyDS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tapplyDS.html","id":null,"dir":"Reference","previous_headings":"","what":"tapplyDS called by ds.tapply — tapplyDS","title":"tapplyDS called by ds.tapply — tapplyDS","text":"Apply one selected range functions summarize outcome variable one indexing factors write resultant summary clientside","code":""},{"path":"/reference/tapplyDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tapplyDS called by ds.tapply — tapplyDS","text":"","code":"tapplyDS(X.name, INDEX.names.transmit, FUN.name)"},{"path":"/reference/tapplyDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tapplyDS called by ds.tapply — tapplyDS","text":"X.name, name variable summarized. Specified via argument ds.tapply function INDEX.names.transmit, name single factor vector names factors index variable summarized. Specified via argument ds.tapply function FUN.name, name one allowable summarizing functions applied. Specified via argument ds.tapply function.","code":""},{"path":"/reference/tapplyDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tapplyDS called by ds.tapply — tapplyDS","text":"array summarized values created tapplyDS function. array returned clientside. number dimensions INDEX.","code":""},{"path":"/reference/tapplyDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tapplyDS called by ds.tapply — tapplyDS","text":"see details ds.tapply function","code":""},{"path":"/reference/tapplyDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tapplyDS called by ds.tapply — tapplyDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/unListDS.html","id":null,"dir":"Reference","previous_headings":"","what":"unListDS a serverside assign function called by ds.unList — unListDS","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"function based native R function unlist coerces object list class back class coerced list","code":""},{"path":"/reference/unListDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"","code":"unListDS(x.name)"},{"path":"/reference/unListDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"x.name name input object unlisted. must specified inverted commas e.g. x.name=\"input.object.name\". Fully specified x.name argument ds.unList","code":""},{"path":"/reference/unListDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"object specified newobj argument ds.unList function (default \"unlist.newobj\" newobj argument NULL). written serverside. well writing output object newobj serverside, two validity messages returned indicating whether newobj created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.seq also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating newobj studysideMessage saved. outcome object ds.unList typically list object names, errors creating message returned ds.message(\"\") study read \"Outcome object list without names. studysideMessage may hidden. Please check output OK\". suggests - case specific function - one check far one can nature output call ds.unList - e.g. ds.class, ds.length etc","code":""},{"path":"/reference/unListDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"See details native R function unlist. function represents substantive restructuring earlier version created Amadou Gaye. details working please see 'details' help ds.unList.","code":""},{"path":"/reference/unListDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"Amadou Gaye (2016), Paul Burton (19/09/2019) DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/uniqueDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Applies the unique method to a server-side variable. — uniqueDS","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"function similar R function unique.","code":""},{"path":"/reference/uniqueDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"","code":"uniqueDS(x.name.transmit = NULL)"},{"path":"/reference/uniqueDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"x.name.transmit name variable upon unique method applied","code":""},{"path":"/reference/uniqueDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"object specified newobj argument written server-side.","code":""},{"path":"/reference/uniqueDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"function computes uniques values variable.","code":""},{"path":"/reference/uniqueDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"Stuart Wheater DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/varDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the variance of vector — varDS","title":"Computes the variance of vector — varDS","text":"Calculates variance.","code":""},{"path":"/reference/varDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the variance of vector — varDS","text":"","code":"varDS(x)"},{"path":"/reference/varDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the variance of vector — varDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/varDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the variance of vector — varDS","text":"list, sum input variable, sum squares input variable, number missing values, number valid values, number total length variable, class, class input object client-side consistency checking","code":""},{"path":"/reference/varDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the variance of vector — varDS","text":"length input vector less set filter missing value returned.","code":""},{"path":"/reference/varDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the variance of vector — varDS","text":"Amadou Gaye, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/vectorDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates a vector on the server-side. — vectorDS","title":"Creates a vector on the server-side. — vectorDS","text":"function similar R function c.","code":""},{"path":"/reference/vectorDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates a vector on the server-side. — vectorDS","text":"","code":"vectorDS(...)"},{"path":"/reference/vectorDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates a vector on the server-side. — vectorDS","text":"... parameter used form vector.","code":""},{"path":"/reference/vectorDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates a vector on the server-side. — vectorDS","text":"object specified newobj argument written server-side.","code":""},{"path":"/reference/vectorDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates a vector on the server-side. — vectorDS","text":"function computes vectors values.","code":""},{"path":"/reference/vectorDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Creates a vector on the server-side. — vectorDS","text":"Stuart Wheater DataSHIELD Development Team","code":""}] diff --git a/docs/sitemap.xml b/docs/sitemap.xml index d094f396..f9770fa1 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -16,6 +16,7 @@ /reference/asMatrixDS.html /reference/asNumericDS.html /reference/aucDS.html +/reference/booleDS.html /reference/boxPlotGGDS.html /reference/boxPlotGG_data_TreatmentDS.html /reference/boxPlotGG_data_Treatment_numericDS.html diff --git a/inst/DATASHIELD b/inst/DATASHIELD index c2e916a7..87e9a67b 100644 --- a/inst/DATASHIELD +++ b/inst/DATASHIELD @@ -75,7 +75,7 @@ AssignMethods: asLogicalDS, asMatrixDS, asNumericDS, - BooleDS, + booleDS, boxPlotGG_data_TreatmentDS, boxPlotGG_data_Treatment_numericDS, bp_standardsDS, diff --git a/man/BooleDS.Rd b/man/booleDS.Rd similarity index 96% rename from man/BooleDS.Rd rename to man/booleDS.Rd index 57587a93..70bb7395 100644 --- a/man/BooleDS.Rd +++ b/man/booleDS.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/booleDS.R -\name{BooleDS} -\alias{BooleDS} -\title{BooleDS} +\name{booleDS} +\alias{booleDS} +\title{booleDS} \usage{ -BooleDS( +booleDS( V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, From c7975ac003122887d29b39ef33092656b2d3f91a Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 2 Nov 2026 21:49:54 +0000 Subject: [PATCH 3/6] Phase 3 of renaming test file --- ...k-asFactorDS1.R => test-smk-asFactor1DS.R} | 10 ++-- ...k-asFactorDS2.R => test-smk-asFactor2DS.R} | 14 ++--- ...setDS1.R => test-smk-dataFrameSubset1DS.R} | 24 ++++----- ...setDS2.R => test-smk-dataFrameSubset2DS.R} | 24 ++++----- .../{test-smk-glmDS1.R => test-smk-glm1DS.R} | 30 +++++------ .../{test-smk-glmDS2.R => test-smk-glm2DS.R} | 30 +++++------ ...smk-glmSLMADS1.R => test-smk-glmSLMA1DS.R} | 26 ++++----- ...smk-glmSLMADS2.R => test-smk-glmSLMA2DS.R} | 26 ++++----- ...glmerSLMADS2.R => test-smk-glmerSLMA2DS.R} | 26 ++++----- tests/testthat/test-smk-histogram1DS.R | 51 ++++++++++++++++++ tests/testthat/test-smk-histogram2DS.R | 47 ++++++++++++++++ tests/testthat/test-smk-histogramDS1.R | 51 ------------------ tests/testthat/test-smk-histogramDS2.R | 47 ---------------- ...k-kurtosisDS1.R => test-smk-kurtosis1DS.R} | 38 ++++++------- ...k-kurtosisDS2.R => test-smk-kurtosis2DS.R} | 26 ++++----- ...est-smk-lexisDS1.R => test-smk-lexis1DS.R} | 16 +++--- ...est-smk-lexisDS2.R => test-smk-lexis2DS.R} | 36 ++++++------- ...k-lmerSLMADS2.R => test-smk-lmerSLMA2DS.R} | 26 ++++----- tests/testthat/test-smk-matrixDet1DS.R | 54 +++++++++++++++++++ tests/testthat/test-smk-matrixDet2DS.R | 39 ++++++++++++++ tests/testthat/test-smk-matrixDetDS1.R | 54 ------------------- tests/testthat/test-smk-matrixDetDS2.R | 39 -------------- ...k-skewnessDS1.R => test-smk-skewness1DS.R} | 38 ++++++------- ...k-skewnessDS2.R => test-smk-skewness2DS.R} | 26 ++++----- ...est-smk-tableDS2.R => test-smk-table2DS.R} | 16 +++--- 25 files changed, 407 insertions(+), 407 deletions(-) rename tests/testthat/{test-smk-asFactorDS1.R => test-smk-asFactor1DS.R} (79%) rename tests/testthat/{test-smk-asFactorDS2.R => test-smk-asFactor2DS.R} (76%) rename tests/testthat/{test-smk-dataFrameSubsetDS1.R => test-smk-dataFrameSubset1DS.R} (85%) rename tests/testthat/{test-smk-dataFrameSubsetDS2.R => test-smk-dataFrameSubset2DS.R} (82%) rename tests/testthat/{test-smk-glmDS1.R => test-smk-glm1DS.R} (71%) rename tests/testthat/{test-smk-glmDS2.R => test-smk-glm2DS.R} (75%) rename tests/testthat/{test-smk-glmSLMADS1.R => test-smk-glmSLMA1DS.R} (72%) rename tests/testthat/{test-smk-glmSLMADS2.R => test-smk-glmSLMA2DS.R} (78%) rename tests/testthat/{test-smk-glmerSLMADS2.R => test-smk-glmerSLMA2DS.R} (76%) create mode 100644 tests/testthat/test-smk-histogram1DS.R create mode 100644 tests/testthat/test-smk-histogram2DS.R delete mode 100644 tests/testthat/test-smk-histogramDS1.R delete mode 100644 tests/testthat/test-smk-histogramDS2.R rename tests/testthat/{test-smk-kurtosisDS1.R => test-smk-kurtosis1DS.R} (70%) rename tests/testthat/{test-smk-kurtosisDS2.R => test-smk-kurtosis2DS.R} (70%) rename tests/testthat/{test-smk-lexisDS1.R => test-smk-lexis1DS.R} (57%) rename tests/testthat/{test-smk-lexisDS2.R => test-smk-lexis2DS.R} (76%) rename tests/testthat/{test-smk-lmerSLMADS2.R => test-smk-lmerSLMA2DS.R} (75%) create mode 100644 tests/testthat/test-smk-matrixDet1DS.R create mode 100644 tests/testthat/test-smk-matrixDet2DS.R delete mode 100644 tests/testthat/test-smk-matrixDetDS1.R delete mode 100644 tests/testthat/test-smk-matrixDetDS2.R rename tests/testthat/{test-smk-skewnessDS1.R => test-smk-skewness1DS.R} (70%) rename tests/testthat/{test-smk-skewnessDS2.R => test-smk-skewness2DS.R} (70%) rename tests/testthat/{test-smk-tableDS2.R => test-smk-table2DS.R} (63%) diff --git a/tests/testthat/test-smk-asFactorDS1.R b/tests/testthat/test-smk-asFactor1DS.R similarity index 79% rename from tests/testthat/test-smk-asFactorDS1.R rename to tests/testthat/test-smk-asFactor1DS.R index e7f0abb8..31a01047 100644 --- a/tests/testthat/test-smk-asFactorDS1.R +++ b/tests/testthat/test-smk-asFactor1DS.R @@ -13,7 +13,7 @@ # Set up # -# context("asFactorDS1::smk::setup") +# context("asFactor1DS::smk::setup") set.standard.disclosure.settings() @@ -21,10 +21,10 @@ set.standard.disclosure.settings() # Tests # -test_that("simple asFactorDS1", { +test_that("simple asFactor1DS", { input <- c(2.0, 1.0, 3.0, 3.0, 3.0, 1.0, 2.0, 2.0, 1.0, 2.0) - res <- asFactorDS1("input") + res <- asFactor1DS("input") expect_equal(class(res), "character") expect_length(res, 3) @@ -33,6 +33,6 @@ test_that("simple asFactorDS1", { expect_equal(res[3], "3") }) -test_that("asFactorDS1 errors when serverside object does not exist", { - expect_error(asFactorDS1("nonexistent_object"), regexp = "does not exist") +test_that("asFactor1DS errors when serverside object does not exist", { + expect_error(asFactor1DS("nonexistent_object"), regexp = "does not exist") }) diff --git a/tests/testthat/test-smk-asFactorDS2.R b/tests/testthat/test-smk-asFactor2DS.R similarity index 76% rename from tests/testthat/test-smk-asFactorDS2.R rename to tests/testthat/test-smk-asFactor2DS.R index d9f2ae83..8670e676 100644 --- a/tests/testthat/test-smk-asFactorDS2.R +++ b/tests/testthat/test-smk-asFactor2DS.R @@ -12,7 +12,7 @@ # Set up # -# context("asFactorDS2::smk::setup") +# context("asFactor2DS::smk::setup") set.standard.disclosure.settings() @@ -20,20 +20,20 @@ set.standard.disclosure.settings() # Tests # -test_that("simple asFactorDS2", { +test_that("simple asFactor2DS", { input <- c(2, 1, 3, 3, 3, 1, 2, 2, 1, 2) - res <- asFactorDS2("input", "1,2,3,4", FALSE, NULL) + res <- asFactor2DS("input", "1,2,3,4", FALSE, NULL) expect_equal(class(res), "factor") expect_length(res, 10) expect_equal(levels(res), c("1", "2", "3", "4")) }) -test_that("asFactorDS2 with fixed dummy variables", { +test_that("asFactor2DS with fixed dummy variables", { input <- c(2, 1, 3, 3, 3, 1, 2, 2, 1, 2) - res <- asFactorDS2("input", "1,2,3,4", TRUE, 1) + res <- asFactor2DS("input", "1,2,3,4", TRUE, 1) expect_true(is.matrix(res)) expect_equal(dim(res), c(10L, 3L)) @@ -43,6 +43,6 @@ test_that("asFactorDS2 with fixed dummy variables", { expect_equal(unname(res[, "DV4"]), rep(0, 10)) }) -test_that("asFactorDS2 errors when serverside object does not exist", { - expect_error(asFactorDS2("nonexistent_object", "1,2", FALSE, NULL), regexp = "does not exist") +test_that("asFactor2DS errors when serverside object does not exist", { + expect_error(asFactor2DS("nonexistent_object", "1,2", FALSE, NULL), regexp = "does not exist") }) diff --git a/tests/testthat/test-smk-dataFrameSubsetDS1.R b/tests/testthat/test-smk-dataFrameSubset1DS.R similarity index 85% rename from tests/testthat/test-smk-dataFrameSubsetDS1.R rename to tests/testthat/test-smk-dataFrameSubset1DS.R index b70c7993..9e5bfdd0 100644 --- a/tests/testthat/test-smk-dataFrameSubsetDS1.R +++ b/tests/testthat/test-smk-dataFrameSubset1DS.R @@ -22,8 +22,8 @@ set.standard.disclosure.settings() # Tests # -# context("dataFrameSubsetDS1::smk::test1") -test_that("test1 dataFrameSubsetDS1", { +# context("dataFrameSubset1DS::smk::test1") +test_that("test1 dataFrameSubset1DS", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) colnames(D) <- c('integer','numeric','binary') @@ -35,7 +35,7 @@ test_that("test1 dataFrameSubsetDS1", { Boolean.operator.n <- 1 keep.NAs <- FALSE - res <- dataFrameSubsetDS1(df.name="D", V1.name="D$binary", V2.name="2", + res <- dataFrameSubset1DS(df.name="D", V1.name="D$binary", V2.name="2", Boolean.operator.n=Boolean.operator.n, keep.NAs = keep.NAs) expect_equal(class(res), "character") @@ -43,8 +43,8 @@ test_that("test1 dataFrameSubsetDS1", { }) -# context("dataFrameSubsetDS1::smk::test2") -test_that("test2 dataFrameSubsetDS1", { +# context("dataFrameSubset1DS::smk::test2") +test_that("test2 dataFrameSubset1DS", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) colnames(D) <- c('integer','numeric','binary') @@ -56,7 +56,7 @@ test_that("test2 dataFrameSubsetDS1", { Boolean.operator.n <- 3 keep.NAs <- FALSE - res <- dataFrameSubsetDS1(df.name="D", V1.name="D$numeric", V2.name="41.10", + res <- dataFrameSubset1DS(df.name="D", V1.name="D$numeric", V2.name="41.10", Boolean.operator.n=Boolean.operator.n, keep.NAs = keep.NAs) expect_equal(class(res), "list") @@ -74,15 +74,15 @@ test_that("test2 dataFrameSubsetDS1", { }) -test_that("dataFrameSubsetDS1 errors when df does not exist", { +test_that("dataFrameSubset1DS errors when df does not exist", { expect_error( - dataFrameSubsetDS1(df.name="nonexistent", V1.name="x", V2.name="1", + dataFrameSubset1DS(df.name="nonexistent", V1.name="x", V2.name="1", Boolean.operator.n=1, keep.NAs=FALSE), regexp = "does not exist" ) }) -test_that("dataFrameSubsetDS1 errors when V1 object does not exist", { +test_that("dataFrameSubset1DS errors when V1 object does not exist", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) colnames(D) <- c('integer','numeric','binary') D$integer <- rep(1, 20) @@ -90,7 +90,7 @@ test_that("dataFrameSubsetDS1 errors when V1 object does not exist", { D$binary <- rep(1, 20) expect_error( - dataFrameSubsetDS1(df.name="D", V1.name="nonexistent$col", V2.name="1", + dataFrameSubset1DS(df.name="D", V1.name="nonexistent$col", V2.name="1", Boolean.operator.n=1, keep.NAs=FALSE), regexp = "does not exist" ) @@ -100,6 +100,6 @@ test_that("dataFrameSubsetDS1 errors when V1 object does not exist", { # Done # -# context("dataFrameSubsetDS1::smk::shutdown") +# context("dataFrameSubset1DS::smk::shutdown") -# context("dataFrameSubsetDS1::smk::done") +# context("dataFrameSubset1DS::smk::done") diff --git a/tests/testthat/test-smk-dataFrameSubsetDS2.R b/tests/testthat/test-smk-dataFrameSubset2DS.R similarity index 82% rename from tests/testthat/test-smk-dataFrameSubsetDS2.R rename to tests/testthat/test-smk-dataFrameSubset2DS.R index eab140b1..ae777911 100644 --- a/tests/testthat/test-smk-dataFrameSubsetDS2.R +++ b/tests/testthat/test-smk-dataFrameSubset2DS.R @@ -22,8 +22,8 @@ set.standard.disclosure.settings() # Tests # -# context("dataFrameSubsetDS2::smk::test1") -test_that("test1 dataFrameSubsetDS2", { +# context("dataFrameSubset2DS::smk::test1") +test_that("test1 dataFrameSubset2DS", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) colnames(D) <- c('integer','numeric','binary') @@ -35,7 +35,7 @@ test_that("test1 dataFrameSubsetDS2", { Boolean.operator.n <- 1 keep.NAs <- FALSE - res <- dataFrameSubsetDS2(df.name="D", V1.name="D$binary", V2.name="2", + res <- dataFrameSubset2DS(df.name="D", V1.name="D$binary", V2.name="2", Boolean.operator.n=Boolean.operator.n, keep.NAs = keep.NAs) expect_equal(class(res), "data.frame") @@ -48,8 +48,8 @@ test_that("test1 dataFrameSubsetDS2", { }) -# context("dataFrameSubsetDS2::smk::test2") -test_that("test2 dataFrameSubsetDS2", { +# context("dataFrameSubset2DS::smk::test2") +test_that("test2 dataFrameSubset2DS", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) colnames(D) <- c('integer','numeric','binary') @@ -61,7 +61,7 @@ test_that("test2 dataFrameSubsetDS2", { Boolean.operator.n <- 3 keep.NAs <- FALSE - res <- dataFrameSubsetDS2(df.name="D", V1.name="D$numeric", V2.name="41.10", + res <- dataFrameSubset2DS(df.name="D", V1.name="D$numeric", V2.name="41.10", Boolean.operator.n=Boolean.operator.n, keep.NAs = keep.NAs) expect_equal(class(res), "data.frame") @@ -71,15 +71,15 @@ test_that("test2 dataFrameSubsetDS2", { }) -test_that("dataFrameSubsetDS2 errors when df does not exist", { +test_that("dataFrameSubset2DS errors when df does not exist", { expect_error( - dataFrameSubsetDS2(df.name="nonexistent", V1.name="x", V2.name="1", + dataFrameSubset2DS(df.name="nonexistent", V1.name="x", V2.name="1", Boolean.operator.n=1, keep.NAs=FALSE), regexp = "does not exist" ) }) -test_that("dataFrameSubsetDS2 errors when V1 object does not exist", { +test_that("dataFrameSubset2DS errors when V1 object does not exist", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) colnames(D) <- c('integer','numeric','binary') D$integer <- rep(1, 20) @@ -87,7 +87,7 @@ test_that("dataFrameSubsetDS2 errors when V1 object does not exist", { D$binary <- rep(1, 20) expect_error( - dataFrameSubsetDS2(df.name="D", V1.name="nonexistent$col", V2.name="1", + dataFrameSubset2DS(df.name="D", V1.name="nonexistent$col", V2.name="1", Boolean.operator.n=1, keep.NAs=FALSE), regexp = "does not exist" ) @@ -97,6 +97,6 @@ test_that("dataFrameSubsetDS2 errors when V1 object does not exist", { # Done # -# context("dataFrameSubsetDS2::smk::shutdown") +# context("dataFrameSubset2DS::smk::shutdown") -# context("dataFrameSubsetDS2::smk::done") +# context("dataFrameSubset2DS::smk::done") diff --git a/tests/testthat/test-smk-glmDS1.R b/tests/testthat/test-smk-glm1DS.R similarity index 71% rename from tests/testthat/test-smk-glmDS1.R rename to tests/testthat/test-smk-glm1DS.R index 5ccb00a0..f1935294 100644 --- a/tests/testthat/test-smk-glmDS1.R +++ b/tests/testthat/test-smk-glm1DS.R @@ -2,7 +2,7 @@ # Set up # -# context("glmDS1::smk::setup") +# context("glm1DS::smk::setup") set.standard.disclosure.settings() @@ -10,8 +10,8 @@ set.standard.disclosure.settings() # Tests # -# context("glmDS1::smk::gaussian") -test_that("simple glmDS1, gaussian", { +# context("glm1DS::smk::gaussian") +test_that("simple glm1DS, gaussian", { D <- data.frame( y = c(4.1, 4.2, 3.9, 2.9, 3.6, 3.8, 4.2, 4.2, 2.5, 3.5, 2.8, 3.7, 3.3, 3.3, 2.4, 3.5, 3.0, 3.1, 3.5, 3.4), @@ -20,7 +20,7 @@ test_that("simple glmDS1, gaussian", { ) expect_warning( - res <- glmDS1(formula = stats::as.formula("y ~ x"), family = "gaussian", + res <- glm1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D"), regexp = "did not converge" ) @@ -37,24 +37,24 @@ test_that("simple glmDS1, gaussian", { expect_equal(res$errorMessage, "No errors") }) -test_that("glmDS1 throws error when data does not exist", { +test_that("glm1DS throws error when data does not exist", { expect_error( - glmDS1(formula = stats::as.formula("y ~ x"), family = "gaussian", + glm1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "nonexistent_object"), regexp = "does not exist" ) }) -test_that("glmDS1 throws error when data is not a data.frame or list", { +test_that("glm1DS throws error when data is not a data.frame or list", { bad_input <- c(1, 2, 3) expect_error( - glmDS1(formula = stats::as.formula("y ~ x"), family = "gaussian", + glm1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "bad_input"), regexp = "must be of type" ) }) -test_that("glmDS1 gives the same result for data as a list as for a data.frame", { +test_that("glm1DS gives the same result for data as a list as for a data.frame", { D <- data.frame( y = c(4.1, 4.2, 3.9, 2.9, 3.6, 3.8, 4.2, 4.2, 2.5, 3.5, 2.8, 3.7, 3.3, 3.3, 2.4, 3.5, 3.0, 3.1, 3.5, 3.4), @@ -63,16 +63,16 @@ test_that("glmDS1 gives the same result for data as a list as for a data.frame", ) D.list <- as.list(D) - res.df <- suppressWarnings(glmDS1(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D")) - res.list <- suppressWarnings(glmDS1(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D.list")) + res.df <- suppressWarnings(glm1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D")) + res.list <- suppressWarnings(glm1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D.list")) expect_equal(res.list, res.df) }) -test_that("glmDS1 throws error when data is a matrix", { +test_that("glm1DS throws error when data is a matrix", { D.matrix <- cbind(y = c(1, 2, 3), x = c(4, 5, 6)) expect_error( - glmDS1(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D.matrix"), + glm1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D.matrix"), regexp = "must be of type data.frame or list" ) }) @@ -81,6 +81,6 @@ test_that("glmDS1 throws error when data is a matrix", { # Done # -# context("glmDS1::smk::shutdown") +# context("glm1DS::smk::shutdown") -# context("glmDS1::smk::done") +# context("glm1DS::smk::done") diff --git a/tests/testthat/test-smk-glmDS2.R b/tests/testthat/test-smk-glm2DS.R similarity index 75% rename from tests/testthat/test-smk-glmDS2.R rename to tests/testthat/test-smk-glm2DS.R index 01d52c09..81676c08 100644 --- a/tests/testthat/test-smk-glmDS2.R +++ b/tests/testthat/test-smk-glm2DS.R @@ -2,7 +2,7 @@ # Set up # -# context("glmDS2::smk::setup") +# context("glm2DS::smk::setup") set.standard.disclosure.settings() @@ -10,8 +10,8 @@ set.standard.disclosure.settings() # Tests # -# context("glmDS2::smk::gaussian") -test_that("simple glmDS2, gaussian", { +# context("glm2DS::smk::gaussian") +test_that("simple glm2DS, gaussian", { D <- data.frame( y = c(4.1, 4.2, 3.9, 2.9, 3.6, 3.8, 4.2, 4.2, 2.5, 3.5, 2.8, 3.7, 3.3, 3.3, 2.4, 3.5, 3.0, 3.1, 3.5, 3.4), @@ -20,7 +20,7 @@ test_that("simple glmDS2, gaussian", { ) expect_warning( - res <- glmDS2(formula = stats::as.formula("y ~ x"), family = "gaussian", + res <- glm2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", beta.vect = "0,0", offset = NULL, weights = NULL, dataName = "D"), regexp = "did not converge" ) @@ -42,24 +42,24 @@ test_that("simple glmDS2, gaussian", { expect_equal(res$errorMessage2, "No errors") }) -test_that("glmDS2 throws error when dataName does not exist", { +test_that("glm2DS throws error when dataName does not exist", { expect_error( - glmDS2(formula = stats::as.formula("y ~ x"), family = "gaussian", + glm2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", beta.vect = "0,0", offset = NULL, weights = NULL, dataName = "nonexistent_object"), regexp = "does not exist" ) }) -test_that("glmDS2 throws error when dataName is not a data.frame or list", { +test_that("glm2DS throws error when dataName is not a data.frame or list", { bad_input <- c(1, 2, 3) expect_error( - glmDS2(formula = stats::as.formula("y ~ x"), family = "gaussian", + glm2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", beta.vect = "0,0", offset = NULL, weights = NULL, dataName = "bad_input"), regexp = "must be of type" ) }) -test_that("glmDS2 gives the same result for data as a list as for a data.frame", { +test_that("glm2DS gives the same result for data as a list as for a data.frame", { D <- data.frame( y = c(4.1, 4.2, 3.9, 2.9, 3.6, 3.8, 4.2, 4.2, 2.5, 3.5, 2.8, 3.7, 3.3, 3.3, 2.4, 3.5, 3.0, 3.1, 3.5, 3.4), @@ -68,16 +68,16 @@ test_that("glmDS2 gives the same result for data as a list as for a data.frame", ) D.list <- as.list(D) - res.df <- suppressWarnings(glmDS2(formula = stats::as.formula("y ~ x"), family = "gaussian", beta.vect = "0,0", offset = NULL, weights = NULL, dataName = "D")) - res.list <- suppressWarnings(glmDS2(formula = stats::as.formula("y ~ x"), family = "gaussian", beta.vect = "0,0", offset = NULL, weights = NULL, dataName = "D.list")) + res.df <- suppressWarnings(glm2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", beta.vect = "0,0", offset = NULL, weights = NULL, dataName = "D")) + res.list <- suppressWarnings(glm2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", beta.vect = "0,0", offset = NULL, weights = NULL, dataName = "D.list")) expect_equal(res.list, res.df) }) -test_that("glmDS2 throws error when data is a matrix", { +test_that("glm2DS throws error when data is a matrix", { D.matrix <- cbind(y = c(1, 2, 3), x = c(4, 5, 6)) expect_error( - glmDS2(formula = stats::as.formula("y ~ x"), family = "gaussian", beta.vect = "0,0", offset = NULL, weights = NULL, dataName = "D.matrix"), + glm2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", beta.vect = "0,0", offset = NULL, weights = NULL, dataName = "D.matrix"), regexp = "must be of type data.frame or list" ) }) @@ -86,6 +86,6 @@ test_that("glmDS2 throws error when data is a matrix", { # Done # -# context("glmDS2::smk::shutdown") +# context("glm2DS::smk::shutdown") -# context("glmDS2::smk::done") +# context("glm2DS::smk::done") diff --git a/tests/testthat/test-smk-glmSLMADS1.R b/tests/testthat/test-smk-glmSLMA1DS.R similarity index 72% rename from tests/testthat/test-smk-glmSLMADS1.R rename to tests/testthat/test-smk-glmSLMA1DS.R index 18641903..f346828e 100644 --- a/tests/testthat/test-smk-glmSLMADS1.R +++ b/tests/testthat/test-smk-glmSLMA1DS.R @@ -2,7 +2,7 @@ # Set up # -# context("glmSLMADS1::smk::setup") +# context("glmSLMA1DS::smk::setup") set.standard.disclosure.settings() @@ -10,8 +10,8 @@ set.standard.disclosure.settings() # Tests # -# context("glmSLMADS1::smk::gaussian") -test_that("simple glmSLMADS1, gaussian", { +# context("glmSLMA1DS::smk::gaussian") +test_that("simple glmSLMA1DS, gaussian", { D <- data.frame( y = c(4.1, 4.2, 3.9, 2.9, 3.6, 3.8, 4.2, 4.2, 2.5, 3.5, 2.8, 3.7, 3.3, 3.3, 2.4, 3.5, 3.0, 3.1, 3.5, 3.4), @@ -20,7 +20,7 @@ test_that("simple glmSLMADS1, gaussian", { ) expect_warning( - res <- glmSLMADS1(formula = stats::as.formula("y ~ x"), family = "gaussian", + res <- glmSLMA1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D"), regexp = "did not converge" ) @@ -37,24 +37,24 @@ test_that("simple glmSLMADS1, gaussian", { expect_equal(res$errorMessage, "No errors") }) -test_that("glmSLMADS1 throws error when data does not exist", { +test_that("glmSLMA1DS throws error when data does not exist", { expect_error( - glmSLMADS1(formula = stats::as.formula("y ~ x"), family = "gaussian", + glmSLMA1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "nonexistent_object"), regexp = "does not exist" ) }) -test_that("glmSLMADS1 throws error when data is not a data.frame or list", { +test_that("glmSLMA1DS throws error when data is not a data.frame or list", { bad_input <- c(1, 2, 3) expect_error( - glmSLMADS1(formula = stats::as.formula("y ~ x"), family = "gaussian", + glmSLMA1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "bad_input"), regexp = "must be of type" ) }) -test_that("glmSLMADS1 gives the same result for data as a list as for a data.frame", { +test_that("glmSLMA1DS gives the same result for data as a list as for a data.frame", { D <- data.frame( y = c(4.1, 4.2, 3.9, 2.9, 3.6, 3.8, 4.2, 4.2, 2.5, 3.5, 2.8, 3.7, 3.3, 3.3, 2.4, 3.5, 3.0, 3.1, 3.5, 3.4), @@ -63,8 +63,8 @@ test_that("glmSLMADS1 gives the same result for data as a list as for a data.fra ) D.list <- as.list(D) - res.df <- suppressWarnings(glmSLMADS1(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D")) - res.list <- suppressWarnings(glmSLMADS1(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D.list")) + res.df <- suppressWarnings(glmSLMA1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D")) + res.list <- suppressWarnings(glmSLMA1DS(formula = stats::as.formula("y ~ x"), family = "gaussian", weights = NULL, offset = NULL, data = "D.list")) expect_equal(res.list, res.df) }) @@ -73,6 +73,6 @@ test_that("glmSLMADS1 gives the same result for data as a list as for a data.fra # Done # -# context("glmSLMADS1::smk::shutdown") +# context("glmSLMA1DS::smk::shutdown") -# context("glmSLMADS1::smk::done") +# context("glmSLMA1DS::smk::done") diff --git a/tests/testthat/test-smk-glmSLMADS2.R b/tests/testthat/test-smk-glmSLMA2DS.R similarity index 78% rename from tests/testthat/test-smk-glmSLMADS2.R rename to tests/testthat/test-smk-glmSLMA2DS.R index 02965fdf..c2ce4f03 100644 --- a/tests/testthat/test-smk-glmSLMADS2.R +++ b/tests/testthat/test-smk-glmSLMA2DS.R @@ -2,7 +2,7 @@ # Set up # -# context("glmSLMADS2::smk::setup") +# context("glmSLMA2DS::smk::setup") set.standard.disclosure.settings() @@ -10,8 +10,8 @@ set.standard.disclosure.settings() # Tests # -# context("glmSLMADS2::smk::gaussian") -test_that("simple glmSLMADS2, gaussian", { +# context("glmSLMA2DS::smk::gaussian") +test_that("simple glmSLMA2DS, gaussian", { D <- data.frame( y = c(4.1, 4.2, 3.9, 2.9, 3.6, 3.8, 4.2, 4.2, 2.5, 3.5, 2.8, 3.7, 3.3, 3.3, 2.4, 3.5, 3.0, 3.1, 3.5, 3.4), @@ -20,7 +20,7 @@ test_that("simple glmSLMADS2, gaussian", { ) my.glm.obj <- glm(y ~ x, family = gaussian(), data = D, x = TRUE) - res <- glmSLMADS2(formula = stats::as.formula("y ~ x"), family = "gaussian", + res <- glmSLMA2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", offset = NULL, weights = NULL, newobj = "my.glm.obj", dataName = "D") expect_equal(class(res), "list") @@ -40,26 +40,26 @@ test_that("simple glmSLMADS2, gaussian", { expect_equal(res$family$family, "gaussian") }) -test_that("glmSLMADS2 throws error when dataName does not exist", { +test_that("glmSLMA2DS throws error when dataName does not exist", { # dataName is validated before newobj is loaded, so no glm object needs to exist here. expect_error( - glmSLMADS2(formula = stats::as.formula("y ~ x"), family = "gaussian", + glmSLMA2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", offset = NULL, weights = NULL, newobj = "my.glm.obj", dataName = "nonexistent_object"), regexp = "does not exist" ) }) -test_that("glmSLMADS2 throws error when dataName is not a data.frame or list", { +test_that("glmSLMA2DS throws error when dataName is not a data.frame or list", { bad_input <- c(1, 2, 3) expect_error( - glmSLMADS2(formula = stats::as.formula("y ~ x"), family = "gaussian", + glmSLMA2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", offset = NULL, weights = NULL, newobj = "my.glm.obj", dataName = "bad_input"), regexp = "must be of type" ) }) -test_that("glmSLMADS2 gives the same result for data as a list as for a data.frame", { +test_that("glmSLMA2DS gives the same result for data as a list as for a data.frame", { D <- data.frame( y = c(4.1, 4.2, 3.9, 2.9, 3.6, 3.8, 4.2, 4.2, 2.5, 3.5, 2.8, 3.7, 3.3, 3.3, 2.4, 3.5, 3.0, 3.1, 3.5, 3.4), @@ -69,9 +69,9 @@ test_that("glmSLMADS2 gives the same result for data as a list as for a data.fra D.list <- as.list(D) my.glm.obj <- glm(y ~ x, family = gaussian(), data = D, x = TRUE) - res.df <- glmSLMADS2(formula = stats::as.formula("y ~ x"), family = "gaussian", + res.df <- glmSLMA2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", offset = NULL, weights = NULL, newobj = "my.glm.obj", dataName = "D") - res.list <- glmSLMADS2(formula = stats::as.formula("y ~ x"), family = "gaussian", + res.list <- glmSLMA2DS(formula = stats::as.formula("y ~ x"), family = "gaussian", offset = NULL, weights = NULL, newobj = "my.glm.obj", dataName = "D.list") expect_equal(res.list$data, "D.list") @@ -82,6 +82,6 @@ test_that("glmSLMADS2 gives the same result for data as a list as for a data.fra # Done # -# context("glmSLMADS2::smk::shutdown") +# context("glmSLMA2DS::smk::shutdown") -# context("glmSLMADS2::smk::done") +# context("glmSLMA2DS::smk::done") diff --git a/tests/testthat/test-smk-glmerSLMADS2.R b/tests/testthat/test-smk-glmerSLMA2DS.R similarity index 76% rename from tests/testthat/test-smk-glmerSLMADS2.R rename to tests/testthat/test-smk-glmerSLMA2DS.R index adb47e47..4488223f 100644 --- a/tests/testthat/test-smk-glmerSLMADS2.R +++ b/tests/testthat/test-smk-glmerSLMA2DS.R @@ -2,7 +2,7 @@ # Set up # -# context("glmerSLMADS2::smk::setup") +# context("glmerSLMA2DS::smk::setup") set.standard.disclosure.settings() @@ -10,8 +10,8 @@ set.standard.disclosure.settings() # Tests # -# context("glmerSLMADS2::smk::binomial random intercept") -test_that("simple glmerSLMADS2, binomial random intercept", { +# context("glmerSLMA2DS::smk::binomial random intercept") +test_that("simple glmerSLMA2DS, binomial random intercept", { set.seed(7) D <- data.frame( group = factor(rep(1:5, each = 10)), @@ -21,7 +21,7 @@ test_that("simple glmerSLMADS2, binomial random intercept", { D$y <- rbinom(50, 1, plogis(lp)) res <- suppressWarnings( - glmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + glmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "D", family = "binomial", control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL) @@ -39,9 +39,9 @@ test_that("simple glmerSLMADS2, binomial random intercept", { expect_equal(res$family, "binomial") }) -test_that("glmerSLMADS2 throws error when dataName does not exist", { +test_that("glmerSLMA2DS throws error when dataName does not exist", { expect_error( - glmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + glmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "nonexistent_object", family = "binomial", control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL), @@ -49,10 +49,10 @@ test_that("glmerSLMADS2 throws error when dataName does not exist", { ) }) -test_that("glmerSLMADS2 throws error when dataName is not a data.frame or list", { +test_that("glmerSLMA2DS throws error when dataName is not a data.frame or list", { bad_input <- c(1, 2, 3) expect_error( - glmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + glmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "bad_input", family = "binomial", control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL), @@ -60,7 +60,7 @@ test_that("glmerSLMADS2 throws error when dataName is not a data.frame or list", ) }) -test_that("glmerSLMADS2 gives the same result for data as a list as for a data.frame", { +test_that("glmerSLMA2DS gives the same result for data as a list as for a data.frame", { set.seed(7) D <- data.frame( group = factor(rep(1:5, each = 10)), @@ -70,11 +70,11 @@ test_that("glmerSLMADS2 gives the same result for data as a list as for a data.f D$y <- rbinom(50, 1, plogis(lp)) D.list <- as.list(D) - res.df <- suppressWarnings(glmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + res.df <- suppressWarnings(glmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "D", family = "binomial", control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL)) - res.list <- suppressWarnings(glmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + res.list <- suppressWarnings(glmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "D.list", family = "binomial", control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL)) @@ -86,6 +86,6 @@ test_that("glmerSLMADS2 gives the same result for data as a list as for a data.f # Done # -# context("glmerSLMADS2::smk::shutdown") +# context("glmerSLMA2DS::smk::shutdown") -# context("glmerSLMADS2::smk::done") +# context("glmerSLMA2DS::smk::done") diff --git a/tests/testthat/test-smk-histogram1DS.R b/tests/testthat/test-smk-histogram1DS.R new file mode 100644 index 00000000..62ee3257 --- /dev/null +++ b/tests/testthat/test-smk-histogram1DS.R @@ -0,0 +1,51 @@ +# +# Set up +# + +# context("histogram1DS::smk::setup") + +set.standard.disclosure.settings() +set.random.seed.setting(1234) + +# +# Tests +# + +# context("histogram1DS::smk") +test_that("histogram1DS, smallCellsRule method", { + xvect <- c(1:100) + + res <- histogram1DS("xvect", method.indicator=1, k=3, noise=0.25) + + expect_length(res, 2) + expect_equal(res$class, "integer") + expect_length(res$range, 2) +}) + +test_that("histogram1DS fails when x references nonexistent object", { + expect_error(histogram1DS("nonexistent_obj", method.indicator=1, k=3, noise=0.25), "does not exist") +}) + +test_that("histogram1DS fails when x is not numeric or integer", { + xvect <- c("a", "b", "c") + expect_error(histogram1DS("xvect", method.indicator=1, k=3, noise=0.25), "must be of type numeric or integer") +}) + +test_that("histogram1DS gives the same result for numeric input as for integer", { + x.integer <- c(1:100) + x.numeric <- as.numeric(x.integer) + + res.integer <- histogram1DS("x.integer", method.indicator=1, k=3, noise=0.25) + res.numeric <- histogram1DS("x.numeric", method.indicator=1, k=3, noise=0.25) + + expect_equal(res.numeric$class, "numeric") + expect_equal(res.numeric[names(res.numeric) != "class"], res.integer[names(res.integer) != "class"]) +}) + +# +# Done +# + +# context("histogram1DS::smk::shutdown") + +# context("histogram1DS::smk::done") diff --git a/tests/testthat/test-smk-histogram2DS.R b/tests/testthat/test-smk-histogram2DS.R new file mode 100644 index 00000000..b37733fa --- /dev/null +++ b/tests/testthat/test-smk-histogram2DS.R @@ -0,0 +1,47 @@ +# +# Set up +# + +# context("histogram2DS::smk::setup") + +set.standard.disclosure.settings() + +# +# Tests +# + +# context("histogram2DS::smk") +test_that("histogram2DS, smallCellsRule method", { + xvect <- c(1:100) + + res <- histogram2DS("xvect", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25) + + expect_length(res, 2) + expect_true(inherits(res$histobject, "histogram")) + expect_equal(res$invalidcells, 0) +}) + +test_that("histogram2DS fails when x references nonexistent object", { + expect_error(histogram2DS("nonexistent_obj", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25), "does not exist") +}) + +test_that("histogram2DS fails when x is not numeric or integer", { + xvect <- c("a", "b", "c") + expect_error(histogram2DS("xvect", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25), "must be of type numeric or integer") +}) + +test_that("histogram2DS gives the same result for numeric input as for integer", { + x.integer <- c(1:100) + x.numeric <- as.numeric(x.integer) + + expect_equal(histogram2DS("x.numeric", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25), + histogram2DS("x.integer", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25)) +}) + +# +# Done +# + +# context("histogram2DS::smk::shutdown") + +# context("histogram2DS::smk::done") diff --git a/tests/testthat/test-smk-histogramDS1.R b/tests/testthat/test-smk-histogramDS1.R deleted file mode 100644 index 905c5841..00000000 --- a/tests/testthat/test-smk-histogramDS1.R +++ /dev/null @@ -1,51 +0,0 @@ -# -# Set up -# - -# context("histogramDS1::smk::setup") - -set.standard.disclosure.settings() -set.random.seed.setting(1234) - -# -# Tests -# - -# context("histogramDS1::smk") -test_that("histogramDS1, smallCellsRule method", { - xvect <- c(1:100) - - res <- histogramDS1("xvect", method.indicator=1, k=3, noise=0.25) - - expect_length(res, 2) - expect_equal(res$class, "integer") - expect_length(res$range, 2) -}) - -test_that("histogramDS1 fails when x references nonexistent object", { - expect_error(histogramDS1("nonexistent_obj", method.indicator=1, k=3, noise=0.25), "does not exist") -}) - -test_that("histogramDS1 fails when x is not numeric or integer", { - xvect <- c("a", "b", "c") - expect_error(histogramDS1("xvect", method.indicator=1, k=3, noise=0.25), "must be of type numeric or integer") -}) - -test_that("histogramDS1 gives the same result for numeric input as for integer", { - x.integer <- c(1:100) - x.numeric <- as.numeric(x.integer) - - res.integer <- histogramDS1("x.integer", method.indicator=1, k=3, noise=0.25) - res.numeric <- histogramDS1("x.numeric", method.indicator=1, k=3, noise=0.25) - - expect_equal(res.numeric$class, "numeric") - expect_equal(res.numeric[names(res.numeric) != "class"], res.integer[names(res.integer) != "class"]) -}) - -# -# Done -# - -# context("histogramDS1::smk::shutdown") - -# context("histogramDS1::smk::done") diff --git a/tests/testthat/test-smk-histogramDS2.R b/tests/testthat/test-smk-histogramDS2.R deleted file mode 100644 index 1176ddf7..00000000 --- a/tests/testthat/test-smk-histogramDS2.R +++ /dev/null @@ -1,47 +0,0 @@ -# -# Set up -# - -# context("histogramDS2::smk::setup") - -set.standard.disclosure.settings() - -# -# Tests -# - -# context("histogramDS2::smk") -test_that("histogramDS2, smallCellsRule method", { - xvect <- c(1:100) - - res <- histogramDS2("xvect", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25) - - expect_length(res, 2) - expect_true(inherits(res$histobject, "histogram")) - expect_equal(res$invalidcells, 0) -}) - -test_that("histogramDS2 fails when x references nonexistent object", { - expect_error(histogramDS2("nonexistent_obj", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25), "does not exist") -}) - -test_that("histogramDS2 fails when x is not numeric or integer", { - xvect <- c("a", "b", "c") - expect_error(histogramDS2("xvect", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25), "must be of type numeric or integer") -}) - -test_that("histogramDS2 gives the same result for numeric input as for integer", { - x.integer <- c(1:100) - x.numeric <- as.numeric(x.integer) - - expect_equal(histogramDS2("x.numeric", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25), - histogramDS2("x.integer", num.breaks=10, min=1, max=100, method.indicator=1, k=3, noise=0.25)) -}) - -# -# Done -# - -# context("histogramDS2::smk::shutdown") - -# context("histogramDS2::smk::done") diff --git a/tests/testthat/test-smk-kurtosisDS1.R b/tests/testthat/test-smk-kurtosis1DS.R similarity index 70% rename from tests/testthat/test-smk-kurtosisDS1.R rename to tests/testthat/test-smk-kurtosis1DS.R index 41a84c11..91527bde 100644 --- a/tests/testthat/test-smk-kurtosisDS1.R +++ b/tests/testthat/test-smk-kurtosis1DS.R @@ -13,7 +13,7 @@ # Set up # -# context("kurtosisDS1::smk::setup") +# context("kurtosis1DS::smk::setup") set.standard.disclosure.settings() @@ -21,11 +21,11 @@ set.standard.disclosure.settings() # Tests # -# context("kurtosisDS1::smk::method 1") -test_that("simple kurtosisDS1, method 1", { +# context("kurtosis1DS::smk::method 1") +test_that("simple kurtosis1DS, method 1", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) - res <- kurtosisDS1("input", 1) + res <- kurtosis1DS("input", 1) expect_length(res, 3) expect_equal(class(res), "list") @@ -36,11 +36,11 @@ test_that("simple kurtosisDS1, method 1", { expect_equal(res$class, "numeric") }) -# context("kurtosisDS1::smk::method 2") -test_that("simple kurtosisDS1, method 2", { +# context("kurtosis1DS::smk::method 2") +test_that("simple kurtosis1DS, method 2", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) - res <- kurtosisDS1("input", 2) + res <- kurtosis1DS("input", 2) expect_length(res, 3) expect_equal(class(res), "list") @@ -51,11 +51,11 @@ test_that("simple kurtosisDS1, method 2", { expect_equal(res$class, "numeric") }) -# context("kurtosisDS1::smk::method 3") -test_that("simple kurtosisDS1, method 3", { +# context("kurtosis1DS::smk::method 3") +test_that("simple kurtosis1DS, method 3", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) - res <- kurtosisDS1("input", 3) + res <- kurtosis1DS("input", 3) expect_length(res, 3) expect_equal(class(res), "list") @@ -66,21 +66,21 @@ test_that("simple kurtosisDS1, method 3", { expect_equal(res$class, "numeric") }) -test_that("kurtosisDS1 throws error when object does not exist", { - expect_error(kurtosisDS1("nonexistent_object", 1), regexp = "does not exist") +test_that("kurtosis1DS throws error when object does not exist", { + expect_error(kurtosis1DS("nonexistent_object", 1), regexp = "does not exist") }) -test_that("kurtosisDS1 throws error when object is not numeric or integer", { +test_that("kurtosis1DS throws error when object is not numeric or integer", { bad_input <- c("a", "b", "c") - expect_error(kurtosisDS1("bad_input", 1), regexp = "must be of type numeric or integer") + expect_error(kurtosis1DS("bad_input", 1), regexp = "must be of type numeric or integer") }) -test_that("kurtosisDS1 gives the same result for integer input as for numeric", { +test_that("kurtosis1DS gives the same result for integer input as for numeric", { input.numeric <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) input.integer <- as.integer(input.numeric) - res.numeric <- kurtosisDS1("input.numeric", 1) - res.integer <- kurtosisDS1("input.integer", 1) + res.numeric <- kurtosis1DS("input.numeric", 1) + res.integer <- kurtosis1DS("input.integer", 1) expect_equal(res.integer$class, "integer") expect_equal(res.integer[names(res.integer) != "class"], res.numeric[names(res.numeric) != "class"]) @@ -90,6 +90,6 @@ test_that("kurtosisDS1 gives the same result for integer input as for numeric", # Done # -# context("kurtosisDS1::smk::shutdown") +# context("kurtosis1DS::smk::shutdown") -# context("kurtosisDS1::smk::done") +# context("kurtosis1DS::smk::done") diff --git a/tests/testthat/test-smk-kurtosisDS2.R b/tests/testthat/test-smk-kurtosis2DS.R similarity index 70% rename from tests/testthat/test-smk-kurtosisDS2.R rename to tests/testthat/test-smk-kurtosis2DS.R index f0b880f0..945571a6 100644 --- a/tests/testthat/test-smk-kurtosisDS2.R +++ b/tests/testthat/test-smk-kurtosis2DS.R @@ -13,7 +13,7 @@ # Set up # -# context("kurtosisDS2::smk::setup") +# context("kurtosis2DS::smk::setup") set.standard.disclosure.settings() @@ -21,12 +21,12 @@ set.standard.disclosure.settings() # Tests # -# context("kurtosisDS2::smk") -test_that("simple kurtosisDS2", { +# context("kurtosis2DS::smk") +test_that("simple kurtosis2DS", { input <- c(1.0, 2.0, 2.0, 3.0, 3.0) global.mean <- 2.5 - res <- kurtosisDS2("input", global.mean) + res <- kurtosis2DS("input", global.mean) expect_length(res, 4) expect_equal(class(res), "list") @@ -39,21 +39,21 @@ test_that("simple kurtosisDS2", { expect_equal(res$class, "numeric") }) -test_that("kurtosisDS2 throws error when object does not exist", { - expect_error(kurtosisDS2("nonexistent_object", 2.5), regexp = "does not exist") +test_that("kurtosis2DS throws error when object does not exist", { + expect_error(kurtosis2DS("nonexistent_object", 2.5), regexp = "does not exist") }) -test_that("kurtosisDS2 throws error when object is not numeric or integer", { +test_that("kurtosis2DS throws error when object is not numeric or integer", { bad_input <- c("a", "b", "c") - expect_error(kurtosisDS2("bad_input", 2.5), regexp = "must be of type numeric or integer") + expect_error(kurtosis2DS("bad_input", 2.5), regexp = "must be of type numeric or integer") }) -test_that("kurtosisDS2 gives the same result for integer input as for numeric", { +test_that("kurtosis2DS gives the same result for integer input as for numeric", { input.numeric <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) input.integer <- as.integer(input.numeric) - res.numeric <- kurtosisDS2("input.numeric", 1.8) - res.integer <- kurtosisDS2("input.integer", 1.8) + res.numeric <- kurtosis2DS("input.numeric", 1.8) + res.integer <- kurtosis2DS("input.integer", 1.8) expect_equal(res.integer$class, "integer") expect_equal(res.integer[names(res.integer) != "class"], res.numeric[names(res.numeric) != "class"]) @@ -63,6 +63,6 @@ test_that("kurtosisDS2 gives the same result for integer input as for numeric", # Done # -# context("kurtosisDS2::smk::shutdown") +# context("kurtosis2DS::smk::shutdown") -# context("kurtosisDS2::smk::done") +# context("kurtosis2DS::smk::done") diff --git a/tests/testthat/test-smk-lexisDS1.R b/tests/testthat/test-smk-lexis1DS.R similarity index 57% rename from tests/testthat/test-smk-lexisDS1.R rename to tests/testthat/test-smk-lexis1DS.R index c0453a77..3d4b2ffa 100644 --- a/tests/testthat/test-smk-lexisDS1.R +++ b/tests/testthat/test-smk-lexis1DS.R @@ -2,7 +2,7 @@ # Set up # -# context("lexisDS1::smk::setup") +# context("lexis1DS::smk::setup") set.standard.disclosure.settings() @@ -10,11 +10,11 @@ set.standard.disclosure.settings() # Tests # -# context("lexisDS1::smk") -test_that("simple lexisDS1", { +# context("lexis1DS::smk") +test_that("simple lexis1DS", { input <- c(1, 5, 3, 9, 2) - res <- lexisDS1("input") + res <- lexis1DS("input") expect_equal(class(res), "list") expect_equal(names(res), "max.time") @@ -23,9 +23,9 @@ test_that("simple lexisDS1", { expect_lte(res$max.time, 9 * 1.05) }) -test_that("lexisDS1 throws error when object does not exist", { +test_that("lexis1DS throws error when object does not exist", { expect_error( - lexisDS1("nonexistent_object"), + lexis1DS("nonexistent_object"), regexp = "does not exist" ) }) @@ -34,6 +34,6 @@ test_that("lexisDS1 throws error when object does not exist", { # Done # -# context("lexisDS1::smk::shutdown") +# context("lexis1DS::smk::shutdown") -# context("lexisDS1::smk::done") +# context("lexis1DS::smk::done") diff --git a/tests/testthat/test-smk-lexisDS2.R b/tests/testthat/test-smk-lexis2DS.R similarity index 76% rename from tests/testthat/test-smk-lexisDS2.R rename to tests/testthat/test-smk-lexis2DS.R index b29655cb..103d11c4 100644 --- a/tests/testthat/test-smk-lexisDS2.R +++ b/tests/testthat/test-smk-lexis2DS.R @@ -2,7 +2,7 @@ # Set up # -# context("lexisDS2::smk::setup") +# context("lexis2DS::smk::setup") set.standard.disclosure.settings() @@ -10,28 +10,28 @@ set.standard.disclosure.settings() # Tests # -# context("lexisDS2::smk::datatext") -test_that("simple lexisDS2, datatext names a whole data.frame", { +# context("lexis2DS::smk::datatext") +test_that("simple lexis2DS, datatext names a whole data.frame", { D <- data.frame(id = 1:6, start = rep(0, 6), end = rep(5, 6), status = rep(1, 6), extra = 101:106) - res <- lexisDS2( + res <- lexis2DS( datatext = "D", intervalWidth = "10", maxmaxtime = 10, idCol = "D$id", entryCol = "D$start", exitCol = "D$end", statusCol = "D$status", vartext = NULL ) expect_equal(class(res), "list") # carried-forward columns must keep D's own column names, not be corrupted - # or misaligned by the data.frame construction (see lexisDS2 datatext/vartext handling) + # or misaligned by the data.frame construction (see lexis2DS datatext/vartext handling) expect_true(all(c("id", "start", "end", "status", "extra") %in% names(res$expanded.table))) expect_equal(res$expanded.table$extra, 101:106) expect_equal(nrow(res$expanded.table), 6) }) -# context("lexisDS2::smk::vartext") -test_that("simple lexisDS2, vartext names individual $-qualified columns", { +# context("lexis2DS::smk::vartext") +test_that("simple lexis2DS, vartext names individual $-qualified columns", { D <- data.frame(id = 1:6, start = rep(0, 6), end = rep(5, 6), status = rep(1, 6), extra = 101:106, extra2 = 201:206) - res <- lexisDS2( + res <- lexis2DS( datatext = NULL, intervalWidth = "10", maxmaxtime = 10, idCol = "D$id", entryCol = "D$start", exitCol = "D$end", statusCol = "D$status", vartext = "D$extra,D$extra2" @@ -43,11 +43,11 @@ test_that("simple lexisDS2, vartext names individual $-qualified columns", { expect_equal(res$expanded.table$D.extra2, 201:206) }) -# context("lexisDS2::smk::no.carry.forward") -test_that("simple lexisDS2, no datatext or vartext", { +# context("lexis2DS::smk::no.carry.forward") +test_that("simple lexis2DS, no datatext or vartext", { D <- data.frame(id = 1:6, start = rep(0, 6), end = rep(5, 6), status = rep(1, 6)) - res <- lexisDS2( + res <- lexis2DS( datatext = NULL, intervalWidth = "10", maxmaxtime = 10, idCol = "D$id", entryCol = "D$start", exitCol = "D$end", statusCol = "D$status", vartext = NULL ) @@ -56,11 +56,11 @@ test_that("simple lexisDS2, no datatext or vartext", { expect_equal(nrow(res$expanded.table), 6) }) -test_that("lexisDS2 throws error when object does not exist", { +test_that("lexis2DS throws error when object does not exist", { D <- data.frame(id = 1:6, start = rep(0, 6), end = rep(5, 6), status = rep(1, 6)) expect_error( - lexisDS2( + lexis2DS( datatext = NULL, intervalWidth = "10", maxmaxtime = 10, idCol = "D$id", entryCol = "D$start", exitCol = "nonexistent_object", statusCol = "D$status", vartext = NULL ), @@ -68,11 +68,11 @@ test_that("lexisDS2 throws error when object does not exist", { ) }) -# context("lexisDS2::smk::no.entryCol") -test_that("simple lexisDS2, entryCol not given defaults entry times to 0", { +# context("lexis2DS::smk::no.entryCol") +test_that("simple lexis2DS, entryCol not given defaults entry times to 0", { D <- data.frame(id = 1:6, end = rep(5, 6), status = rep(1, 6)) - res <- lexisDS2( + res <- lexis2DS( datatext = NULL, intervalWidth = "10", maxmaxtime = 10, idCol = "D$id", entryCol = NULL, exitCol = "D$end", statusCol = "D$status", vartext = NULL ) @@ -86,6 +86,6 @@ test_that("simple lexisDS2, entryCol not given defaults entry times to 0", { # Done # -# context("lexisDS2::smk::shutdown") +# context("lexis2DS::smk::shutdown") -# context("lexisDS2::smk::done") +# context("lexis2DS::smk::done") diff --git a/tests/testthat/test-smk-lmerSLMADS2.R b/tests/testthat/test-smk-lmerSLMA2DS.R similarity index 75% rename from tests/testthat/test-smk-lmerSLMADS2.R rename to tests/testthat/test-smk-lmerSLMA2DS.R index e4d84aad..9f8af881 100644 --- a/tests/testthat/test-smk-lmerSLMADS2.R +++ b/tests/testthat/test-smk-lmerSLMA2DS.R @@ -2,7 +2,7 @@ # Set up # -# context("lmerSLMADS2::smk::setup") +# context("lmerSLMA2DS::smk::setup") set.standard.disclosure.settings() @@ -10,8 +10,8 @@ set.standard.disclosure.settings() # Tests # -# context("lmerSLMADS2::smk::random intercept") -test_that("simple lmerSLMADS2, random intercept", { +# context("lmerSLMA2DS::smk::random intercept") +test_that("simple lmerSLMA2DS, random intercept", { set.seed(42) D <- data.frame( group = factor(rep(1:4, each = 6)), @@ -20,7 +20,7 @@ test_that("simple lmerSLMADS2, random intercept", { D$y <- 2 + 0.5 * D$x + rep(rnorm(4, sd = 1), each = 6) + rnorm(24, sd = 0.3) res <- suppressWarnings( - lmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + lmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "D", REML = TRUE, control_type = NULL, control_value.transmit = NULL, optimizer = NULL, verbose = 0) @@ -38,9 +38,9 @@ test_that("simple lmerSLMADS2, random intercept", { expect_equal(res$sigma, 0.3874094, tolerance = 1e-5) }) -test_that("lmerSLMADS2 throws error when dataName does not exist", { +test_that("lmerSLMA2DS throws error when dataName does not exist", { expect_error( - lmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + lmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "nonexistent_object", REML = TRUE, control_type = NULL, control_value.transmit = NULL, optimizer = NULL, verbose = 0), @@ -48,10 +48,10 @@ test_that("lmerSLMADS2 throws error when dataName does not exist", { ) }) -test_that("lmerSLMADS2 throws error when dataName is not a data.frame or list", { +test_that("lmerSLMA2DS throws error when dataName is not a data.frame or list", { bad_input <- c(1, 2, 3) expect_error( - lmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + lmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "bad_input", REML = TRUE, control_type = NULL, control_value.transmit = NULL, optimizer = NULL, verbose = 0), @@ -59,7 +59,7 @@ test_that("lmerSLMADS2 throws error when dataName is not a data.frame or list", ) }) -test_that("lmerSLMADS2 gives the same result for data as a list as for a data.frame", { +test_that("lmerSLMA2DS gives the same result for data as a list as for a data.frame", { set.seed(42) D <- data.frame( group = factor(rep(1:4, each = 6)), @@ -68,10 +68,10 @@ test_that("lmerSLMADS2 gives the same result for data as a list as for a data.fr D$y <- 2 + 0.5 * D$x + rep(rnorm(4, sd = 1), each = 6) + rnorm(24, sd = 0.3) D.list <- as.list(D) - res.df <- suppressWarnings(lmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + res.df <- suppressWarnings(lmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "D", REML = TRUE, control_type = NULL, control_value.transmit = NULL, optimizer = NULL, verbose = 0)) - res.list <- suppressWarnings(lmerSLMADS2(formula = stats::as.formula("y ~ x + (1|group)"), + res.list <- suppressWarnings(lmerSLMA2DS(formula = stats::as.formula("y ~ x + (1|group)"), offset = NULL, weights = NULL, dataName = "D.list", REML = TRUE, control_type = NULL, control_value.transmit = NULL, optimizer = NULL, verbose = 0)) @@ -82,6 +82,6 @@ test_that("lmerSLMADS2 gives the same result for data as a list as for a data.fr # Done # -# context("lmerSLMADS2::smk::shutdown") +# context("lmerSLMA2DS::smk::shutdown") -# context("lmerSLMADS2::smk::done") +# context("lmerSLMA2DS::smk::done") diff --git a/tests/testthat/test-smk-matrixDet1DS.R b/tests/testthat/test-smk-matrixDet1DS.R new file mode 100644 index 00000000..cb9b402f --- /dev/null +++ b/tests/testthat/test-smk-matrixDet1DS.R @@ -0,0 +1,54 @@ + +# +# Set up +# + +# context("matrixDet1DS::smk::setup") + +set.standard.disclosure.settings() + +# +# Tests +# + +test_that("simple matrixDet1DS passes with matrix of sufficient dimensions", { + M1 <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 10), 3, 3) + res <- matrixDet1DS("M1", logarithm=FALSE) + + expect_true(is.list(res)) + expect_equal(res$matrix.determinant, determinant(M1, logarithm=FALSE)) +}) + +test_that("matrixDet1DS errors when serverside object does not exist", { + expect_error(matrixDet1DS("nonexistent_object", logarithm=FALSE), regexp = "does not exist") +}) + +test_that("matrixDet1DS errors when input is wrong type", { + bad_input <- c("a", "b", "c") + expect_error(matrixDet1DS("bad_input", logarithm=FALSE), regexp = "must be of type") +}) + +test_that("matrixDet1DS errors when matrix is too small (disclosure guard)", { + M1x1 <- matrix(7, 1, 1) + M2x2 <- matrix(c(1, 2, 3, 4), 2, 2) + + expect_error(matrixDet1DS("M1x1", logarithm=FALSE), regexp = "too small") + expect_error(matrixDet1DS("M2x2", logarithm=FALSE), regexp = "too small") +}) + +test_that("matrixDet1DS is blocked in non-permissive mode", { + options(datashield.privacyControlLevel = "non-permissive") + on.exit(options(datashield.privacyControlLevel = NULL), add = TRUE) + M1 <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 10), 3, 3) + expect_error(matrixDet1DS("M1", logarithm=FALSE), regexp = "non-permissive") +}) + +test_that("matrixDet1DS gives the same result for a data.frame as for a matrix", { + M1 <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 10), 3, 3) + M1.df <- as.data.frame(M1) + + res.matrix <- matrixDet1DS("M1", logarithm=FALSE) + res.df <- matrixDet1DS("M1.df", logarithm=FALSE) + + expect_equal(res.df, res.matrix) +}) diff --git a/tests/testthat/test-smk-matrixDet2DS.R b/tests/testthat/test-smk-matrixDet2DS.R new file mode 100644 index 00000000..26fd542f --- /dev/null +++ b/tests/testthat/test-smk-matrixDet2DS.R @@ -0,0 +1,39 @@ + +# +# Set up +# + +# context("matrixDet2DS::smk::setup") + +set.standard.disclosure.settings() + +# +# Tests +# + +test_that("simple matrixDet2DS", { + M1 <- matrix(c(1, 2, 3, 4), 2, 2) + + res <- matrixDet2DS("M1", logarithm=FALSE) + + expect_equal(res, determinant(M1, logarithm=FALSE)) +}) + +test_that("matrixDet2DS errors when serverside object does not exist", { + expect_error(matrixDet2DS("nonexistent_object", logarithm=FALSE), regexp = "does not exist") +}) + +test_that("matrixDet2DS errors when input is wrong type", { + bad_input <- c("a", "b", "c") + expect_error(matrixDet2DS("bad_input", logarithm=FALSE), regexp = "must be of type") +}) + +test_that("matrixDet2DS gives the same result for a data.frame as for a matrix", { + M1 <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 10), 3, 3) + M1.df <- as.data.frame(M1) + + res.matrix <- matrixDet2DS("M1", logarithm=FALSE) + res.df <- matrixDet2DS("M1.df", logarithm=FALSE) + + expect_equal(res.df, res.matrix) +}) diff --git a/tests/testthat/test-smk-matrixDetDS1.R b/tests/testthat/test-smk-matrixDetDS1.R deleted file mode 100644 index 7b5be4a1..00000000 --- a/tests/testthat/test-smk-matrixDetDS1.R +++ /dev/null @@ -1,54 +0,0 @@ - -# -# Set up -# - -# context("matrixDetDS1::smk::setup") - -set.standard.disclosure.settings() - -# -# Tests -# - -test_that("simple matrixDetDS1 passes with matrix of sufficient dimensions", { - M1 <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 10), 3, 3) - res <- matrixDetDS1("M1", logarithm=FALSE) - - expect_true(is.list(res)) - expect_equal(res$matrix.determinant, determinant(M1, logarithm=FALSE)) -}) - -test_that("matrixDetDS1 errors when serverside object does not exist", { - expect_error(matrixDetDS1("nonexistent_object", logarithm=FALSE), regexp = "does not exist") -}) - -test_that("matrixDetDS1 errors when input is wrong type", { - bad_input <- c("a", "b", "c") - expect_error(matrixDetDS1("bad_input", logarithm=FALSE), regexp = "must be of type") -}) - -test_that("matrixDetDS1 errors when matrix is too small (disclosure guard)", { - M1x1 <- matrix(7, 1, 1) - M2x2 <- matrix(c(1, 2, 3, 4), 2, 2) - - expect_error(matrixDetDS1("M1x1", logarithm=FALSE), regexp = "too small") - expect_error(matrixDetDS1("M2x2", logarithm=FALSE), regexp = "too small") -}) - -test_that("matrixDetDS1 is blocked in non-permissive mode", { - options(datashield.privacyControlLevel = "non-permissive") - on.exit(options(datashield.privacyControlLevel = NULL), add = TRUE) - M1 <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 10), 3, 3) - expect_error(matrixDetDS1("M1", logarithm=FALSE), regexp = "non-permissive") -}) - -test_that("matrixDetDS1 gives the same result for a data.frame as for a matrix", { - M1 <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 10), 3, 3) - M1.df <- as.data.frame(M1) - - res.matrix <- matrixDetDS1("M1", logarithm=FALSE) - res.df <- matrixDetDS1("M1.df", logarithm=FALSE) - - expect_equal(res.df, res.matrix) -}) diff --git a/tests/testthat/test-smk-matrixDetDS2.R b/tests/testthat/test-smk-matrixDetDS2.R deleted file mode 100644 index da9395ba..00000000 --- a/tests/testthat/test-smk-matrixDetDS2.R +++ /dev/null @@ -1,39 +0,0 @@ - -# -# Set up -# - -# context("matrixDetDS2::smk::setup") - -set.standard.disclosure.settings() - -# -# Tests -# - -test_that("simple matrixDetDS2", { - M1 <- matrix(c(1, 2, 3, 4), 2, 2) - - res <- matrixDetDS2("M1", logarithm=FALSE) - - expect_equal(res, determinant(M1, logarithm=FALSE)) -}) - -test_that("matrixDetDS2 errors when serverside object does not exist", { - expect_error(matrixDetDS2("nonexistent_object", logarithm=FALSE), regexp = "does not exist") -}) - -test_that("matrixDetDS2 errors when input is wrong type", { - bad_input <- c("a", "b", "c") - expect_error(matrixDetDS2("bad_input", logarithm=FALSE), regexp = "must be of type") -}) - -test_that("matrixDetDS2 gives the same result for a data.frame as for a matrix", { - M1 <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 10), 3, 3) - M1.df <- as.data.frame(M1) - - res.matrix <- matrixDetDS2("M1", logarithm=FALSE) - res.df <- matrixDetDS2("M1.df", logarithm=FALSE) - - expect_equal(res.df, res.matrix) -}) diff --git a/tests/testthat/test-smk-skewnessDS1.R b/tests/testthat/test-smk-skewness1DS.R similarity index 70% rename from tests/testthat/test-smk-skewnessDS1.R rename to tests/testthat/test-smk-skewness1DS.R index 7f272db8..8e756753 100644 --- a/tests/testthat/test-smk-skewnessDS1.R +++ b/tests/testthat/test-smk-skewness1DS.R @@ -13,7 +13,7 @@ # Set up # -# context("skewnessDS1::smk::setup") +# context("skewness1DS::smk::setup") set.standard.disclosure.settings() @@ -21,11 +21,11 @@ set.standard.disclosure.settings() # Tests # -# context("skewnessDS1::smk::method 1") -test_that("simple skewnessDS1, method 1", { +# context("skewness1DS::smk::method 1") +test_that("simple skewness1DS, method 1", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) - res <- skewnessDS1("input", 1) + res <- skewness1DS("input", 1) expect_length(res, 3) expect_equal(class(res), "list") @@ -36,11 +36,11 @@ test_that("simple skewnessDS1, method 1", { expect_equal(res$class, "numeric") }) -# context("skewnessDS1::smk::method 2") -test_that("simple skewnessDS1, method 2", { +# context("skewness1DS::smk::method 2") +test_that("simple skewness1DS, method 2", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) - res <- skewnessDS1("input", 2) + res <- skewness1DS("input", 2) expect_length(res, 3) expect_equal(class(res), "list") @@ -51,11 +51,11 @@ test_that("simple skewnessDS1, method 2", { expect_equal(res$class, "numeric") }) -# context("skewnessDS1::smk::method 3") -test_that("simple skewnessDS1, method 3", { +# context("skewness1DS::smk::method 3") +test_that("simple skewness1DS, method 3", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) - res <- skewnessDS1("input", 3) + res <- skewness1DS("input", 3) expect_length(res, 3) expect_equal(class(res), "list") @@ -66,21 +66,21 @@ test_that("simple skewnessDS1, method 3", { expect_equal(res$class, "numeric") }) -test_that("skewnessDS1 throws error when object does not exist", { - expect_error(skewnessDS1("nonexistent_object", 1), regexp = "does not exist") +test_that("skewness1DS throws error when object does not exist", { + expect_error(skewness1DS("nonexistent_object", 1), regexp = "does not exist") }) -test_that("skewnessDS1 throws error when object is not numeric or integer", { +test_that("skewness1DS throws error when object is not numeric or integer", { bad_input <- c("a", "b", "c") - expect_error(skewnessDS1("bad_input", 1), regexp = "must be of type numeric or integer") + expect_error(skewness1DS("bad_input", 1), regexp = "must be of type numeric or integer") }) -test_that("skewnessDS1 gives the same result for integer input as for numeric", { +test_that("skewness1DS gives the same result for integer input as for numeric", { input.numeric <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) input.integer <- as.integer(input.numeric) - res.numeric <- skewnessDS1("input.numeric", 1) - res.integer <- skewnessDS1("input.integer", 1) + res.numeric <- skewness1DS("input.numeric", 1) + res.integer <- skewness1DS("input.integer", 1) expect_equal(res.integer$class, "integer") expect_equal(res.integer[names(res.integer) != "class"], res.numeric[names(res.numeric) != "class"]) @@ -90,6 +90,6 @@ test_that("skewnessDS1 gives the same result for integer input as for numeric", # Done # -# context("skewnessDS1::smk::shutdown") +# context("skewness1DS::smk::shutdown") -# context("skewnessDS1::smk::done") +# context("skewness1DS::smk::done") diff --git a/tests/testthat/test-smk-skewnessDS2.R b/tests/testthat/test-smk-skewness2DS.R similarity index 70% rename from tests/testthat/test-smk-skewnessDS2.R rename to tests/testthat/test-smk-skewness2DS.R index 6e36b51e..5403264a 100644 --- a/tests/testthat/test-smk-skewnessDS2.R +++ b/tests/testthat/test-smk-skewness2DS.R @@ -13,7 +13,7 @@ # Set up # -# context("skewnessDS2::smk::setup") +# context("skewness2DS::smk::setup") set.standard.disclosure.settings() @@ -21,12 +21,12 @@ set.standard.disclosure.settings() # Tests # -# context("skewnessDS2::smk") -test_that("simple skewnessDS2", { +# context("skewness2DS::smk") +test_that("simple skewness2DS", { input <- c(1.0, 2.0, 2.0, 3.0, 3.0) global.mean <- 2.5 - res <- skewnessDS2("input", global.mean) + res <- skewness2DS("input", global.mean) expect_length(res, 4) expect_equal(class(res), "list") @@ -39,21 +39,21 @@ test_that("simple skewnessDS2", { expect_equal(res$class, "numeric") }) -test_that("skewnessDS2 throws error when object does not exist", { - expect_error(skewnessDS2("nonexistent_object", 2.5), regexp = "does not exist") +test_that("skewness2DS throws error when object does not exist", { + expect_error(skewness2DS("nonexistent_object", 2.5), regexp = "does not exist") }) -test_that("skewnessDS2 throws error when object is not numeric or integer", { +test_that("skewness2DS throws error when object is not numeric or integer", { bad_input <- c("a", "b", "c") - expect_error(skewnessDS2("bad_input", 2.5), regexp = "must be of type numeric or integer") + expect_error(skewness2DS("bad_input", 2.5), regexp = "must be of type numeric or integer") }) -test_that("skewnessDS2 gives the same result for integer input as for numeric", { +test_that("skewness2DS gives the same result for integer input as for numeric", { input.numeric <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) input.integer <- as.integer(input.numeric) - res.numeric <- skewnessDS2("input.numeric", 1.8) - res.integer <- skewnessDS2("input.integer", 1.8) + res.numeric <- skewness2DS("input.numeric", 1.8) + res.integer <- skewness2DS("input.integer", 1.8) expect_equal(res.integer$class, "integer") expect_equal(res.integer[names(res.integer) != "class"], res.numeric[names(res.numeric) != "class"]) @@ -63,6 +63,6 @@ test_that("skewnessDS2 gives the same result for integer input as for numeric", # Done # -# context("skewnessDS2::smk::shutdown") +# context("skewness2DS::smk::shutdown") -# context("skewnessDS2::smk::done") +# context("skewness2DS::smk::done") diff --git a/tests/testthat/test-smk-tableDS2.R b/tests/testthat/test-smk-table2DS.R similarity index 63% rename from tests/testthat/test-smk-tableDS2.R rename to tests/testthat/test-smk-table2DS.R index c787816c..54cfb53f 100644 --- a/tests/testthat/test-smk-tableDS2.R +++ b/tests/testthat/test-smk-table2DS.R @@ -2,7 +2,7 @@ # Set up # -# context("tableDS2::smk::setup") +# context("table2DS::smk::setup") set.standard.disclosure.settings() @@ -10,13 +10,13 @@ set.standard.disclosure.settings() # Tests # -# context("tableDS2::smk") -test_that("simple tableDS2", { +# context("table2DS::smk") +test_that("simple table2DS", { rvar <- factor(rep(c("a", "b"), each = 10)) cvar <- factor(rep(rep(c("x", "y"), each = 5), 2)) res.assign <- tableDS.assign("rvar", "cvar", NULL, "a,b", "x,y", NULL, NULL, "no") - res <- tableDS2("res.assign", "rvar", "cvar", NULL) + res <- table2DS("res.assign", "rvar", "cvar", NULL) expect_equal(class(res), "list") expect_equal( @@ -27,9 +27,9 @@ test_that("simple tableDS2", { expect_equal(res$table.cell.IDs, 1:4) }) -test_that("tableDS2 throws error when object does not exist", { +test_that("table2DS throws error when object does not exist", { expect_error( - tableDS2("nonexistent_object", "rvar", "cvar", NULL), + table2DS("nonexistent_object", "rvar", "cvar", NULL), regexp = "does not exist" ) }) @@ -38,6 +38,6 @@ test_that("tableDS2 throws error when object does not exist", { # Done # -# context("tableDS2::smk::shutdown") +# context("table2DS::smk::shutdown") -# context("tableDS2::smk::done") +# context("table2DS::smk::done") From 27016ad1c73f23f0e624d4fe188d6e6894b0d12e Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 2 Nov 2026 23:06:18 +0000 Subject: [PATCH 4/6] Minor updates --- .../hp-laptop-quay_perf-profile.csv | 8 +- ...{test-smk-BooleDS.R => test-smk-booleDS.R} | 110 +++++++++--------- 2 files changed, 59 insertions(+), 59 deletions(-) rename tests/testthat/{test-smk-BooleDS.R => test-smk-booleDS.R} (69%) diff --git a/tests/testthat/perf_files/hp-laptop-quay_perf-profile.csv b/tests/testthat/perf_files/hp-laptop-quay_perf-profile.csv index 7ab03037..b66f7cfb 100644 --- a/tests/testthat/perf_files/hp-laptop-quay_perf-profile.csv +++ b/tests/testthat/perf_files/hp-laptop-quay_perf-profile.csv @@ -1,5 +1,5 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"meanDS::perf::numeric::0","11557.1204746495","0.5","2" -"meanDS::perf::numberAndNA::0","11718.8520447749","0.5","2" -"varDS::perf::numeric::0","12758.5511531009","0.5","2" -"varDS::perf::numberAndNA::0","12545.8819532662","0.5","2" +"meanDS::perf::numeric::0","8870.0","0.5","2" +"meanDS::perf::numberAndNA::0","8730.0","0.5","2" +"varDS::perf::numeric::0","9450.0","0.5","2" +"varDS::perf::numberAndNA::0","9470.0","0.5","2" diff --git a/tests/testthat/test-smk-BooleDS.R b/tests/testthat/test-smk-booleDS.R similarity index 69% rename from tests/testthat/test-smk-BooleDS.R rename to tests/testthat/test-smk-booleDS.R index e517e6f1..8af0e976 100644 --- a/tests/testthat/test-smk-BooleDS.R +++ b/tests/testthat/test-smk-booleDS.R @@ -13,7 +13,7 @@ # Set up # -# context("BooleDS::smk::setup") +# context("booleDS::smk::setup") set.standard.disclosure.settings() @@ -21,11 +21,11 @@ set.standard.disclosure.settings() # Tests # -# context("BooleDS::smk::simple equal") -test_that("simple BooleDS, equal numeric", { +# context("booleDS::smk::simple equal") +test_that("simple booleDS, equal numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 1, "NA", TRUE) + res <- booleDS("input$v1", "input$v2", 1, "NA", TRUE) expect_length(res, 5) expect_equal(class(res), "numeric") @@ -36,10 +36,10 @@ test_that("simple BooleDS, equal numeric", { expect_equal(res[5], 0) }) -test_that("simple BooleDS, equal logical", { +test_that("simple booleDS, equal logical", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 1, "NA", FALSE) + res <- booleDS("input$v1", "input$v2", 1, "NA", FALSE) expect_length(res, 5) expect_equal(class(res), "logical") @@ -50,11 +50,11 @@ test_that("simple BooleDS, equal logical", { expect_equal(res[5], FALSE) }) -# context("BooleDS::smk::simple not-equal") -test_that("simple BooleDS, not-equal numeric", { +# context("booleDS::smk::simple not-equal") +test_that("simple booleDS, not-equal numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 2, "NA", TRUE) + res <- booleDS("input$v1", "input$v2", 2, "NA", TRUE) expect_length(res, 5) expect_equal(class(res), "numeric") @@ -65,10 +65,10 @@ test_that("simple BooleDS, not-equal numeric", { expect_equal(res[5], 1) }) -test_that("simple BooleDS, not-equal logical", { +test_that("simple booleDS, not-equal logical", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 2, "NA", FALSE) + res <- booleDS("input$v1", "input$v2", 2, "NA", FALSE) expect_length(res, 5) expect_equal(class(res), "logical") @@ -79,11 +79,11 @@ test_that("simple BooleDS, not-equal logical", { expect_equal(res[5], TRUE) }) -# context("BooleDS::smk::simple less-than") -test_that("simple BooleDS, less-than numeric", { +# context("booleDS::smk::simple less-than") +test_that("simple booleDS, less-than numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 3, "NA", TRUE) + res <- booleDS("input$v1", "input$v2", 3, "NA", TRUE) expect_length(res, 5) expect_equal(class(res), "numeric") @@ -94,10 +94,10 @@ test_that("simple BooleDS, less-than numeric", { expect_equal(res[5], 0) }) -test_that("simple BooleDS, less-than logical", { +test_that("simple booleDS, less-than logical", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 3, "NA", FALSE) + res <- booleDS("input$v1", "input$v2", 3, "NA", FALSE) expect_length(res, 5) expect_equal(class(res), "logical") @@ -108,11 +108,11 @@ test_that("simple BooleDS, less-than logical", { expect_equal(res[5], FALSE) }) -# context("BooleDS::smk::simple less-than-equal") -test_that("simple BooleDS, less-than-equal numeric", { +# context("booleDS::smk::simple less-than-equal") +test_that("simple booleDS, less-than-equal numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 4, "NA", TRUE) + res <- booleDS("input$v1", "input$v2", 4, "NA", TRUE) expect_length(res, 5) expect_equal(class(res), "numeric") @@ -123,10 +123,10 @@ test_that("simple BooleDS, less-than-equal numeric", { expect_equal(res[5], 0) }) -test_that("simple BooleDS, less-than-equal logical", { +test_that("simple booleDS, less-than-equal logical", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 4, "NA", FALSE) + res <- booleDS("input$v1", "input$v2", 4, "NA", FALSE) expect_length(res, 5) expect_equal(class(res), "logical") @@ -137,11 +137,11 @@ test_that("simple BooleDS, less-than-equal logical", { expect_equal(res[5], FALSE) }) -# context("BooleDS::smk::simple greater-than") -test_that("simple BooleDS, greater-than numeric", { +# context("booleDS::smk::simple greater-than") +test_that("simple booleDS, greater-than numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 5, "NA", TRUE) + res <- booleDS("input$v1", "input$v2", 5, "NA", TRUE) expect_length(res, 5) expect_equal(class(res), "numeric") @@ -152,10 +152,10 @@ test_that("simple BooleDS, greater-than numeric", { expect_equal(res[5], 1) }) -test_that("simple BooleDS, greater-than logical", { +test_that("simple booleDS, greater-than logical", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 5, "NA", FALSE) + res <- booleDS("input$v1", "input$v2", 5, "NA", FALSE) expect_length(res, 5) expect_equal(class(res), "logical") @@ -166,11 +166,11 @@ test_that("simple BooleDS, greater-than logical", { expect_equal(res[5], TRUE) }) -# context("BooleDS::smk::simple greater-than-equal") -test_that("simple BooleDS, greater-than-equal numeric", { +# context("booleDS::smk::simple greater-than-equal") +test_that("simple booleDS, greater-than-equal numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 6, "NA", TRUE) + res <- booleDS("input$v1", "input$v2", 6, "NA", TRUE) expect_length(res, 5) expect_equal(class(res), "numeric") @@ -181,10 +181,10 @@ test_that("simple BooleDS, greater-than-equal numeric", { expect_equal(res[5], 1) }) -test_that("simple BooleDS, greater-than-equal logical", { +test_that("simple booleDS, greater-than-equal logical", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) - res <- BooleDS("input$v1", "input$v2", 6, "NA", FALSE) + res <- booleDS("input$v1", "input$v2", 6, "NA", FALSE) expect_length(res, 5) expect_equal(class(res), "logical") @@ -195,11 +195,11 @@ test_that("simple BooleDS, greater-than-equal logical", { expect_equal(res[5], TRUE) }) -# context("BooleDS::smk::na-check numeric") -test_that("na-check BooleDS, numeric, NA=NA", { +# context("booleDS::smk::na-check numeric") +test_that("na-check booleDS, numeric, NA=NA", { input <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, NA), v2 = c(NA, 3.0, 2.0, 1.0, NA)) - res <- BooleDS("input$v1", "input$v2", 1, "NA", TRUE) + res <- booleDS("input$v1", "input$v2", 1, "NA", TRUE) expect_length(res, 5) expect_equal(class(res), "numeric") @@ -210,10 +210,10 @@ test_that("na-check BooleDS, numeric, NA=NA", { expect_true(is.na(res[5])) }) -test_that("na-check BooleDS, numeric, NA=0", { +test_that("na-check booleDS, numeric, NA=0", { input <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, NA), v2 = c(NA, 3.0, 2.0, 1.0, NA)) - res <- BooleDS("input$v1", "input$v2", 1, "0", TRUE) + res <- booleDS("input$v1", "input$v2", 1, "0", TRUE) expect_length(res, 5) expect_equal(class(res), "numeric") @@ -224,10 +224,10 @@ test_that("na-check BooleDS, numeric, NA=0", { expect_equal(res[5], 0) }) -test_that("na-check BooleDS, numeric, NA=1", { +test_that("na-check booleDS, numeric, NA=1", { input <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, NA), v2 = c(NA, 3.0, 2.0, 1.0, NA)) - res <- BooleDS("input$v1", "input$v2", 1, "1", TRUE) + res <- booleDS("input$v1", "input$v2", 1, "1", TRUE) expect_length(res, 5) expect_equal(class(res), "numeric") @@ -238,11 +238,11 @@ test_that("na-check BooleDS, numeric, NA=1", { expect_equal(res[5], 1) }) -# context("BooleDS::smk::na-check logical") -test_that("na-check BooleDS, logical, NA=NA", { +# context("booleDS::smk::na-check logical") +test_that("na-check booleDS, logical, NA=NA", { input <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, NA), v2 = c(NA, 3.0, 2.0, 1.0, NA)) - res <- BooleDS("input$v1", "input$v2", 1, "NA", FALSE) + res <- booleDS("input$v1", "input$v2", 1, "NA", FALSE) expect_length(res, 5) expect_equal(class(res), "logical") @@ -253,10 +253,10 @@ test_that("na-check BooleDS, logical, NA=NA", { expect_true(is.na(res[5])) }) -test_that("na-check BooleDS, logical, NA=0", { +test_that("na-check booleDS, logical, NA=0", { input <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, NA), v2 = c(NA, 3.0, 2.0, 1.0, NA)) - res <- BooleDS("input$v1", "input$v2", 1, "0", FALSE) + res <- booleDS("input$v1", "input$v2", 1, "0", FALSE) expect_length(res, 5) expect_equal(class(res), "logical") @@ -267,10 +267,10 @@ test_that("na-check BooleDS, logical, NA=0", { expect_equal(res[5], FALSE) }) -test_that("na-check BooleDS, logical, NA=1", { +test_that("na-check booleDS, logical, NA=1", { input <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, NA), v2 = c(NA, 3.0, 2.0, 1.0, NA)) - res <- BooleDS("input$v1", "input$v2", 1, "1", FALSE) + res <- booleDS("input$v1", "input$v2", 1, "1", FALSE) expect_length(res, 5) expect_equal(class(res), "logical") @@ -281,36 +281,36 @@ test_that("na-check BooleDS, logical, NA=1", { expect_equal(res[5], TRUE) }) -test_that("BooleDS errors when V1 object does not exist", { +test_that("booleDS errors when V1 object does not exist", { input <- data.frame(v2 = c(1.0, 2.0, 3.0, 4.0, 5.0)) expect_error( - BooleDS("nonexistent$v1", "input$v2", 1, "NA", TRUE), + booleDS("nonexistent$v1", "input$v2", 1, "NA", TRUE), regexp = "does not exist" ) }) -test_that("BooleDS errors when V2 object does not exist", { +test_that("booleDS errors when V2 object does not exist", { input <- data.frame(v1 = c(1.0, 2.0, 3.0, 4.0, 5.0)) expect_error( - BooleDS("input$v1", "nonexistent$v2", 1, "NA", TRUE), + booleDS("input$v1", "nonexistent$v2", 1, "NA", TRUE), regexp = "does not exist" ) }) -test_that("BooleDS accepts a literal TRUE for V2", { +test_that("booleDS accepts a literal TRUE for V2", { input <- data.frame(flag = c(TRUE, FALSE, TRUE, FALSE)) - res <- BooleDS("input$flag", "TRUE", 1, "NA", TRUE) + res <- booleDS("input$flag", "TRUE", 1, "NA", TRUE) expect_equal(res, c(1, 0, 1, 0)) }) -test_that("BooleDS accepts a literal FALSE for V2", { +test_that("booleDS accepts a literal FALSE for V2", { input <- data.frame(flag = c(TRUE, FALSE, TRUE, FALSE)) - res <- BooleDS("input$flag", "FALSE", 1, "NA", TRUE) + res <- booleDS("input$flag", "FALSE", 1, "NA", TRUE) expect_equal(res, c(0, 1, 0, 1)) }) @@ -319,6 +319,6 @@ test_that("BooleDS accepts a literal FALSE for V2", { # Done # -# context("BooleDS::smk::shutdown") +# context("booleDS::smk::shutdown") -# context("BooleDS::smk::done") +# context("booleDS::smk::done") From 8371ae427a2ea37ff13ec69f2c62d0c6f29328df Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 3 Nov 2026 10:27:51 +0000 Subject: [PATCH 5/6] Fix typo in glmSLMA1DS.R --- R/glmSLMA1DS.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/glmSLMA1DS.R b/R/glmSLMA1DS.R index 05e2d4e8..e54d42b3 100644 --- a/R/glmSLMA1DS.R +++ b/R/glmSLMA1DS.R @@ -20,7 +20,7 @@ #' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands #' @export -glmSLMA11DS<- function(formula, family, weights, offset, data){ +glmSLMA1DS<- function(formula, family, weights, offset, data){ errorMessage="No errors" From 1fe96625864aee01dca06f01ef471082211d3321 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 3 Nov 2026 11:07:32 +0000 Subject: [PATCH 6/6] Updates to documents --- NAMESPACE | 2 +- docs/llms.txt | 4 +- docs/pkgdown.yml | 2 +- docs/reference/glmSLMA1DS.html | 111 ++++++++++++++++++++++++++ docs/reference/glmSLMA1DS.md | 56 +++++++++++++ docs/reference/index.html | 2 +- docs/reference/index.md | 4 +- docs/search.json | 2 +- docs/sitemap.xml | 1 + man/{glmSLMA11DS.Rd => glmSLMA1DS.Rd} | 6 +- 10 files changed, 179 insertions(+), 11 deletions(-) create mode 100644 docs/reference/glmSLMA1DS.html create mode 100644 docs/reference/glmSLMA1DS.md rename man/{glmSLMA11DS.Rd => glmSLMA1DS.Rd} (94%) diff --git a/NAMESPACE b/NAMESPACE index 1652fc26..0beed367 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -48,7 +48,7 @@ export(glm1DS) export(glm2DS) export(glmPredictDS.ag) export(glmPredictDS.as) -export(glmSLMA11DS) +export(glmSLMA1DS) export(glmSLMA2DS) export(glmSLMADS.assign) export(glmSummaryDS.ag) diff --git a/docs/llms.txt b/docs/llms.txt index 14688ab9..ee6d20bd 100644 --- a/docs/llms.txt +++ b/docs/llms.txt @@ -238,8 +238,8 @@ analysis platform.” *Bioinformatics Advances*, *5*(1), 1-21. - [`glmPredictDS.as()`](glmPredictDS.as.md) : predict regression responses from a glm object -- [`glmSLMA11DS()`](glmSLMA11DS.md) : Fit a Generalized Linear Model - (GLM) with pooling via Study Level Meta-Analysis (SLMA) +- [`glmSLMA1DS()`](glmSLMA1DS.md) : Fit a Generalized Linear Model (GLM) + with pooling via Study Level Meta-Analysis (SLMA) - [`glmSLMA2DS()`](glmSLMA2DS.md) : Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index f5b3507a..249b2972 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,4 +2,4 @@ pandoc: 3.7.0.2 pkgdown: 2.2.1 pkgdown_sha: ~ articles: {} -last_built: 2026-11-02T20:31Z +last_built: 2026-11-03T11:01Z diff --git a/docs/reference/glmSLMA1DS.html b/docs/reference/glmSLMA1DS.html new file mode 100644 index 00000000..746f1018 --- /dev/null +++ b/docs/reference/glmSLMA1DS.html @@ -0,0 +1,111 @@ + +Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA1DS • dsBase + Skip to contents + + +
+
+
+ +

Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)

+ +
glmSLMA1DS.Rd
+
+ +
+

Fits a generalized linear model (GLM) on data from single or multiple sources +with pooled co-analysis across studies being based on SLMA (Study Level Meta Analysis).

+
+ +
+

Usage

+ 
glmSLMA1DS(formula, family, weights, offset, data)
+
+ +
+

Arguments

+ + +
formula
+

a glm formula, specified in call to ds.glmSLMA

+ + +
family
+

a glm family, specified in call to ds.glmSLMA

+ + +
weights
+

a character string specifying a variable to be used as regression weights. +Specified in call to ds.glmSLMA. Specified in call to ds.glmSLMA.

+ + +
offset
+

a character string specifying a variable to be used as an offset. +Specified in call to ds.glmSLMA.

+ + +
data
+

a character string specifying the name of a data.frame +holding the data for the model. Specified as dataName in call to ds.glmSLMA.

+ +
+
+

Value

+

assesses and returns information about failure to pass disclosure traps +such as test of model complexity (saturation). +For more detailed information see help for ds.glmSLMA.

+
+
+

Details

+

glmSLMADS.assign is an aggregate function called by clientside function ds.glmSLMA. +ds.glmSLMA also calls another aggregate function glmSLMA2DS +and an assign function glmSLMADS.assign +For more detailed information see help for ds.glmSLMA.

+
+
+

Author

+

Paul Burton for DataSHIELD Development Team (14/7/20)

+

Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands

+
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.2.1.

+
+ +
+ + + + + + + diff --git a/docs/reference/glmSLMA1DS.md b/docs/reference/glmSLMA1DS.md new file mode 100644 index 00000000..fe4681e9 --- /dev/null +++ b/docs/reference/glmSLMA1DS.md @@ -0,0 +1,56 @@ +# Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) + +Fits a generalized linear model (GLM) on data from single or multiple +sources with pooled co-analysis across studies being based on SLMA +(Study Level Meta Analysis). + +## Usage + +``` r +glmSLMA1DS(formula, family, weights, offset, data) +``` + +## Arguments + +- formula: + + a glm formula, specified in call to ds.glmSLMA + +- family: + + a glm family, specified in call to ds.glmSLMA + +- weights: + + a character string specifying a variable to be used as regression + weights. Specified in call to ds.glmSLMA. Specified in call to + ds.glmSLMA. + +- offset: + + a character string specifying a variable to be used as an offset. + Specified in call to ds.glmSLMA. + +- data: + + a character string specifying the name of a data.frame holding the + data for the model. Specified as dataName in call to ds.glmSLMA. + +## Value + +assesses and returns information about failure to pass disclosure traps +such as test of model complexity (saturation). For more detailed +information see help for ds.glmSLMA. + +## Details + +glmSLMADS.assign is an aggregate function called by clientside function +ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS +and an assign function glmSLMADS.assign For more detailed information +see help for ds.glmSLMA. + +## Author + +Paul Burton for DataSHIELD Development Team (14/7/20) + +Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands diff --git a/docs/reference/index.html b/docs/reference/index.html index 3c540198..ac3baadc 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -377,7 +377,7 @@

All functionsglmSLMA11DS() + glmSLMA1DS()

Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)
diff --git a/docs/reference/index.md b/docs/reference/index.md index 7e60db06..94b719c1 100644 --- a/docs/reference/index.md +++ b/docs/reference/index.md @@ -136,8 +136,8 @@ - [`glmPredictDS.as()`](glmPredictDS.as.md) : predict regression responses from a glm object -- [`glmSLMA11DS()`](glmSLMA11DS.md) : Fit a Generalized Linear Model - (GLM) with pooling via Study Level Meta-Analysis (SLMA) +- [`glmSLMA1DS()`](glmSLMA1DS.md) : Fit a Generalized Linear Model (GLM) + with pooling via Study Level Meta-Analysis (SLMA) - [`glmSLMA2DS()`](glmSLMA2DS.md) : Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) diff --git a/docs/search.json b/docs/search.json index f33cae8f..ad0e3e77 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Paul Burton. Author. Rebecca Wilson. Author. Olly Butters. Author. Patricia Ryser-Welch. Author. Alex Westerberg. Author. Leire Abarrategui. Author. Roberto Villegas-Diaz. Author. Demetris Avraam. Author. Yannick Marcon. Author. Tom Bishop. Author. Amadou Gaye. Author. Xavier Escribà-Montagut. Author. Stuart Wheater. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg , Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye , Escribà-Montagut X, Wheater S (????). dsBase: 'DataSHIELD' Server Side Base Functions. R package version 7.0.0.9000. Gaye , Marcon Y, Isaeva J, LaFlamme P, Turner , Jones E, Minion J, Boyd , Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir , Doiron D, Giepmans L, Wallace S, Budin-Ljøsne , Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry , Peters , Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier , Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking analysis data, data analysis.” International Journal Epidemiology, 43(6), 1929–1944. doi:10.1093/ije/dyu188. Wilson R, Butters O, Avraam D, Baker J, Tedds J, Turner , Murtagh M, Burton P (2017). “DataSHIELD – New Directions Dimensions.” Data Science Journal, 16(21), 1–21. doi:10.5334/dsj-2017-021. Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan , Murtagh M, Nestor M, Nybo Andersen , Parker S, Pinot de Moira , Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1–21. doi:10.1093/bioadv/vbaf046.","code":"@Manual{, title = {dsBase: 'DataSHIELD' Server Side Base Functions}, author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater}, note = {R package version 7.0.0.9000}, } @Article{, title = {{DataSHIELD: taking the analysis to the data, not the data to the analysis}}, author = {Amadou Gaye and Yannick Marcon and Julia Isaeva and Philippe {LaFlamme} and Andrew Turner and Elinor M Jones and Joel Minion and Andrew W Boyd and Christopher J Newby and Marja-Liisa Nuotio and Rebecca Wilson and Oliver Butters and Barnaby Murtagh and Ipek Demir and Dany Doiron and Lisette Giepmans and Susan E Wallace and Isabelle Budin-Lj{\\o}sne and Carsten O. Schmidt and Paolo Boffetta and Mathieu Boniol and Maria Bota and Kim W Carter and Nick {deKlerk} and Chris Dibben and Richard W Francis and Tero Hiekkalinna and Kristian Hveem and Kirsti Kval{\\o}y and Sean Millar and Ivan J Perry and Annette Peters and Catherine M Phillips and Frank Popham and Gillian Raab and Eva Reischl and Nuala Sheehan and Melanie Waldenberger and Markus Perola and Edwin {{van den Heuvel}} and John Macleod and Bartha M Knoppers and Ronald P Stolk and Isabel Fortier and Jennifer R Harris and Bruce H R Woffenbuttel and Madeleine J Murtagh and Vincent Ferretti and Paul R Burton}, journal = {International Journal of Epidemiology}, year = {2014}, volume = {43}, number = {6}, pages = {1929--1944}, doi = {10.1093/ije/dyu188}, } @Article{, title = {{DataSHIELD – New Directions and Dimensions}}, author = {Rebecca C. Wilson and Oliver W. Butters and Demetris Avraam and James Baker and Jonathan A. Tedds and Andrew Turner and Madeleine Murtagh and Paul R. Burton}, journal = {Data Science Journal}, year = {2017}, volume = {16}, number = {21}, pages = {1--21}, doi = {10.5334/dsj-2017-021}, } @Article{, title = {{DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform}}, author = {Demetris Avraam and Rebecca C Wilson and Noemi {{Aguirre Chan}} and Soumya Banerjee and Tom R P Bishop and Olly Butters and Tim Cadman and Luise Cederkvist and Liesbeth Duijts and Xavier {{Escrib{\\a`a} Montagut}} and Hugh Garner and Gon{\\c c}alo {Gon{\\c c}alves} and Juan R Gonz{\\a'a}lez and Sido Haakma and Mette Hartlev and Jan Hasenauer and Manuel Huth and Eleanor Hyde and Vincent W V Jaddoe and Yannick Marcon and Michaela Th Mayrhofer and Fruzsina Molnar-Gabor and Andrei Scott Morgan and Madeleine Murtagh and Marc Nestor and Anne-Marie {{Nybo Andersen}} and Simon Parker and Angela {{Pinot de Moira}} and Florian Schwarz and Katrine Strandberg-Larsen and Morris A Swertz and Marieke Welten and Stuart Wheater and Paul R Burton}, journal = {Bioinformatics Advances}, year = {2024}, volume = {5}, number = {1}, pages = {1--21}, doi = {10.1093/bioadv/vbaf046}, editor = {Thomas Lengauer}, publisher = {Oxford University Press (OUP)}, }"},{"path":[]},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"DataSHIELD Server Side Base Functions","text":"can install released version dsBase CRAN : development version GitHub : full list development branches, checkout https://github.com/datashield/dsBase/branches","code":"install.packages(\"dsBase\") install.packages(\"remotes\") remotes::install_github(\"datashield/dsBase\", \"\") # Install v6.3.6 with the following remotes::install_github(\"datashield/dsBase\", \"6.3.6\")"},{"path":"/index.html","id":"about","dir":"","previous_headings":"","what":"About","title":"DataSHIELD Server Side Base Functions","text":"DataSHIELD software package allows non-disclosive federated analysis sensitive data. website (https://www.datashield.org) depth descriptions , works install . key point highlight DataSHIELD client-server infrastructure, dsBase package (https://github.com/datashield/dsBase) needs used conjunction dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying use one without makes sense. Detailed instructions install DataSHIELD https://wiki.datashield.org/. code organised :","code":""},{"path":"/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"DataSHIELD Server Side Base Functions","text":"[1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg , Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye , Escribà Montagut X, Wheater S (2025). dsBase: ‘DataSHIELD’ Server Side Base Functions. R package version 6.3.4. https://doi.org/10.32614/CRAN.package.dsBase. [2] Gaye , Marcon Y, Isaeva J, LaFlamme P, Turner , Jones E, Minion J, Boyd , Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir , Doiron D, Giepmans L, Wallace S, Budin-Ljøsne , Oliver Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry , Peters , Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier , Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking analysis data, data analysis.” International Journal Epidemiology, 43(6), 1929-1944. https://doi.org/10.1093/ije/dyu188. [3] Wilson R, W. Butters O, Avraam D, Baker J, Tedds J, Turner , Murtagh M, R. Burton P (2017). “DataSHIELD – New Directions Dimensions.” Data Science Journal, 16(21), 1-21. https://doi.org/10.5334/dsj-2017-021. [4] Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan , Murtagh M, Nestor M, Nybo Andersen , Parker S, Pinot de Moira , Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1-21. https://doi.org/10.1093/bioadv/vbaf046. Note: Apple Mx architecture users, please aware numerical limitations platform, leads unexpected results using base R packages, like stats​. x <- c(0, 3, 7) 1 - cor(x, x)​ result value zero. Also See: details see https://cran.r-project.org/doc/FAQ/R-FAQ.html#-doesn_0027t-R-think--numbers--equal_003f bug report: https://bugs.r-project.org/show_bug.cgi?id=18941","code":""},{"path":"/reference/BooleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"BooleDS — BooleDS","title":"BooleDS — BooleDS","text":"Converts individual elements vector object Boolean indicators.","code":""},{"path":"/reference/BooleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BooleDS — BooleDS","text":"","code":"BooleDS( V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, na.assign.text, numeric.output = TRUE )"},{"path":"/reference/BooleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BooleDS — BooleDS","text":"V1.name character string specifying name vector Boolean operator applied V2.name character string specifying name vector scalar compared. Boolean.operator.n integer value (1 6) providing numeric coding character string specifying one six possible Boolean operators: '==', '!=', '>', '>=','<', '<=' legally passed client server via DataSHIELD parser na.assign.text character string taking values 'NA', '1' '0'. 'NA' NA values input vector remain NAs output vector. '1' '0' NA values input vector converted 1 0 respectively. numeric.output TRUE/FALSE indicator defaulting TRUE determining whether final output variable class numeric (1/0) class logical (TRUE/FALSE).","code":""},{"path":"/reference/BooleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"BooleDS — BooleDS","text":"levels input variable.","code":""},{"path":"/reference/BooleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"BooleDS — BooleDS","text":"function converts input vector Boolean indicators.","code":""},{"path":"/reference/BooleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"BooleDS — BooleDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/absDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the absolute values of the input variable — absDS","title":"Computes the absolute values of the input variable — absDS","text":"function similar R function abs.","code":""},{"path":"/reference/absDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the absolute values of the input variable — absDS","text":"","code":"absDS(x)"},{"path":"/reference/absDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the absolute values of the input variable — absDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/absDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the absolute values of the input variable — absDS","text":"object specified newobj argument ds.abs (default name abs.newobj) written serverside. output object class numeric integer.","code":""},{"path":"/reference/absDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the absolute values of the input variable — absDS","text":"function computes absolute values input numeric integer vector.","code":""},{"path":"/reference/absDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the absolute values of the input variable — absDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asCharacterDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class character — asCharacterDS","title":"Coerces an R object into class character — asCharacterDS","text":"function based native R function .character","code":""},{"path":"/reference/asCharacterDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class character — asCharacterDS","text":"","code":"asCharacterDS(x.name)"},{"path":"/reference/asCharacterDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class character — asCharacterDS","text":"x.name name input object coerced class character. 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class","code":""},{"path":"/reference/asDataMatrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactor1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Determines the levels of the input variable in each single study — asFactor1DS","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"function aggregate DataSHIELD function returns levels input variable single study client-side function.","code":""},{"path":"/reference/asFactor1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"","code":"asFactor1DS(input.var.name = NULL)"},{"path":"/reference/asFactor1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"input.var.name name variable converted factor.","code":""},{"path":"/reference/asFactor1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"levels input variable.","code":""},{"path":"/reference/asFactor1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"function encodes input vector factor returns levels ascending order levels numerical alphabetical order levels type character.","code":""},{"path":"/reference/asFactor1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactor2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts a numeric vector into a factor — asFactor2DS","title":"Converts a numeric vector into a factor — asFactor2DS","text":"function assign DataSHIELD function converts numeric vector factor type presented vector matrix dummy variables.","code":""},{"path":"/reference/asFactor2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts a numeric vector into a factor — asFactor2DS","text":"","code":"asFactor2DS( input.var.name = NULL, all.unique.levels.transmit = NULL, fixed.dummy.vars = NULL, baseline.level = NULL )"},{"path":"/reference/asFactor2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts a numeric vector into a factor — asFactor2DS","text":"input.var.name name variable converted factor. .unique.levels.transmit levels variable transmitted . fixed.dummy.vars boolean determines whether new object represented vector matrix dummy variables indicating factor level data point. argument set FALSE (default) input variable converted factor assigned vector. set TRUE input variable converted factor assigned matrix dummy variables. baseline.level number indicating baseline level used creation matrix dummy variables.","code":""},{"path":"/reference/asFactor2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts a numeric vector into a factor — asFactor2DS","text":"object class factor","code":""},{"path":"/reference/asFactor2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Converts a numeric vector into a factor — asFactor2DS","text":"functions converts input variable factor presented vector fixed.dummy.vars set FALSE matrix dummy variables fixed.dummy.vars set TRUE (see help file ds.asFactor.b details).","code":""},{"path":"/reference/asFactor2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts a numeric vector into a factor — asFactor2DS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactorSimpleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts a numeric vector into a factor — asFactorSimpleDS","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"function assign DataSHIELD function coerces numeric character vector factor","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"","code":"asFactorSimpleDS(input.var.name = NULL)"},{"path":"/reference/asFactorSimpleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"input.var.name name variable converted factor.","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"object class factor","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"functions converts input variable factor. Unlike ds.asFactor serverside functions, ds.asFactorSimple coerce class variable factor study. check enforce consistency factor levels across sources allow force arbitrary set levels unless levels actually exist sources. addition, allow create array binary dummy variables equivalent factor. need things use ds.asFactor function.","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asIntegerDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class integer — asIntegerDS","title":"Coerces an R object into class integer — asIntegerDS","text":"function based native R function .integer.","code":""},{"path":"/reference/asIntegerDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class integer — asIntegerDS","text":"","code":"asIntegerDS(x.name)"},{"path":"/reference/asIntegerDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class integer — asIntegerDS","text":"x.name name input object coerced class integer. Must specified inverted commas. argument usually specified directly argument clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class integer — asIntegerDS","text":"object specified argument (default name \"asinteger.newobj\") written serverside. details see help clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class integer — asIntegerDS","text":"See help function .integer native R, details section help file clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class integer — asIntegerDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asListDS.html","id":null,"dir":"Reference","previous_headings":"","what":"asListDS a serverside assign function called by ds.asList — asListDS","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"Coerces R object list","code":""},{"path":"/reference/asListDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"","code":"asListDS(x.name)"},{"path":"/reference/asListDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"x.name name input object coerced class data.matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asList","code":""},{"path":"/reference/asListDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"input object coerced list, ds.asList writes serverside. way .list coerces objects list depends class object","code":""},{"path":"/reference/asListDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"assign function based native R function .list additional information can found help .list","code":""},{"path":"/reference/asListDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asLogicalDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class logical — asLogicalDS","title":"Coerces an R object into class logical — asLogicalDS","text":"function based native R function .logical","code":""},{"path":"/reference/asLogicalDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class logical — asLogicalDS","text":"","code":"asLogicalDS(x.name)"},{"path":"/reference/asLogicalDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class logical — asLogicalDS","text":"x.name name input object coerced class logical. Must specified inverted commas. argument usually specified directly argument clientside function ds.asLogical","code":""},{"path":"/reference/asLogicalDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class logical — asLogicalDS","text":"object specified argument (default name .logic) written serverside. details see help clientside function ds.asLogical","code":""},{"path":"/reference/asLogicalDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class logical — asLogicalDS","text":"See help function .logical native R","code":""},{"path":"/reference/asLogicalDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class logical — asLogicalDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asMatrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into a matrix — asMatrixDS","title":"Coerces an R object into a matrix — asMatrixDS","text":"function based native R function .matrix","code":""},{"path":"/reference/asMatrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into a matrix — asMatrixDS","text":"","code":"asMatrixDS(x.name)"},{"path":"/reference/asMatrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into a matrix — asMatrixDS","text":"x.name name input object coerced class matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asMatrix","code":""},{"path":"/reference/asMatrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into a matrix — asMatrixDS","text":"object specified argument (default name .mat) written serverside. details see help clientside function ds.asMatrix","code":""},{"path":"/reference/asMatrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into a matrix — asMatrixDS","text":"See help function .matrix native R","code":""},{"path":"/reference/asMatrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into a matrix — asMatrixDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asNumericDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class numeric — asNumericDS","title":"Coerces an R object into class numeric — asNumericDS","text":"function based native R function .numeric.","code":""},{"path":"/reference/asNumericDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class numeric — asNumericDS","text":"","code":"asNumericDS(x.name)"},{"path":"/reference/asNumericDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class numeric — asNumericDS","text":"x.name name input object coerced class numeric. Must specified inverted commas. argument usually specified directly argument clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class numeric — asNumericDS","text":"object specified argument (default name .num) written serverside. details see help clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class numeric — asNumericDS","text":"See help function .numeric native R, details section help file clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class numeric — asNumericDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/aucDS.html","id":null,"dir":"Reference","previous_headings":"","what":"aucDS an aggregate function called by ds.auc — aucDS","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"function calculates C-statistic AUC logistic regression models.","code":""},{"path":"/reference/aucDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"","code":"aucDS(pred = pred, y = y)"},{"path":"/reference/aucDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"pred name vector predicted values y name outcome variable. Note variable include complete cases used regression model.","code":""},{"path":"/reference/aucDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"returns AUC standard error","code":""},{"path":"/reference/aucDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"AUC determines discriminative ability model.","code":""},{"path":"/reference/aucDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/booleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"booleDS — booleDS","title":"booleDS — booleDS","text":"Converts individual elements vector object Boolean indicators.","code":""},{"path":"/reference/booleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"booleDS — booleDS","text":"","code":"booleDS( V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, na.assign.text, numeric.output = TRUE )"},{"path":"/reference/booleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"booleDS — booleDS","text":"V1.name character string specifying name vector Boolean operator applied V2.name character string specifying name vector scalar compared. Boolean.operator.n integer value (1 6) providing numeric coding character string specifying one six possible Boolean operators: '==', '!=', '>', '>=','<', '<=' legally passed client server via DataSHIELD parser na.assign.text character string taking values 'NA', '1' '0'. 'NA' NA values input vector remain NAs output vector. '1' '0' NA values input vector converted 1 0 respectively. numeric.output TRUE/FALSE indicator defaulting TRUE determining whether final output variable class numeric (1/0) class logical (TRUE/FALSE).","code":""},{"path":"/reference/booleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"booleDS — booleDS","text":"levels input variable.","code":""},{"path":"/reference/booleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"booleDS — booleDS","text":"function converts input vector Boolean indicators.","code":""},{"path":"/reference/booleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"booleDS — booleDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGGDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"order create non disclosive box plot, data passed client purely geometrical aspects plot, ggplot object contains data inside, graphical parameters passed. three different cases depending grouping variables. outliers also removed graphical parameters.","code":""},{"path":"/reference/boxPlotGGDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"","code":"boxPlotGGDS(data_table.name, group = NULL, group2 = NULL)"},{"path":"/reference/boxPlotGGDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"data_table.name character Name server-side data frame holds information plotted, arranged : Column 'x': Names X axis boxplot, aka variables plot Column 'value': Values variable (raw data columns rbinded) Column 'group': (Optional) Values grouping variable Column 'group2': (Optional) Values second grouping variable group character (default NULL) Name first grouping variable. group2 character (default NULL) Name second grouping variable.","code":""},{"path":"/reference/boxPlotGGDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"list : -data frame Geometrical parameters (identity stats ggplot) -character Type plot (single_group, double_group no_group)","code":""},{"path":"/reference/boxPlotGGDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"Arrange data frame pass boxplot function","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"","code":"boxPlotGG_data_TreatmentDS(table.name, variables, group = NULL, group2 = NULL)"},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"table.name character Name server-side data frame holds information plotted later variables character vector Name column(s) data frame include boxplot group character (default NULL) Name first grouping variable. group2 character (default NULL) Name second grouping variable.","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"data frame following structure: Column 'x': Names X axis boxplot, aka variables plot Column 'value': Values variable (raw data columns rbinded) Column 'group': (Optional) Values grouping variable Column 'group2': (Optional) Values second grouping variable","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"Arrange vector pass boxplot function","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"","code":"boxPlotGG_data_Treatment_numericDS(vector.name)"},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"vector.name character Name server-side numeric vector arrange plotted later","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"data frame following structure: Column 'x': Names X axis boxplot, aka name vector (vector.name argument) Column 'value': Values variable","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/bp_standardsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates Blood pressure z-scores — bp_standardsDS","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"function calculates blood pressure z-scores two steps: Step 1. Calculates z-score height according CDC growth chart (growth chart!). Step 2. Calculates z-score BP according fourth report BP management, USA","code":""},{"path":"/reference/bp_standardsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"","code":"bp_standardsDS( sex = sex, age = age, height = height, bp = bp, systolic = systolic )"},{"path":"/reference/bp_standardsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"sex name sex variable. variable coded 1 males 2 females. coded differently (e.g. 0/1), can use ds.recodeValues function recode categories 1/2 use ds.bp_standards age name age variable years. height name height variable cm bp name blood pressure variable. systolic logical. TRUE (default) function assumes conversion systolic blood pressure. FALSE function assumes conversion diastolic blood pressure.","code":""},{"path":"/reference/bp_standardsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"assigns new object server-side. assigned object list two elements: 'Zbp' zscores blood pressure 'perc' percentiles BP zscores.","code":""},{"path":"/reference/bp_standardsDS.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"z-scores height based CDC growth charts calculated sds function childsds R package.","code":""},{"path":"/reference/bp_standardsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/cDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenates objects into a vector or list — cDS","title":"Concatenates objects into a vector or list — cDS","text":"function similar R base function 'c'.","code":""},{"path":"/reference/cDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenates objects into a vector or list — cDS","text":"","code":"cDS(x.names)"},{"path":"/reference/cDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenates objects into a vector or list — cDS","text":"x.names character vector object names concatenate.","code":""},{"path":"/reference/cDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenates objects into a vector or list — cDS","text":"vector list","code":""},{"path":"/reference/cDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Concatenates objects into a vector or list — cDS","text":"Unlike R base function 'c' vector list certain length allowed output","code":""},{"path":"/reference/cDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Concatenates objects into a vector or list — cDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/cbindDS.html","id":null,"dir":"Reference","previous_headings":"","what":"cbindDS called by ds.cbind — cbindDS","title":"cbindDS called by ds.cbind — cbindDS","text":"serverside assign function takes sequence vector, matrix data-frame arguments combines column produce data-frame.","code":""},{"path":"/reference/cbindDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cbindDS called by ds.cbind — cbindDS","text":"","code":"cbindDS(x.names.transmit = NULL, colnames.transmit = NULL)"},{"path":"/reference/cbindDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"cbindDS called by ds.cbind — cbindDS","text":"x.names.transmit vector character strings representing names elemental components combined converted transmittable format. argument fully specified x argument client-side ds.cbind function. colnames.transmit vector character strings representing column names output object converted transmittable format.","code":""},{"path":"/reference/cbindDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"cbindDS called by ds.cbind — cbindDS","text":"object specified newobj argument ds.cbind (default name cbind.newobj) written serverside. output object class data.frame.","code":""},{"path":"/reference/cbindDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"cbindDS called by ds.cbind — cbindDS","text":"sequence vector, matrix data-frame arguments combined column column produce data-frame written serverside. critical requirement length component variables, number rows component data.frames matrices must . output data.frame number rows. details see help ds.cbind native R function cbind.","code":""},{"path":"/reference/cbindDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"cbindDS called by ds.cbind — cbindDS","text":"Paul Burton Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/changeRefGroupDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Changes a reference level of a factor — changeRefGroupDS","title":"Changes a reference level of a factor — changeRefGroupDS","text":"function similar R function relevel,","code":""},{"path":"/reference/changeRefGroupDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Changes a reference level of a factor — changeRefGroupDS","text":"","code":"changeRefGroupDS(x, ref = NULL, reorderByRef = NULL)"},{"path":"/reference/changeRefGroupDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Changes a reference level of a factor — changeRefGroupDS","text":"x character string, name factor vector. ref character, reference level reorderByRef boolean tells whether new vector ordered reference group.","code":""},{"path":"/reference/changeRefGroupDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Changes a reference level of a factor — changeRefGroupDS","text":"factor length input vector","code":""},{"path":"/reference/changeRefGroupDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Changes a reference level of a factor — changeRefGroupDS","text":"addition R function , function allows user re-order vector, putting reference group first. user chooses re-order warning issued can introduce mismatch values vector put back table reordered way. mismatch can render results operations table invalid.","code":""},{"path":"/reference/changeRefGroupDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Changes a reference level of a factor — changeRefGroupDS","text":"Isaeva, J., Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/checkNegValueDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if a numeric variable has negative values — checkNegValueDS","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"function called client function ds.glm.","code":""},{"path":"/reference/checkNegValueDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"","code":"checkNegValueDS(weights)"},{"path":"/reference/checkNegValueDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"weights numeric vector","code":""},{"path":"/reference/checkNegValueDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"boolean; TRUE vector one negative values FALSE otherwise","code":""},{"path":"/reference/checkNegValueDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"user sets parameter 'weights' client side function ds.glm server side function called verify 'weights' vector negative values negative allowed weights.","code":""},{"path":"/reference/checkNegValueDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"Gaye, .","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":null,"dir":"Reference","previous_headings":"","what":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"server-side function check server running \"permissive\" privacy control level.","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"","code":"checkPermissivePrivacyControlLevel(privacyControlLevels)"},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"privacyControlLevels vector strings contains privacy control level names permitted calling method.","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"return value, called side effects","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"Tests whether R option \"datashield.privacyControlLevel\" set \"permissive\", cause call stop() message \"BLOCKED: server running 'non-permissive' mode caused method blocked\".","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"Wheater, Dr SM., DataSHIELD Development Team.","code":""},{"path":"/reference/classDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the class of an object — classDS","title":"Returns the class of an object — classDS","text":"function similar R function class.","code":""},{"path":"/reference/classDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the class of an object — classDS","text":"","code":"classDS(x)"},{"path":"/reference/classDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the class of an object — classDS","text":"x string character, name object","code":""},{"path":"/reference/classDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the class of an object — classDS","text":"class input object","code":""},{"path":"/reference/classDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the class of an object — classDS","text":"function returns class object","code":""},{"path":"/reference/classDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the class of an object — classDS","text":"Stuart Wheater, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/colnamesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the column names of a data frame or matrix — colnamesDS","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"function similar R function colnames.","code":""},{"path":"/reference/colnamesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"","code":"colnamesDS(x)"},{"path":"/reference/colnamesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"x string character, name dataframe matrix","code":""},{"path":"/reference/colnamesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"column names input object","code":""},{"path":"/reference/colnamesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"function returns column names input dataframe matrix","code":""},{"path":"/reference/colnamesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"Demetris Avraam, DataSHIELD Development Team","code":""},{"path":"/reference/completeCasesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"Identifies strips rows data.frame, matrix vector contain NAs.","code":""},{"path":"/reference/completeCasesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"","code":"completeCasesDS(x1.transmit)"},{"path":"/reference/completeCasesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"x1.transmit argument determines input data.frame, matrix vector rows NAs stripped. argument fully specified argument ds.completeCases function.","code":""},{"path":"/reference/completeCasesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"modified data.frame, matrix vector rows containing least one NA deleted. modified object written serverside source. addition, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.completeCases also returns studysideMessages can help explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/completeCasesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"case data.frame matrix, completeCasesDS identifies rows containing one NAs deletes rows altogether. one variable NA given row lead deletion whole row. case vector, completeCasesDS acts equivalent manner equivalent 'row' simply strips observations recorded NA. ds.completeCASES analogous complete.cases function native R. Limited additional information can therefore found help(\"complete.cases\") native R.","code":""},{"path":"/reference/completeCasesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/corDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"function computes sum vector variable sum products two variables (.e. scalar product two vectors).","code":""},{"path":"/reference/corDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"","code":"corDS(x = NULL, y = NULL)"},{"path":"/reference/corDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"x character, name vector, matrix dataframe variables(s) correlation(s) () going calculated . y NULL (default) name vector, matrix dataframe compatible dimensions x.","code":""},{"path":"/reference/corDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"list includes matrix elements sum products two variables, matrix elements sum values variable, matrix elements number complete cases pair variables, list number missing values variable separately (columnwise) number missing values casewise, vector elements sum squares variable. first disclosure control checks number variables bigger percentage individual-level records (allowed percentage pre-specified 'nfilter.glm'). second disclosure control checks none dichotomous level fewer counts pre-specified 'nfilter.tab' threshold. list also includes class, class input object client-side consistency checking.","code":""},{"path":"/reference/corDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"computes sum vector variable sum products two variables","code":""},{"path":"/reference/corDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/corTestDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests for correlation between paired samples — corTestDS","title":"Tests for correlation between paired samples — corTestDS","text":"function similar R function cor.test.","code":""},{"path":"/reference/corTestDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests for correlation between paired samples — corTestDS","text":"","code":"corTestDS(x, y, method, exact, conf.level)"},{"path":"/reference/corTestDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests for correlation between paired samples — corTestDS","text":"x character string providing name numerical vector. y character string providing name numerical vector. method character string indicating correlation coefficient used test. One \"pearson\", \"kendall\", \"spearman\", can abbreviated. exact logical indicating whether exact p-value computed. Used Kendall's tau Spearman's rho. conf.level confidence level returned confidence interval. Currently used Pearson product moment correlation coefficient least 4 complete pairs observations.","code":""},{"path":"/reference/corTestDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tests for correlation between paired samples — corTestDS","text":"list results correlation test class, class input object client-side consistency checking.","code":""},{"path":"/reference/corTestDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tests for correlation between paired samples — corTestDS","text":"function runs two-sided correlation test","code":""},{"path":"/reference/corTestDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Tests for correlation between paired samples — corTestDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/covDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"function computes sum vector variable sum products two variables (.e. scalar product two vectors).","code":""},{"path":"/reference/covDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"","code":"covDS(x = NULL, y = NULL, use = NULL)"},{"path":"/reference/covDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"x character, name vector, matrix dataframe variable(s) covariance(s) correlation(s) () going calculated . y NULL (default) name vector, matrix dataframe compatible dimensions x. use character string giving method computing covariances presence missing values. must one strings \"casewise.complete\" \"pairwise.complete\". use set 'casewise.complete' rows missing values omitted vector, matrix dataframe calculations sums. use set 'pairwise.complete' (default case set client-side), sums products computed two variables using complete pairs observations two variables.","code":""},{"path":"/reference/covDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"list includes matrix elements sum products two variables, matrix elements sum values variable, matrix elements number complete cases pair variables, list number missing values variable separately (columnwise) number missing values casewise pairwise depending argument use, error message indicates whether input variables pass disclosure controls. first disclosure control checks number variables bigger percentage individual-level records (allowed percentage pre-specified 'nfilter.glm'). second disclosure control checks none dichotomous level fewer counts pre-specified 'nfilter.tab' threshold. input variables pass disclosure controls output values replaced NAs. list also includes class, class input object client-side consistency checking.","code":""},{"path":"/reference/covDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"computes sum vector variable sum products two variables","code":""},{"path":"/reference/covDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameDS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameDS called by ds.dataFrame — dataFrameDS","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"serverside function creates data frame elemental components. : pre-existing data frames; single variables; /matrices","code":""},{"path":"/reference/dataFrameDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"","code":"dataFrameDS( vectors = NULL, r.names = NULL, ch.rows = FALSE, ch.names = TRUE, clnames = NULL, strAsFactors = TRUE, completeCases = FALSE )"},{"path":"/reference/dataFrameDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"vectors list contains elemental components combine. correspond vector character strings specified argument x clientside function ds.dataFrame() r.names NULL character vector specifying names rows. Default NULL. ch.rows logical, TRUE rows checked consistency length names. Default FALSE. ch.names logical, TRUE names variables data frame checked ensure syntactically valid variable names duplicated. Default TRUE. fact, clientside function ensures duplicated names can presented dataFrameDS argument kept check forms syntactic validity. clnames list characters, column names output data frame. generated clientside function names vectors, column names data.frames matrices combined producing output data.frame strAsFactors logical, TRUE determines whether character vectors automatically converted factors? Default TRUE. completeCases logical. TRUE indicates complete cases included: rows missing values component excluded. Default FALSE.","code":""},{"path":"/reference/dataFrameDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"dataframe composed specified elemental components created serverside named according argument clientside function ds.dataFrame()","code":""},{"path":"/reference/dataFrameDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"data frame list variables number rows unique row names, class 'data.frame'. ds.dataFrame create data frame combining series elemental components may pre-existing data.frames, matrices variables. critical requirement length component variables, number rows component data.frames matrices must . output data.frame number rows. serverside function dataFrameDS() calls native R function data.frame() several arguments precisely data.frame(). consequence, additional information can sought help() data.frame().","code":""},{"path":"/reference/dataFrameDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSortDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Sorts data frame using specified alphanumeric numeric sort key","code":""},{"path":"/reference/dataFrameSortDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"","code":"dataFrameSortDS( df.name = NULL, sort.key.name = NULL, sort.descending, sort.method )"},{"path":"/reference/dataFrameSortDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"df.name character string providing name serverside data.frame sorted. parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.key.name character string providing name sort key. serverside vector may sit inside data frame sorted independently serverside analysis environment. , sits outside data frame must length data frame. parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.descending logical, TRUE data.frame sorted sort key descending order. Default = FALSE (sort order ascending). parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.method character string taking one values: \"default\", \"d\", \"alphabetic\", \"\", \"numeric\", \"n\", NULL. Default value \"default\". parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\").","code":""},{"path":"/reference/dataFrameSortDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"appropriately re-sorted data.frame written serverside R environment data.frame named according argument(default name 'dataframesort.newobj') name specified","code":""},{"path":"/reference/dataFrameSortDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Serverside assign function dataFrameSortDS called clientside function ds.dataFrameSort. vector matrix can added , coerced , data frame (using function [ds.dataFrame]) means can sorted/reordered using ds.dataFrameSort. Fundamentally, function [ds.dataFrameSort] sort specified data frame serverside using sort key also serverside. details see help clientside function: [ds.dataFrameShort]","code":""},{"path":"/reference/dataFrameSortDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Paul Burton, critical error identification Leire Abarrategui-Martinez, DataSHIELD Development Team, 2/4/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"First serverside function subsetting data frame row column.","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"","code":"dataFrameSubset1DS( df.name = NULL, V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, keep.cols = NULL, rm.cols = NULL, keep.NAs = NULL )"},{"path":"/reference/dataFrameSubset1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"df.name character string providing name data.frame sorted. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset V1.name character string specifying name subsetting vector Boolean operator applied define subset created. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset V2.name character string specifying name vector scalar values vector specified argument compared. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset Boolean.operator.n character string specifying one six possible Boolean operators: '==', '!=', '>', '>=', '<', '<=' argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset keep.cols numeric vector specifying numbers columns kept final subset subsetting column. example: keep.cols=c(2:5,7,12) keep columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset rm.cols numeric vector specifying numbers columns removed creating final subset subsetting column. example: rm.cols=c(2:5,7,12) remove columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset keep.NAs logical, TRUE NAs vector holding final Boolean vector indicating whether given row included subset converted 1s included subset. NAs caused NAs either . FALSE NULL NAs final Boolean vector converted 0s corresponding row therefore excluded subset. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"first serverside function called ds.dataFrameSubset provides first level traps comprehensive series disclosure risks can returned directly clientside dataFrameSubset1DS aggregate function. second serverside function called ds.dataFrameSubset (dataFrameSubset2DS) carries disclosure tests, assign function writes subsetted data.frame serverside. consequence, records error messages studysideMessages can retrieved using ds.message","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"data frame list variables number rows, class 'data.frame'. details see help header ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"Second serverside function subsetting data frame row column.","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"","code":"dataFrameSubset2DS( df.name = NULL, V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, keep.cols = NULL, rm.cols = NULL, keep.NAs = NULL )"},{"path":"/reference/dataFrameSubset2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"df.name character string providing name data.frame sorted. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset V1.name character string specifying name subsetting vector Boolean operator applied define subset created. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset V2.name character string specifying name vector scalar values vector specified argument compared. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset Boolean.operator.n character string specifying one six possible Boolean operators: '==', '!=', '>', '>=', '<', '<=' argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset keep.cols numeric vector specifying numbers columns kept final subset subsetting column. example: keep.cols=c(2:5,7,12) keep columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset rm.cols numeric vector specifying numbers columns removed creating final subset subsetting column. example: rm.cols=c(2:5,7,12) remove columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset keep.NAs logical, TRUE NAs vector holding final Boolean vector indicating whether given row included subset converted 1s included subset. NAs caused NAs either . FALSE NULL NAs final Boolean vector converted 0s corresponding row therefore excluded subset. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"object specified argument (default name '_subset') initially specified calling ds.dataFrameSubset. output object (required subsetted data.frame called written serverside. addition, two validity messages returned via ds.dataFrameSubset indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - dataFrameSubset2DS (via ds.dataFrame()) also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"data frame list variables number rows, class 'data.frame'. details see help header ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/densityGridDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates a density grid with or without a priori defined limits — densityGridDS","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Generates density grid can used heatmap contour plots.","code":""},{"path":"/reference/densityGridDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"","code":"densityGridDS( x, y, limits = FALSE, x.min = NULL, x.max = NULL, y.min = NULL, y.max = NULL, numints = 20 )"},{"path":"/reference/densityGridDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"x character string providing name server-side numerical vector y character string providing name server-side numerical vector limits logical expression whether limits density grid defined user. limits set \"FALSE\", min max x y used range. limits set \"TRUE\", limits defined x.min, x.max, y.min y.max used. x.min minimum value x axis grid density object, needed x.max maximum value x axis grid density object, needed y.min minimum value y axis grid density object, needed y.max maximum value y axis grid density object, needed numints number intervals grid density object, default 20","code":""},{"path":"/reference/densityGridDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"list grid density matrix (grid) classes x y inputs (class.x class.y)","code":""},{"path":"/reference/densityGridDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Invalid cells (cells count < set filter value minimum allowed counts table cells) turn 0.","code":""},{"path":"/reference/densityGridDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Julia Isaeva, Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dimDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the dimension of a data frame or matrix — dimDS","title":"Returns the dimension of a data frame or matrix — dimDS","text":"function similar R function dim.","code":""},{"path":"/reference/dimDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the dimension of a data frame or matrix — dimDS","text":"","code":"dimDS(x)"},{"path":"/reference/dimDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the dimension of a data frame or matrix — dimDS","text":"x string character, name dataframe matrix","code":""},{"path":"/reference/dimDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the dimension of a data frame or matrix — dimDS","text":"list two elements: dim (dimension input object) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/dimDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the dimension of a data frame or matrix — dimDS","text":"function returns dimension input dataframe matrix","code":""},{"path":"/reference/dimDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the dimension of a data frame or matrix — dimDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dmtC2SDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"Creates data.frame, matrix tibble serverside equivalent data.frame, matrix tibble (DMT) clientside.","code":""},{"path":"/reference/dmtC2SDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"","code":"dmtC2SDS( dfdata.mat.transmit, inout.object.transmit, from, nrows.transmit, ncols.transmit, colnames.transmit, colclass.transmit, byrow )"},{"path":"/reference/dmtC2SDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"dfdata.mat.transmit character string format can pass DataSHIELD R parser specifies name DMT copied clientside serverside. Value fully specified argument ds.dmtC2S. inout.object.transmit character string taking values \"DF\", \"MAT\" \"TBL\". value argument automatically set ds.dmtC2S depending whether clientside DMT data.frame, matrix tibble. Correspondingly, value determines whether object created serverside data.frame, matrix tibble. unlikely always work (class misspecifications may occur) works test cases. character string specifying source . Fixed clientside function \"clientside.matdftbl\". nrows.transmit specifies number rows matrix created. Fixed clientside function equal number rows clientside DMT transferred. ncols.transmit specifies number columns matrix created. Fixed clientside function equal number columns clientside DMT transferred. colnames.transmit parser-transmissible vector specifying name column DMT transferred clientside serverside. Generated automatically clientside function colnames clientside DMT. colclass.transmit parser-transmissible vector specifying class vector representing individual column DMT transferred. Generated automatically clientside function. allows transmission DMTs containing columns different classes.something going go wrong class misspecification (see inout.object.transmit) DMT complex combination data/column types likely cause. suggests always check class serverside DMT individual columns (latter important). situation arises class columns crucial function needed please contact DataSHIELD forum can try remedy problem. byrow logical value specifying whether DMT created serverside filled row row column column. fixed clientside function FALSE (fill column column).","code":""},{"path":"/reference/dmtC2SDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"object specified argument (default name \"matdftbl.copied.C2S\") written data.frame, matrix tibble serverside.","code":""},{"path":"/reference/dmtC2SDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"dmtC2SDS serverside assign function called ds.dmtC2S. information works see help ds.dmtC2S","code":""},{"path":"/reference/dmtC2SDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"Paul Burton DataSHIELD Development Team - 3rd June, 2021","code":""},{"path":"/reference/dsBase-package.html","id":null,"dir":"Reference","previous_headings":"","what":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","title":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","text":"Base 'DataSHIELD' functions server side. 'DataSHIELD' software package allows non-disclosive federated analysis sensitive data. 'DataSHIELD' analytic functions designed share non disclosive summary statistics, built automated output checking based statistical disclosure control. data sites setting threshold values automated output checks. details, see 'citation(\"dsBase\")'.","code":""},{"path":"/reference/dsBase-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","text":"Maintainer: Stuart Wheater stuart.wheater@arjuna.com (ORCID) Authors: Stuart Wheater stuart.wheater@arjuna.com (ORCID) Paul Burton (ORCID) Rebecca Wilson (ORCID) Olly Butters (ORCID) Patricia Ryser-Welch (ORCID) Alex Westerberg Leire Abarrategui Roberto Villegas-Diaz (ORCID) Demetris Avraam (ORCID) Yannick Marcon yannick.marcon@obiba.org (ORCID) Tom Bishop Amadou Gaye (ORCID) Xavier Escribà-Montagut (ORCID)","code":""},{"path":"/reference/elsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"function based native R function elspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/elsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"","code":"elsplineDS(x = x, n = n, marginal = FALSE, names = NULL)"},{"path":"/reference/elsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"x name input numeric variable n integer greater 2, knots computed cut n equally-spaced intervals along range x marginal logical, parametrize spline, see Details names character, vector names constructed variables","code":""},{"path":"/reference/elsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"elspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/elsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment. Function elspline wraps lspline computes knot positions cut range x n equal-width intervals.","code":""},{"path":"/reference/elsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/expDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the exponential values of the input variable — expDS","title":"Computes the exponential values of the input variable — expDS","text":"function similar R function exp.","code":""},{"path":"/reference/expDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the exponential values of the input variable — expDS","text":"","code":"expDS(x)"},{"path":"/reference/expDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the exponential values of the input variable — expDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/expDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the exponential values of the input variable — expDS","text":"object specified newobj argument ds.exp (default name exp.newobj) written serverside. output object class numeric.","code":""},{"path":"/reference/expDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the exponential values of the input variable — expDS","text":"function computes exponential values input numeric integer vector.","code":""},{"path":"/reference/expDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the exponential values of the input variable — expDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/fixClassDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Change Class of Target Variables in a Data Frame — fixClassDS","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"Change Class Target Variables Data Frame","code":""},{"path":"/reference/fixClassDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"","code":"fixClassDS(df.name, target_vars, target_class)"},{"path":"/reference/fixClassDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"df.name string representing name data frame. target_vars character vector specifying columns modified. target_class character vector specifying new classes column (1 = factor, 2 = integer, 3 = numeric, 4 = character, 5 = logical).","code":""},{"path":"/reference/fixClassDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"modified data frame specified columns converted target classes.","code":""},{"path":"/reference/fixColsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Missing Columns with NA Values — fixColsDS","title":"Add Missing Columns with NA Values — fixColsDS","text":"Add Missing Columns NA Values","code":""},{"path":"/reference/fixColsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Missing Columns with NA Values — fixColsDS","text":"","code":"fixColsDS(.data, cols)"},{"path":"/reference/fixColsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Missing Columns with NA Values — fixColsDS","text":".data string representing name data frame. cols character vector specifying columns added missing.","code":""},{"path":"/reference/fixColsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Missing Columns with NA Values — fixColsDS","text":"modified data frame missing columns added filled NA.","code":""},{"path":"/reference/fixLevelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"Set Factor Levels Specific Columns Data Frame","code":""},{"path":"/reference/fixLevelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"","code":"fixLevelsDS(df.name, vars, levels)"},{"path":"/reference/fixLevelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"df.name string representing name data frame modify. vars character vector specifying columns modified. levels named list element contains levels corresponding factor variable.","code":""},{"path":"/reference/fixLevelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"modified data frame specified columns converted factors provided levels.","code":""},{"path":"/reference/gamlssDS.html","id":null,"dir":"Reference","previous_headings":"","what":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"function calls gamlssDS wrapper function gamlss R package. function returns object class \"gamlss\", generalized additive model location, scale shape (GAMLSS). function also saves residuals object server-side name specified newobj argument. addition, argument centiles set TRUE, function calls centiles function gamlss package returns sample percentages centile curve.","code":""},{"path":"/reference/gamlssDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"","code":"gamlssDS( formula = formula, sigma.formula = sigma.formula, nu.formula = nu.formula, tau.formula = tau.formula, family = family, data = data, method = method, mu.fix = mu.fix, sigma.fix = sigma.fix, nu.fix = nu.fix, tau.fix = tau.fix, control = control, i.control = i.control, centiles = centiles, xvar = xvar, newobj = newobj )"},{"path":"/reference/gamlssDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"formula formula object, response left ~ operator, terms, separated + operators, right. Nonparametric smoothing terms indicated pb() penalised beta splines, cs smoothing splines, lo loess smooth terms random ra random terms, e.g. y~cs(x,df=5)+x1+x2*x3. sigma.formula formula object fitting model sigma parameter, formula , e.g. sigma.formula=~cs(x,df=5). nu.formula formula object fitting model nu parameter, e.g. nu.formula=~x tau.formula formula object fitting model tau parameter, e.g. tau.formula=~cs(x,df=2) family gamlss.family object, used define distribution link functions various parameters. distribution families supported gamlss() can found gamlss.family. Functions BI() (binomial) produce family object. Also can given without parentheses .e. BI. Family functions can take arguments, BI(mu.link=probit). data data frame containing variables occurring formula. missing, variables parent environment. method character indicating algorithm GAMLSS. Can either 'RS', 'CG' 'mixed'. method='RS' function use Rigby Stasinopoulos algorithm, method='CG' function use Cole Green algorithm, method='mixed' function use RS algorithm twice switching Cole Green algorithm 10 extra iterations. mu.fix logical, indicate whether mu parameter kept fixed fitting processes. sigma.fix logical, indicate whether sigma parameter kept fixed fitting processes. nu.fix logical, indicate whether nu parameter kept fixed fitting processes. tau.fix logical, indicate whether tau parameter kept fixed fitting processes. control sets control parameters outer iterations algorithm using gamlss.control function. vector 7 numeric values: () c.crit (convergence criterion algorithm), (ii) n.cyc (number cycles algorithm), (iii) mu.step (step length parameter mu), (iv) sigma.step (step length parameter sigma), (v) nu.step (step length parameter nu), (vi) tau.step (step length parameter tau), (vii) gd.tol (global deviance tolerance level). default values 7 parameters set c(0.001, 20, 1, 1, 1, 1, Inf). .control sets control parameters inner iterations RS algorithm using glim.control function. vector 4 numeric values: () cc (convergence criterion algorithm), (ii) cyc (number cycles algorithm), (iii) bf.cyc (number cycles backfitting algorithm), (iv) bf.tol (convergence criterion (tolerance level) backfitting algorithm). default values 4 parameters set c(0.001, 50, 30, 0.001). centiles logical, indicating whether function centiles() used tabulate sample percentages centile curve. Default set FALSE. xvar unique explanatory variable used centiles() function. variable used centiles argument set TRUE. restriction centiles function applies models one explanatory variable . newobj character string provides name output object stored data servers. Default gamlss_residuals.","code":""},{"path":"/reference/gamlssDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"gamlss object components native R gamlss function. Individual-level information like components y (response response) residuals (normalised quantile residuals model) disclosed client-side.","code":""},{"path":"/reference/gamlssDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"additional details see help header gamlss centiles functions native R gamlss package.","code":""},{"path":"/reference/gamlssDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/getAllLevelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"Retrieve Factor Levels Specific Columns","code":""},{"path":"/reference/getAllLevelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"","code":"getAllLevelsDS(df.name, factor_vars)"},{"path":"/reference/getAllLevelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"df.name string representing name data frame. factor_vars character vector specifying factor columns.","code":""},{"path":"/reference/getAllLevelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"list factor levels specified columns.","code":""},{"path":"/reference/getClassAllColsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"Get Class Columns Data Frame","code":""},{"path":"/reference/getClassAllColsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"","code":"getClassAllColsDS(df.name)"},{"path":"/reference/getClassAllColsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"df.name string representing name data frame.","code":""},{"path":"/reference/getClassAllColsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"tibble class column data frame.","code":""},{"path":"/reference/getWGSRDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"Calculate Growth Reference z-score given anthropometric measurement function similar R function getWGSR zscorer package.","code":""},{"path":"/reference/getWGSRDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"","code":"getWGSRDS(sex, firstPart, secondPart, index, standing = NA, thirdPart = NA)"},{"path":"/reference/getWGSRDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"sex name binary variable indicates sex subject. must coded 1 = male 2 = female. project variable sex different levels, recode levels 1 males 2 females using ds.recodeValues DataSHIELD function use ds.getWGSR. firstPart Name variable specifying: Weight (kg) BMI/, W/, W/H, W/L Head circumference (cm) HC/Height (cm) H/Length (cm) L/MUAC (cm) MUAC/Sub-scapular skinfold (mm) SSF/Triceps skinfold (mm) TSF/Give quoted variable name (e.g.) \"weight\". careful units (weight kg; height, length, head circumference, MUAC cm, skinfolds mm). secondPart Name variable specifying: Age (days) H/, HC/, L/, MUAC/, SSF/, TSF/Height (cm) BMI/, W/H Length (cm) W/L Give quoted variable name (e.g.) \"age\". careful units (age days; height length cm). index index calculated added data. One : bfa BMI age hca Head circumference age hfa Height age lfa Length age mfa MUAC age ssa Sub-scapular skinfold age tsa Triceps skinfold age wfa Weight age wfh Weight height wfl Weight length Give quoted index name (e.g.) \"wfh\". standing Variable specifying stature measured. NA (default) age (\"hfa\" \"lfa\") height rules (\"wfh\" \"wfl\") applied. must coded 1 = Standing; 2 = Supine; 3 = Unknown. Missing values recoded 3 = Unknown. Give single value (e.g.\"1\"). value specified height age rules applied. thirdPart Name variable specifying age (days) BMI/. Give quoted variable name (e.g.) \"age\". careful units (age days).","code":""},{"path":"/reference/getWGSRDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"ds.getWGSR assigns numeric vector includes z-scores specified index.","code":""},{"path":"/reference/getWGSRDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"function computes Growth Reference z-scores anthropometric data weight, height length, MUAC, head circumference, sub-scapular skinfold triceps skinfold. Note function might fail return NAs variables outside ranges given WGS (Child Growth Standards) reference (.e. 45 120 cm height 0 60 months age). user check ranges units data.","code":""},{"path":"/reference/getWGSRDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glm1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"glm1DS called by ds.glm — glm1DS","title":"glm1DS called by ds.glm — glm1DS","text":"first server-side aggregate function called ds.glm","code":""},{"path":"/reference/glm1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"glm1DS called by ds.glm — glm1DS","text":"","code":"glm1DS(formula, family, weights, offset, data)"},{"path":"/reference/glm1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"glm1DS called by ds.glm — glm1DS","text":"formula glm() formula consistent R syntax eg U~x+y+Z regress variables U x,y Z family glm() family consistent R syntax eg \"gaussian\", \"poisson\", \"binomial\" weights optional variable providing regression weights offset offset data optional character string specifying data.frame object holding data analysed specified model","code":""},{"path":"/reference/glm1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"glm1DS called by ds.glm — glm1DS","text":"List values GLM model.","code":""},{"path":"/reference/glm1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"glm1DS called by ds.glm — glm1DS","text":"aggregation function sets model structure creates starting beta.vector feeds, via ds.glm, glm2DS enable iterative fitting generalized linear model specified. details please see extensive header ds.glm.","code":""},{"path":"/reference/glm1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"glm1DS called by ds.glm — glm1DS","text":"Burton PR DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glm2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"glm2DS called by ds.glm — glm2DS","title":"glm2DS called by ds.glm — glm2DS","text":"second server-side aggregate function called ds.glm.","code":""},{"path":"/reference/glm2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"glm2DS called by ds.glm — glm2DS","text":"","code":"glm2DS(formula, family, beta.vect, offset, weights, dataName)"},{"path":"/reference/glm2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"glm2DS called by ds.glm — glm2DS","text":"formula glm() formula consistent R syntax eg U~x+y+Z regress variables U x, y Z family glm() family consistent R syntax eg \"gaussian\", \"poisson\", \"binomial\" beta.vect numeric vector created clientside function specifying vector regression coefficients current iteration offset optional variable providing regression offset weights optional variable providing regression weights dataName optional character string specifying data.frame object holding data analysed specified model ","code":""},{"path":"/reference/glm2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"glm2DS called by ds.glm — glm2DS","text":"List values GLM model","code":""},{"path":"/reference/glm2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"glm2DS called by ds.glm — glm2DS","text":"aggregate function uses model structure starting beta.vector constructed glm1DS iteratively fit generalized linear model specified. function glm2DS also carries series disclosure checks arguments data fail tests, model construction blocked appropriate serverside error message created returned ds.glm clientside. details please see extensive header ds.glm.","code":""},{"path":"/reference/glm2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"glm2DS called by ds.glm — glm2DS","text":"Paul Burton, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmPredictDS.ag.html","id":null,"dir":"Reference","previous_headings":"","what":"predict regression responses from a glm object — glmPredictDS.ag","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"identify return key components/summaries serverside glm_predict object can safely returned clientside without disclosure risk","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"","code":"glmPredictDS.ag( glmname.transmit, newdataname.transmit, output.type, se.fit, dispersion, terms.transmit, na.action )"},{"path":"/reference/glmPredictDS.ag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"glmname.transmit character string specifying name glm object serverside used prediction. Fully specified glmname argument ds.glmPredict newdataname.transmit character string specifying (optional) dataframe serverside look (potentially) new covariate values base predictions. Fully specified newdataname argument ds.glmPredict. output.type character string taking values 'response', 'link' 'terms'. Fully specified corresponding argument ds.glmPredict. se.fit logical standard errors fitted predictions required. Fully specified corresponding argument ds.glmPredict. dispersion numeric value specifying dispersion GLM fit assumed computing standard errors. Fully specified corresponding argument ds.glmPredict. terms.transmit character vector specifying subset terms return prediction. Fully specified 'terms' argument ds.glmPredict. na.action character string determining done missing values data.frame identified . Fully specified na.action argument ds.glmPredict.","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"components/summarising statistics serverside predict_glm object can safely transmitted clientside without risk disclosure. details see DataSHIELD help ds.glmPredict glmPredict.help native R predict.glm predict.glm native R","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"Serverside aggregate function called ds.glmPredict. called immediately assign function glmPredict.created predict_glm object serverside applying equivalent predict.glm() native R glm object serverside. aggregate function, glmPredict.ag, identifies returns components predict_glm object can safely returned clientside without risk disclosure. details see DataSHIELD help ds.glmPredict glmPredict.help native R predict.glm","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmPredictDS.as.html","id":null,"dir":"Reference","previous_headings":"","what":"predict regression responses from a glm object — glmPredictDS.as","title":"predict regression responses from a glm object — glmPredictDS.as","text":"create predict_glm object serverside applying equivalent predict.glm() native R glm object serverside. Identify return components predict_glm object can safely sent clientside without risk disclosure","code":""},{"path":"/reference/glmPredictDS.as.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"predict regression responses from a glm object — glmPredictDS.as","text":"","code":"glmPredictDS.as( glmname.transmit, newdataname.transmit, output.type, se.fit, dispersion, terms.transmit, na.action )"},{"path":"/reference/glmPredictDS.as.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"predict regression responses from a glm object — glmPredictDS.as","text":"glmname.transmit character string specifying name glm object serverside used prediction. Fully specified glmname argument ds.glmPredict newdataname.transmit character string specifying (optional) dataframe serverside look (potentially) new covariate values base predictions. Fully specified newdataname argument ds.glmPredict. output.type character string taking values 'response', 'link' 'terms'. Fully specified corresponding argument ds.glmPredict. se.fit logical standard errors fitted predictions required. Fully specified corresponding argument ds.glmPredict. dispersion numeric value specifying dispersion GLM fit assumed computing standard errors. Fully specified corresponding argument ds.glmPredict. terms.transmit character vector specifying subset terms return prediction. Fully specified 'terms' argument ds.glmPredict. na.action character string determining done missing values data.frame identified . Fully specified na.action argument ds.glmPredict.","code":""},{"path":"/reference/glmPredictDS.as.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"predict regression responses from a glm object — glmPredictDS.as","text":"glmPredict.writes new object serverside containing output precisely equivalent output predict.glm native R. details see DataSHIELD help ds.glmPredict help predict.glm native R","code":""},{"path":"/reference/glmPredictDS.as.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"predict regression responses from a glm object — glmPredictDS.as","text":"Serverside assign function called ds.glmPredict makes predictions regression responses based serverside glm object already created serverside ds.glmSLMA writes predict_glm object serverside. details see help ds.glmPredict help native R predict.glm","code":""},{"path":"/reference/glmPredictDS.as.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"predict regression responses from a glm object — glmPredictDS.as","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMA11DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMA11DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"","code":"glmSLMA11DS(formula, family, weights, offset, data)"},{"path":"/reference/glmSLMA11DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA weights character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. offset character string specifying variable used offset. Specified call ds.glmSLMA. data character string specifying name data.frame holding data model. Specified dataName call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"assesses returns information failure pass disclosure traps test model complexity (saturation). detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"glmSLMADS.assign aggregate function called clientside function ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS assign function glmSLMADS.assign detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"Paul Burton DataSHIELD Development Team (14/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"","code":"glmSLMA2DS(formula, family, offset, weights, newobj, dataName)"},{"path":"/reference/glmSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA offset character string specifying variable used offset. Specified call ds.glmSLMA. weights character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. newobj character string specifying name glm object written serverside glmSLMADS.assign. either name specified newobj argument ds.glmSLMA newobj unspecified NULL called new.glm.obj. dataName character string specifying name data.frame holding data model. Specified call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"quantitative, Boolean, character objects required enable SLMA pooling separate glm models fitted study - particular including study-specific regression coefficients corresponding standard errors.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"glmSLMADS.assign aggregate function called clientside function ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS assign function glmSLMADS.assign detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"Paul Burton DataSHIELD Development Team (14/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"","code":"glmSLMADS.assign(formula, family, offsetName, weightsName, dataName)"},{"path":"/reference/glmSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA offsetName character string specifying variable used offset. Specified call ds.glmSLMA. weightsName character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. dataName character string specifying name data.frame holding data model. Specified call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"writes glm object summarising fitted model serverside. detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"glmSLMADS.assign assign function called clientside function ds.glmSLMA. ds.glmSLMA also calls two aggregate functions glmSLMA1DS glmSLMA2DS. detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"Paul Burton DataSHIELD Development Team (14/7/20)","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize a glm object on the serverside — glmSummaryDS.ag","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"returns non-disclosive elements clientside glm object corresponding object holding output summary(glm object) serverside.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"","code":"glmSummaryDS.ag(x.transmit)"},{"path":"/reference/glmSummaryDS.ag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"x.transmit character string specifying name glm object serverside summarised. specified x.name argument ds.glmSummary","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"returns clientside non-disclosive elements (non-disclosive elements) specified serverside glm corresponding summary_glm object.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"Serverside aggregate function called ds.glmSummary. ds.glmSummary first calls glmSummaryDS.ag create glm_summary object serverside based applying native R's summary.glm() serverside glm object previously created ds.glmSLMA. calls glmSummaryDS.ag return clientside non-disclosive elements (non-disclosive elements) serverside glm corresponding summary_glm object.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSummaryDS.as.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize a glm object on the serverside — glmSummaryDS.as","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"summarize glm object serverside create summary_glm object. Also identify return components glm object summary_glm object can safely sent clientside without risk disclosure","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"","code":"glmSummaryDS.as(x.transmit)"},{"path":"/reference/glmSummaryDS.as.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"x.transmit character string specifying name glm object serverside summarised. specified x.name argument ds.glmSummary","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"writes object serverside precisely equivalent summary(glm object) native R","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"Serverside assign function called ds.glmSummary summarises glm object already created serverside fitting ds.glmSLMA writes summary_glm object serverside. details see help ds.glmSLMA help native R glm() summary.glm","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmerSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"glmerSLMA2DS fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data one multiple sources pooling via SLMA (study level meta-analysis)","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"","code":"glmerSLMA2DS( formula, offset, weights, dataName, family, control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL )"},{"path":"/reference/glmerSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"formula see help ds.glmerSLMA offset see help ds.glmerSLMA weights see help ds.glmerSLMA dataName see help ds.glmerSLMA family see help ds.glmerSLMA control_type see help ds.glmerSLMA control_value.transmit see help argument function ds.glmerSLMA nAGQ integer scalar, defaulting 1L. PRACTICE, MAY NECESSARY SET nAGQ 0L model appears converge perfectly well (e.g. verbose=2 demonstrates good initial convergence log-likelihood regression coefficients) formal convergence get declared - output produced - despite running model many iterations. nAGQ argument set nAGQ argument ds.glmerSLMA details can found help(ds.glmerSLMA) native R help glmer() verbose see help ds.glmerSLMA theta see help argument function ds.glmerSLMA fixef see help argument function ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"key model components see help ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"glmerSLMA2DS serverside function called ds.glmerSLMA clientside. analytic work engine glmer function R sits lme4 package. ds.glmerSLMA fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data single multiple sources. multiple data sources, glme fitted convergence data source independently estimates standard errors returned client thereby enabling cross-study pooling using study level meta-analysis (SLMA). default SLMA undertaken using metafor package, SLMA occurs clientside , far user concerned just standard R environment, user can choose use approach meta-analysis choose. Additional information fitting glmes using glmer engine can obtained using R help glmer lme4 package","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"Tom Bishop, additions Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"glmerSLMADS.assign glmerSLMA2DS fits generalized linear mixed effects model (glme) per study saves outcomes study","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"","code":"glmerSLMADS.assign( formula, offset, weights, dataName, family, control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL )"},{"path":"/reference/glmerSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"formula see help ds.glmerSLMA offset see help ds.glmerSLMA weights see help ds.glmerSLMA dataName see help ds.glmerSLMA family see help ds.glmerSLMA control_type see help ds.glmerSLMA control_value.transmit see help argument function ds.glmerSLMA nAGQ integer scalar, defaulting 1L. PRACTICE, MAY NECESSARY SET nAGQ 0L model appears converge perfectly well (e.g. verbose=2 demonstrates good initial convergence log-likelihood regression coefficients) formal convergence get declared - output produced - despite running model many iterations. nAGQ argument set nAGQ argument ds.glmerSLMA details can found help(ds.glmerSLMA) native R help glmer() verbose see help ds.glmerSLMA theta see help argument function ds.glmerSLMA fixef see help argument function ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"writes glmerMod object summarising fitted model serverside. detailed information see help ds.glmerSLMA.","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"glmerSLMADS.assign serverside function called ds.glmerSLMA clientside. analytic work engine glmer function R sits lme4 package. glmerSLMADS.assign fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data single data source saves regression outcomes serverside.","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/heatmapPlotDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"function calculates coordinates centroids n nearest neighbours.","code":""},{"path":"/reference/heatmapPlotDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"","code":"heatmapPlotDS(x.name, y.name, k, noise, method.indicator)"},{"path":"/reference/heatmapPlotDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"x.name character string providing name server-side numeric vector, x-variable. y.name character string providing name server-side numeric vector, y-variable. k number nearest neighbours centroid calculated method.indicator equal 1 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 2 (.e. probabilistic method). method.indicator number equal either 1 2. value equal 1 'deterministic' method used. value set 2 'probabilistic' method used.","code":""},{"path":"/reference/heatmapPlotDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"list x y coordinates centroids deterministic method used x y coordinated noisy data probabilistic method used, along classes x y inputs (class.x class.y)","code":""},{"path":"/reference/heatmapPlotDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"function finds n-1 nearest neighbours data point 2-dimensional space. nearest neighbours data points minimum Euclidean distances point interest. point interest n-1 nearest neighbours used calculation coordinates centroid n points. Centroid referred centre mass, .e. x-coordinate centroid average value x-coordinates n nearest neighbours y-coordinate centroid average y-coordinates n nearest neighbours. coordinates centroids return client side function can used plot non-disclosive graphs (e.g. scatter plots, heatmap plots, contour plots, etc).","code":""},{"path":"/reference/heatmapPlotDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/hetcorDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Heterogeneous Correlation Matrix — hetcorDS","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"function based hetcor function R package polycor.","code":""},{"path":"/reference/hetcorDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"","code":"hetcorDS(data, ML, std.err, bins, pd, use)"},{"path":"/reference/hetcorDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"data name data frame consisting factors, ordered factors, logical variables, character variables, /numeric variables, first several variables. ML TRUE, compute maximum-likelihood estimates; FALSE (default), compute quick two-step estimates. std.err TRUE (default), compute standard errors. bins number bins use continuous variables testing bivariate normality; default 4. pd TRUE (default) correlation matrix positive-definite, attempt made adjust positive-definite matrix, using nearPD function Matrix package. Note default arguments nearPD used (except corr=TRUE); control call nearPD directly. use \"complete.obs\", remove observations missing data; \"pairwise.complete.obs\", compute correlation using observations valid data pair variables.","code":""},{"path":"/reference/hetcorDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Returns object class \"hetcor\" following components: correlation matrix; type correlation: \"Pearson\", \"Polychoric\", \"Polyserial\"; standard errors correlations, requested; number (numbers) observations correlations based; p-values tests bivariate normality pair variables; method missing data handled: \"complete.obs\" \"pairwise.complete.obs\"; TRUE ML estimates, FALSE two-step estimates.","code":""},{"path":"/reference/hetcorDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Computes heterogeneous correlation matrix, consisting Pearson product-moment correlations numeric variables, polyserial correlations numeric ordinal variables, polychoric correlations ordinal variables.","code":""},{"path":"/reference/hetcorDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/histogram1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"returns the minimum and the maximum of the input numeric vector — histogram1DS","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"function returns minimum maximum input numeric vector depends argument method.indicator. method.indicator set 1 (.e. 'smallCellsRule' used) computed minimum maximum values multiplied small random number. method.indicator set 2 (.e. 'deterministic' method used) function returns minimum maximum values vector scaled centroids. method.indicator set 3 (.e. 'probabilistic' method used) function returns minimum maximum values generated 'noisy' vector.","code":""},{"path":"/reference/histogram1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"","code":"histogram1DS(x, method.indicator, k, noise)"},{"path":"/reference/histogram1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"x character string providing name server-side numeric vector histogram desired. method.indicator number equal either 1, 2 3 indicating method disclosure control used generation histogram. value equal 1 'smallCellsRule' used. value equal 2 'deterministic' method used. value set 3 'probabilistic' method used. k number nearest neighbours centroid calculated method.indicator equal 2 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 3 (.e. probabilistic method).","code":""},{"path":"/reference/histogram1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"list numeric vector containing minimum maximum values vector (range) class input vector (class)","code":""},{"path":"/reference/histogram1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/histogram2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes a histogram of the input variable without plotting. — histogram2DS","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"function produces information required plot histogram. done without allowing bins (cells) number counts less pre-specified disclosure control set minimum cell size table. bin less counts threshold counts density replaced 0 value.","code":""},{"path":"/reference/histogram2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"","code":"histogram2DS(x, num.breaks, min, max, method.indicator, k, noise)"},{"path":"/reference/histogram2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"x character string providing name server-side numeric vector histogram desired. num.breaks number breaks range variable divided. min numeric, lower limit distribution. max numeric, upper limit distribution. method.indicator number equal either 1, 2 3 indicating method disclosure control used generation histogram. value equal 1 'smallCellsRule' used. value equal 2 'deterministic' method used. value set 3 'probabilistic' method used. k number nearest neighbours centroid calculated method.indicator equal 2 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 3 (.e. probabilistic method).","code":""},{"path":"/reference/histogram2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"list object class histogram number invalid cells","code":""},{"path":"/reference/histogram2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"Please find details documentation clientside ds.histogram function.","code":""},{"path":"/reference/histogram2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/igb_standardsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"Converts birth measurements INTERGROWTH z-scores/centiles (generic)","code":""},{"path":"/reference/igb_standardsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"","code":"igb_standardsDS( gagebrth = gagebrth, z = z, p = p, val = val, var = var, sex = sex, fun = fun )"},{"path":"/reference/igb_standardsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"gagebrth name \"gestational age birth days\" variable. z z-score(s) convert (must 0 1). Default value 0. value used fun set \"igb_zscore2value\". p centile(s) convert (must 0 100). Default value p=50. value used fun set \"igb_centile2value\". val name anthropometric variable convert. var name measurement convert (\"lencm\", \"wtkg\", \"hcircm\", \"wlr\") sex name sex factor variable. variable coded Male/Female. coded differently (e.g. 0/1), can use ds.recodeValues function recode categories Male/Female use ds.igb_standards fun name function used. can one : \"igb_centile2value\", \"igb_zscore2value\", \"igb_value2zscore\" (default), \"igb_value2centile\".","code":""},{"path":"/reference/igb_standardsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"assigns converted measurement new object server-side","code":""},{"path":"/reference/igb_standardsDS.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"gestational ages 24 33 weeks, INTERGROWTH early preterm standard used.","code":""},{"path":"/reference/igb_standardsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/isNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if a vector is empty — isNaDS","title":"Checks if a vector is empty — isNaDS","text":"function similar R function .na instead vector booleans returns just one boolean tell element missing values.","code":""},{"path":"/reference/isNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if a vector is empty — isNaDS","text":"","code":"isNaDS(x)"},{"path":"/reference/isNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if a vector is empty — isNaDS","text":"x character string, name server-side vector","code":""},{"path":"/reference/isNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if a vector is empty — isNaDS","text":"list two elements: .na (TRUE vector contains NAs, FALSE otherwise) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/isNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if a vector is empty — isNaDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/isValidDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if an input is valid — isValidDS","title":"Checks if an input is valid — isValidDS","text":"Tells object server side valid.","code":""},{"path":"/reference/isValidDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if an input is valid — isValidDS","text":"","code":"isValidDS(x)"},{"path":"/reference/isValidDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if an input is valid — isValidDS","text":"x character string, name vector (numeric, integer, factor, character, logical), data.frame matrix","code":""},{"path":"/reference/isValidDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if an input is valid — isValidDS","text":"list valid, boolean TRUE input valid FALSE , class, class input object client-side consistency checking","code":""},{"path":"/reference/isValidDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Checks if an input is valid — isValidDS","text":"function checks object valid.","code":""},{"path":"/reference/isValidDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if an input is valid — isValidDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/kurtosis1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the kurtosis of a numeric variable — kurtosis1DS","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"function calculates kurtosis numeric variable study separately.","code":""},{"path":"/reference/kurtosis1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"","code":"kurtosis1DS(x, method)"},{"path":"/reference/kurtosis1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"x string character, name numeric variable. method integer 1 3 selecting one algorithms computing kurtosis detailed headers client-side ds.kurtosis function.","code":""},{"path":"/reference/kurtosis1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"list including kurtosis input numeric variable, number valid observations class, class input object client-side consistency checking.","code":""},{"path":"/reference/kurtosis1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"function calculates kurtosis input variable x three different methods. method specified argument method client-side ds.kurtosis function.","code":""},{"path":"/reference/kurtosis1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/kurtosis2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the kurtosis of a numeric variable — kurtosis2DS","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"function calculates summary statistics returned client-side used estimation combined kurtosis numeric variable across studies.","code":""},{"path":"/reference/kurtosis2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"","code":"kurtosis2DS(x, global.mean)"},{"path":"/reference/kurtosis2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"x string character, name numeric variable. global.mean numeric, combined mean input variable across studies.","code":""},{"path":"/reference/kurtosis2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"list including sum quartic differences values x global mean x across studies, sum squared differences values x global mean x across studies, number valid observations (.e. length x excluding missing values), class, class input object client-side consistency checking.","code":""},{"path":"/reference/kurtosis2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"function calculates sum squared differences values x global mean x across studies, sum quatric differences values x global mean x across studies number valid observations input variable x.","code":""},{"path":"/reference/kurtosis2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lengthDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the length of a vector or list — lengthDS","title":"Returns the length of a vector or list — lengthDS","text":"function similar R function length.","code":""},{"path":"/reference/lengthDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the length of a vector or list — lengthDS","text":"","code":"lengthDS(x)"},{"path":"/reference/lengthDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the length of a vector or list — lengthDS","text":"x string character, name vector list","code":""},{"path":"/reference/lengthDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the length of a vector or list — lengthDS","text":"list two elements: length (number elements input vector list) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/lengthDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the length of a vector or list — lengthDS","text":"function returns length input vector list.","code":""},{"path":"/reference/lengthDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the length of a vector or list — lengthDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/levelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the levels of a factor vector — levelsDS","title":"Returns the levels of a factor vector — levelsDS","text":"function similar R function levels.","code":""},{"path":"/reference/levelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the levels of a factor vector — levelsDS","text":"","code":"levelsDS(x)"},{"path":"/reference/levelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the levels of a factor vector — levelsDS","text":"x character string, name factor vector","code":""},{"path":"/reference/levelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the levels of a factor vector — levelsDS","text":"list one element: Levels (factor levels present vector)","code":""},{"path":"/reference/levelsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the levels of a factor vector — levelsDS","text":"function returns levels input vector list.","code":""},{"path":"/reference/levelsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the levels of a factor vector — levelsDS","text":"Alex Westerberg, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"lexis1DS — lexis1DS","title":"lexis1DS — lexis1DS","text":"first server-side function called ds.lexis.","code":""},{"path":"/reference/lexis1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lexis1DS — lexis1DS","text":"","code":"lexis1DS(exitCol = NULL)"},{"path":"/reference/lexis1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lexis1DS — lexis1DS","text":"exitCol character string specifying variable holding time individual censored fails","code":""},{"path":"/reference/lexis1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lexis1DS — lexis1DS","text":"List `max.time`","code":""},{"path":"/reference/lexis1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lexis1DS — lexis1DS","text":"aggregate function. details see extensive header ds.lexis.","code":""},{"path":"/reference/lexis1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lexis1DS — lexis1DS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"lexis2DS — lexis2DS","title":"lexis2DS — lexis2DS","text":"second serverside function called ds.lexis.","code":""},{"path":"/reference/lexis2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lexis2DS — lexis2DS","text":"","code":"lexis2DS( datatext = NULL, intervalWidth, maxmaxtime, idCol, entryCol, exitCol, statusCol, vartext = NULL )"},{"path":"/reference/lexis2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lexis2DS — lexis2DS","text":"datatext clientside provided character string specifying data.frame holding data set expanded intervalWidth clientside generated character string specifying width survival epochs expanded data maxmaxtime clientside generated object specifying maximum follow time sources idCol clientside generated character string specifying variable holding IDs individuals data set expanded entryCol clientside specified character string identifying variable holding time individual starts follow exitCol clientside specified character string identifying variable holding time individual ends follow (censored fails) statusCol clientside specified character string identifying variable holding final censoring status (failed/censored) vartext clientside provided vector character strings denoting column names additional variables include final expanded table. 'variables' argument set (null) 'data' argument set full data.frame expanded carried forward","code":""},{"path":"/reference/lexis2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lexis2DS — lexis2DS","text":"List `expanded.table`","code":""},{"path":"/reference/lexis2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lexis2DS — lexis2DS","text":"assign function actually creates expanded dataframe containing survival data piecewise exponential regression. lexis2DS also carries series disclosure checks arguments data fail tests, creation expanded dataframe blocked appropriate serverside error message stored. details see extensive header ds.lexis.","code":""},{"path":"/reference/lexis2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lexis2DS — lexis2DS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis3DS.html","id":null,"dir":"Reference","previous_headings":"","what":"@title lexis3DS — lexis3DS","title":"@title lexis3DS — lexis3DS","text":"third serverside function called ds.lexis.","code":""},{"path":"/reference/lexis3DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"@title lexis3DS — lexis3DS","text":"","code":"lexis3DS()"},{"path":"/reference/lexis3DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"@title lexis3DS — lexis3DS","text":"Data frame `messageobj` object","code":""},{"path":"/reference/lexis3DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"@title lexis3DS — lexis3DS","text":"assign function simplifies returned output ds.lexis. Specifically, without lexis3DS output consists table within list, lexis3DS converts directly dataframe. details see extensive header ds.lexis.","code":""},{"path":"/reference/listDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce objects into a list — listDS","title":"Coerce objects into a list — listDS","text":"function similar R function 'list'","code":""},{"path":"/reference/listDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce objects into a list — listDS","text":"","code":"listDS(x.names = NULL, eltnames = NULL)"},{"path":"/reference/listDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce objects into a list — listDS","text":"x.names character vector object names coerce list. eltnames character vector, names elements list.","code":""},{"path":"/reference/listDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce objects into a list — listDS","text":"list","code":""},{"path":"/reference/listDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerce objects into a list — listDS","text":"Unlike R function 'list' takes also vector characters, names elements output list.","code":""},{"path":"/reference/listDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerce objects into a list — listDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"listDisclosureSettingsDS — listDisclosureSettingsDS","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"serverside function aggregate function called ds.listDisclosureSettings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"","code":"listDisclosureSettingsDS()"},{"path":"/reference/listDisclosureSettingsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"List DataSHIELD disclosure settings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"details see extensive header ds.listDisclosureSettings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team","code":""},{"path":"/reference/lmerSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"lmerSLMA2DS serverside function fits linear mixed effects model (lme) - .e. can include fixed random effects - data one multiple sources pooling via SLMA (study level meta-analysis)","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"","code":"lmerSLMA2DS( formula, offset, weights, dataName, REML = TRUE, control_type, control_value.transmit, optimizer, verbose = 0 )"},{"path":"/reference/lmerSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"formula see help ds.lmerSLMA offset see help ds.lmerSLMA weights see help ds.lmerSLMA dataName see help ds.lmerSLMA REML see help ds.lmerSLMA control_type see help ds.lmerSLMA control_value.transmit see help argument function ds.lmerSLMA optimizer see help ds.lmerSLMA verbose see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"key model components see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"lmerSLMA2DS serverside function called ds.lmerSLMA clientside. analytic work engine lmer function R sits lme4 package. ds.lmerSLMA fits linear mixed effects model (lme) - can include fixed random effects - data single multiple sources. multiple data sources, lme fitted convergence data source independently estimates standard errors returned client thereby enabling cross-study pooling using study level meta-analysis (SLMA). default SLMA undertaken using metafor package, SLMA occurs clientside , far user concerned just standard R environment, user can choose use approach meta-analysis choose. detailed help aspect lmerSLM2DS please see extensive help ds.lmerSLMA. Additional information fitting lmes using lmer engine can obtained using R help lmer lme4 package","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"Tom Bishop, additions Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"lmerSLMADS.assign lmerSLMA2DS fits linear mixed effects model (lme) per study saves outcomes study","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"","code":"lmerSLMADS.assign( formula, offset, weights, dataName, REML = TRUE, control_type, control_value.transmit, optimizer, verbose = 0 )"},{"path":"/reference/lmerSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"formula see help ds.lmerSLMA offset see help ds.lmerSLMA weights see help ds.lmerSLMA dataName see help ds.lmerSLMA REML see help ds.lmerSLMA control_type see help ds.lmerSLMA control_value.transmit see help argument function ds.lmerSLMA optimizer see help ds.lmerSLMA verbose see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"writes lmerMod object summarising fitted model serverside. detailed information see help ds.lmerSLMA.","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"lmerSLMADS.assign serverside function called ds.lmerSLMA clientside. analytic work engine lmer function R sits lme4 package. lmerSLMADS.assign fits linear mixed effects model (lme) including fixed random effects - data single data source saves regression outcomes serverside.","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"TDemetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/logDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the logarithm values of the input variable — logDS","title":"Computes the logarithm values of the input variable — logDS","text":"function similar R function log.","code":""},{"path":"/reference/logDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the logarithm values of the input variable — logDS","text":"","code":"logDS(x, base = exp(1))"},{"path":"/reference/logDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the logarithm values of the input variable — logDS","text":"x string character, name numeric integer vector base positive number, base logarithms computed. Default exp(1).","code":""},{"path":"/reference/logDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the logarithm values of the input variable — logDS","text":"object specified newobj argument ds.log (default name log.newobj) written serverside. output object class numeric.","code":""},{"path":"/reference/logDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the logarithm values of the input variable — logDS","text":"function computes logarithm values input numeric integer vector. default natural logarithms computed.","code":""},{"path":"/reference/logDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the logarithm values of the input variable — logDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"lists all objects on a serverside environment — lsDS","title":"lists all objects on a serverside environment — lsDS","text":"creates list names objects specified serverside environment","code":""},{"path":"/reference/lsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lists all objects on a serverside environment — lsDS","text":"","code":"lsDS(search.filter = NULL, env.to.search)"},{"path":"/reference/lsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lists all objects on a serverside environment — lsDS","text":"search.filter either NULL character string (potentially including '*' wildcards) specifying required search criteria. argument fully specified corresponding argument clientside function. env..search integer (e.g. format '2' '5L' format) specifying position search path environment explored. argument fully specified corresponding argument clientside function.","code":""},{"path":"/reference/lsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lists all objects on a serverside environment — lsDS","text":"list containing: (1) name/details serverside R environment ds.ls searched; (2) vector character strings giving names objects meeting naming criteria specified argument specified R serverside environment; (3) nature search filter string actually applied","code":""},{"path":"/reference/lsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lists all objects on a serverside environment — lsDS","text":"Serverside aggregate function lsDS called clientside function ds.ls. running analyses one may want know objects already generated. request disclosive returns names objects contents. default, objects current 'active analytic environment' (\".GlobalEnv\") displayed. environment contains objects serverside DataSHIELD using main analysis written serverside process managing undertaking analysis (variables, scalars, matrices, data.frames etc). details see help ds.ls function native R function ls","code":""},{"path":"/reference/lsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lists all objects on a serverside environment — lsDS","text":"Gaye, (2015). Updated extended Paul Burton (2020).","code":""},{"path":"/reference/lsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"function based native R function lspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/lsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"","code":"lsplineDS(x = x, knots = NULL, marginal = FALSE, names = NULL)"},{"path":"/reference/lsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"x name input numeric variable knots numeric vector knot positions marginal logical, parametrize spline, see Details names, character, vector names constructed variables","code":""},{"path":"/reference/lsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"lspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/lsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment.","code":""},{"path":"/reference/lsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDS assign function called by ds.matrix — matrixDS","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Creates matrix serverside","code":""},{"path":"/reference/matrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"","code":"matrixDS(mdata.transmit, from, nrows.transmit, ncols.transmit, byrow, dimnames)"},{"path":"/reference/matrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"mdata.transmit specifies elements matrix created. Fully specified argument ds.matrix character string specifying source nature . Fully specified <> argument ds.matrix nrows.transmit specifies number rows matrix created. Fully specified argument ds.matrix ncols.transmit specifies number columns matrix created. Fully specified argument ds.matrix byrow logical value specifying whether, vector, matrix created filled row row column column. Fully specified argument ds.matrix dimnames dimnames attribute matrix: NULL list length 2 giving row column names respectively. empty list treated NULL, list length one row names . Fully specified argument ds.matrix","code":""},{"path":"/reference/matrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Output matrix written serverside. details see help ds.matrix","code":""},{"path":"/reference/matrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Similar matrix() function native R. Creates matrix dimensions specified arguments assigns values elements based argument","code":""},{"path":"/reference/matrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDet1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Calculates determinant square matrix returns output clientside","code":""},{"path":"/reference/matrixDet1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"","code":"matrixDet1DS(M1.name = NULL, logarithm)"},{"path":"/reference/matrixDet1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"M1.name character string specifying name matrix determinant calculated logarithm logical. Default FALSE, returns determinant , TRUE returns logarithm modulus determinant.","code":""},{"path":"/reference/matrixDet1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Output determinant matrix identified argument returned clientside. details see help ds.matrixDet","code":""},{"path":"/reference/matrixDet1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Calculates determinant square matrix (additional information see help det function native R). operation possible number columns rows .","code":""},{"path":"/reference/matrixDet1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDet2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Calculates determinant square matrix writes output serverside","code":""},{"path":"/reference/matrixDet2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"","code":"matrixDet2DS(M1.name = NULL, logarithm)"},{"path":"/reference/matrixDet2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"M1.name character string specifying name matrix determinant calculated logarithm logical. Default FALSE, returns determinant , TRUE returns logarithm modulus determinant.","code":""},{"path":"/reference/matrixDet2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Output determinant matrix identified argument written serverside. details see help ds.matrixDet","code":""},{"path":"/reference/matrixDet2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Calculates determinant square matrix (additional information see help det function native R). operation possible number columns rows .","code":""},{"path":"/reference/matrixDet2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDiagDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Extracts diagonal vector square matrix creates diagonal matrix based vector scalar value writes output serverside","code":""},{"path":"/reference/matrixDiagDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"","code":"matrixDiagDS(x1.transmit, aim, nrows.transmit)"},{"path":"/reference/matrixDiagDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"x1.transmit identifies input matrix vector. Fully specified argument ds.matrixDiag. details see help ds.matrixDiag. aim character string specifying behaviour required function. Fully specified argument ds.matrixDiag. details see help ds.matrixDiag. nrows.transmit scalar value forcing number rows columns output matrix.Fully specified argument ds.matrixDiag. details see help ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Output matrix vector specified argument (default name diag_) written serverside. details see help ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"details see help function ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDimnamesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Adds dimnames (row names, column names ) matrix serverside.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"","code":"matrixDimnamesDS(M1.name = NULL, dimnames)"},{"path":"/reference/matrixDimnamesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"M1.name Specifies name serverside matrix dimnames added. Fully specified argument function ds.matrixDimnames. details see help ds.matrixDimnames. dimnames dimnames attribute matrix: NULL list length 2 giving row column names respectively. Fully specified argument function ds.matrixDimnames. details see help ds.matrixDimnames.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Output serverside matrix specified argument (default name diag_) specified dimnames (row column names) written serverside.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Adds dimnames (row names, column names ) matrix serverside. Similar dimnames function native R. details see help function ds.matrixDimnames","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixInvertDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Inverts square matrix writes output serverside","code":""},{"path":"/reference/matrixInvertDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"","code":"matrixInvertDS(M1.name = NULL)"},{"path":"/reference/matrixInvertDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"M1.name character string specifying name matrix inverted","code":""},{"path":"/reference/matrixInvertDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Output matrix representing inverse written serverside. details see help ds.matrixInvert","code":""},{"path":"/reference/matrixInvertDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Undertakes standard matrix inversion. operation possible number columns rows matrix non-singular - positive definite (eg row column zeros)","code":""},{"path":"/reference/matrixInvertDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixMultDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Calculates matrix product two matrices writes output serverside","code":""},{"path":"/reference/matrixMultDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"","code":"matrixMultDS(M1.name = NULL, M2.name = NULL)"},{"path":"/reference/matrixMultDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"M1.name character string specifying name first matrix (M1) argument specified M1 argument original call ds.matrixMult M2.name character string specifying name second matrix (M2) argument specified M1 argument original call ds.matrixMult","code":""},{"path":"/reference/matrixMultDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Output matrix representing product M1 M2 written serverside. details see help ds.matrixMult","code":""},{"path":"/reference/matrixMultDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Undertakes standard matrix multiplication input matrices B dimensions : mxn B: nxp output C dimensions mxp element C[,j] value equal dot product row column j B dot product obtained sum([,1]*B[1,j] + [,2]*B[2,j] + .... + [,n]*B[n,j]). calculation valid number columns number rows B","code":""},{"path":"/reference/matrixMultDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixTransposeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Transposes matrix writes output serverside","code":""},{"path":"/reference/matrixTransposeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"","code":"matrixTransposeDS(M1.name = NULL)"},{"path":"/reference/matrixTransposeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"M1.name character string specifying name matrix transposed","code":""},{"path":"/reference/matrixTransposeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Output matrix representing transpose written serverside. details see help ds.matrixTranspose","code":""},{"path":"/reference/matrixTransposeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Undertakes standard matrix transposition. operation converts matrix matrix C element C[,j] matrix C equals element [j,] matrix . Matrix therefore number rows matrix C columns vice versa.","code":""},{"path":"/reference/matrixTransposeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/mdPatternDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Missing data pattern with disclosure control — mdPatternDS","title":"Missing data pattern with disclosure control — mdPatternDS","text":"function serverside aggregate function computes missing data pattern using mice::md.pattern applies disclosure control prevent revealing small cell counts.","code":""},{"path":"/reference/mdPatternDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Missing data pattern with disclosure control — mdPatternDS","text":"","code":"mdPatternDS(x)"},{"path":"/reference/mdPatternDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Missing data pattern with disclosure control — mdPatternDS","text":"x character string specifying name data frame matrix containing data analyze missing patterns.","code":""},{"path":"/reference/mdPatternDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Missing data pattern with disclosure control — mdPatternDS","text":"list containing: pattern missing data pattern matrix disclosure control applied valid Logical indicating patterns meet disclosure requirements message message describing validity status class class input object, client-side consistency checking","code":""},{"path":"/reference/mdPatternDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Missing data pattern with disclosure control — mdPatternDS","text":"function calls mice::md.pattern function generate matrix showing missing data patterns input data. ensure disclosure control, pattern counts threshold (nfilter.tab, default=3) suppressed. Suppression Method: pattern count threshold: - Row name changed \"suppressed()\" N threshold - pattern values row set NA - Summary row also set NA (prevents back-calculation) Output Matrix Structure: - Rows represent different missing data patterns (plus summary row bottom) - Row names contain pattern counts (\"suppressed()\" invalid patterns) - Columns show 1 variable observed, 0 missing - Last column shows total number missing values per pattern - Last row shows total number missing values per variable Note Pooling: function called ds.mdPattern type='combine', suppressed patterns excluded pooling prevent disclosure subtraction. means pooled counts may underestimate true total patterns suppressed studies.","code":""},{"path":"/reference/mdPatternDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Missing data pattern with disclosure control — mdPatternDS","text":"Xavier Escribà montagut DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/meanDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes statistical mean of a vector — meanDS","title":"Computes statistical mean of a vector — meanDS","text":"Calculates mean value.","code":""},{"path":"/reference/meanDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes statistical mean of a vector — meanDS","text":"","code":"meanDS(x)"},{"path":"/reference/meanDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes statistical mean of a vector — meanDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/meanDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes statistical mean of a vector — meanDS","text":"list, estimated mean, number missing values, number valid values, total number values, class, class input object client-side consistency checking","code":""},{"path":"/reference/meanDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes statistical mean of a vector — meanDS","text":"length input vector less set filter missing value returned.","code":""},{"path":"/reference/meanDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes statistical mean of a vector — meanDS","text":"Gaye , Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/meanSdGpDS.html","id":null,"dir":"Reference","previous_headings":"","what":"MeanSdGpDS — meanSdGpDS","title":"MeanSdGpDS — meanSdGpDS","text":"Server-side function called ds.meanSdGp","code":""},{"path":"/reference/meanSdGpDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MeanSdGpDS — meanSdGpDS","text":"","code":"meanSdGpDS(x, index)"},{"path":"/reference/meanSdGpDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MeanSdGpDS — meanSdGpDS","text":"x client-side supplied character string identifying variable means/SDs calculated index client-side supplied character string identifying factor across means/SDs calculated","code":""},{"path":"/reference/meanSdGpDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MeanSdGpDS — meanSdGpDS","text":"List results group statistics","code":""},{"path":"/reference/meanSdGpDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MeanSdGpDS — meanSdGpDS","text":"Computes mean standard deviation across groups defined one factor","code":""},{"path":"/reference/meanSdGpDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MeanSdGpDS — meanSdGpDS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/mergeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"mergeDS (assign function) called by ds.merge — mergeDS","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"merges (links) two data.frames together based common values defined vectors data.frame","code":""},{"path":"/reference/mergeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"","code":"mergeDS( x.name, y.name, by.x.names.transmit, by.y.names.transmit, all.x, all.y, sort, suffixes.transmit, no.dups, incomparables )"},{"path":"/reference/mergeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"x.name, name first data.frame merged specified inverted commas. Specified via argument ds.merge function y.name, name second data.frame merged specified inverted commas. Specified via argument ds.merge function .x.names.transmit name single variable vector names multiple variables (transmittable form) containing IDs data data.frame x merged/linked data.frame y. Specified via argument <.x.names> ds.merge function .y.names.transmit name single variable vector names multiple variables (transmittable form) containing IDs data data.frame y merged/linked data.frame x. Specified via argument <.y.names> ds.merge function .x logical, TRUE, extra rows added output, one row x matching row y. Specified via argument <.x> ds.merge function. Default = FALSE. .y logical, TRUE, extra rows added output, one row y matching row x. Specified via argument <.y> ds.merge function. Default = FALSE. sort logical, TRUE merged result sorted elements .x.names .y.names columns. Specified via argument ds.merge function. Default = TRUE. suffixes.transmit character vector length 2 (transmittable form) specifying suffixes used making unique common column names two input data.frames appear merged data.frame. Specified via argument ds.merge function. Default '.x' '.y'. .dups logical, TRUE suffixes appended cases rigorously avoid duplicated column names merged data.frame. Specified via argument <.dups> ds.merge function. Default TRUE apparently implicitly FALSE R version 3.5.0. incomparables, values intended merging one column matched. See 'match' help Native R merge function. Specified via argument ds.merge","code":""},{"path":"/reference/mergeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"merged data.frame specified argument ds.merge (default 'x.name_y.name' argument NULL) written serverside. addition, two validity messages returned clientside indicating whether created data source whether valid form. form valid least one study may studysideMessage can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message() print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message() return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/mergeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"information see details native R function merge DataSHIELD clientside function ds.merge.","code":""},{"path":"/reference/mergeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/metadataDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the metadata, if any, about the specified variable — metadataDS","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"function returns metadata, , specified variable.","code":""},{"path":"/reference/metadataDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"","code":"metadataDS(x)"},{"path":"/reference/metadataDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"x string character, containing name specified variable","code":""},{"path":"/reference/metadataDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"list containing metadata. elements list depend metadata available.","code":""},{"path":"/reference/metadataDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"function returns metadata, obtained attributes function.","code":""},{"path":"/reference/metadataDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"Stuart Wheater, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/miceDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Aggregate function called by ds.mice — miceDS","title":"Aggregate function called by ds.mice — miceDS","text":"function wrapper function mice mice R package. function creates multiple imputations (replacement values) multivariate missing data. method based Fully Conditional Specification, incomplete variable imputed separate model. MICE algorithm can impute mixes continuous, binary, unordered categorical ordered categorical data. addition, MICE can impute continuous two-level data, maintain consistency imputations means passive imputation.","code":""},{"path":"/reference/miceDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Aggregate function called by ds.mice — miceDS","text":"","code":"miceDS( data = data, m = m, maxit = maxit, method = method, post = post, seed = seed, predictorMatrix = predictorMatrix, ncol.pred.mat = ncol.pred.mat, newobj_mids = newobj_mids, newobj_df = newobj_df )"},{"path":"/reference/miceDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Aggregate function called by ds.mice — miceDS","text":"data data frame matrix containing incomplete data. m Number multiple imputations. default m=5. maximum allowed number DataSHIELD m=20. maxit scalar giving number iterations. default 5. maximum allowed number DataSHIELD maxit=30. method Can either single string, vector strings length ncol(data), specifying imputation method used column data. specified single string, method used blocks. default imputation method (argument specified) depends measurement level target column, regulated defaultMethod argument native R mice function. Columns need imputed empty method \"\". post vector strings length ncol(data) specifying expressions strings. string parsed executed within sampler() function post-process imputed values iterations. default vector empty strings, indicating post-processing. Multivariate (block) imputation methods ignore post parameter. seed either NA (default) \"fixed\". seed set \"fixed\" fixed seed random number generator study-specific used. predictorMatrix numeric matrix ncol(data) rows ncol(data) columns, containing 0/1 data specifying set predictors used target column. row corresponds variable imputed. value 1 means column variable used predictor target variables (rows). default, predictorMatrix square matrix ncol(data) rows columns 1's, except diagonal. ncol.pred.mat number columns predictorMatrix. newobj_mids character string provides name output mids object stored data servers. Default mids_object. newobj_df character string provides name output dataframes stored data servers. Default imputationSet. example, m=5, newobj_df=\"imputationSet\", five imputed dataframes saved servers names imputationSet.1, imputationSet.2, imputationSet.3, imputationSet.4, imputationSet.5.","code":""},{"path":"/reference/miceDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Aggregate function called by ds.mice — miceDS","text":"list three elements: method, predictorMatrix post. function also saves server mids object completed datasets dataframes.","code":""},{"path":"/reference/miceDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Aggregate function called by ds.mice — miceDS","text":"additional details see help header mice function native R mice package.","code":""},{"path":"/reference/miceDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Aggregate function called by ds.mice — miceDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/namesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the names of a list object — namesDS","title":"Return the names of a list object — namesDS","text":"Returns names designated server-side list","code":""},{"path":"/reference/namesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the names of a list object — namesDS","text":"","code":"namesDS(xname.transmit)"},{"path":"/reference/namesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the names of a list object — namesDS","text":"xname.transmit character string specifying name list.","code":""},{"path":"/reference/namesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the names of a list object — namesDS","text":"namesDS returns client-side names list object stored server-side.","code":""},{"path":"/reference/namesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Return the names of a list object — namesDS","text":"namesDS aggregate function called ds.names. function similar native R function names subsume functionality, example, works extract names already exist, create new names objects. function restricted objects type list, includes objects primary class list return TRUE native R function .list. example, includes multi-component object created fitting generalized linear model using ds.glmSLMA. resultant object saved separate server formally double class \"glm\" \"ls\" responds TRUE .list(),","code":""},{"path":"/reference/namesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Return the names of a list object — namesDS","text":"Amadou Gaye, updated Paul Burton 25/06/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/nsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"function based native R function ns splines package. function generate B-spline basis matrix natural cubic spline.","code":""},{"path":"/reference/nsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"","code":"nsDS(x, df, knots, intercept, Boundary.knots)"},{"path":"/reference/nsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"x predictor variable. Missing values allowed. df degrees freedom. One can supply df rather knots; ns() chooses df - 1 - intercept knots suitably chosen quantiles x (ignore missing values). default, df = NULL, sets number inner knots length(knots). knots breakpoints define spline. default knots; together natural boundary conditions results basis linear regression x. Typical values mean median one knot, quantiles knots. See also Boundary.knots. intercept TRUE, intercept included basis; default FALSE. Boundary.knots boundary points impose natural boundary conditions anchor B-spline basis (default range data). knots Boundary.knots supplied, basis parameters depend x. Data can extend beyond Boundary.knots","code":""},{"path":"/reference/nsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"matrix dimension length(x) * df either df supplied knots supplied, df = length(knots) + 1 + intercept. Attributes returned correspond arguments ns, explicitly give knots, Boundary.knots etc use predict.ns(). object assigned serverside.","code":""},{"path":"/reference/nsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"ns native R based function splineDesign. generates basis matrix representing family piecewise-cubic splines specified sequence interior knots, natural boundary conditions. enforce constraint function linear beyond boundary knots, can either supplied default extremes data. primary use modeling formula directly specify natural spline term model.","code":""},{"path":"/reference/nsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/numNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Counts the number of missing values — numNaDS","title":"Counts the number of missing values — numNaDS","text":"function just counts number missing entries vector.","code":""},{"path":"/reference/numNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Counts the number of missing values — numNaDS","text":"","code":"numNaDS(x)"},{"path":"/reference/numNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Counts the number of missing values — numNaDS","text":"x character string, name server-side vector","code":""},{"path":"/reference/numNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Counts the number of missing values — numNaDS","text":"list two elements: numNA (integer, number missing values) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/numNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Counts the number of missing values — numNaDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/qlsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"function based native R function qlspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/qlsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"","code":"qlsplineDS(x = x, q = q, na.rm = TRUE, marginal = FALSE, names = NULL)"},{"path":"/reference/qlsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"x name input numeric variable q numeric, single scalar greater equal 2 number equal-frequency intervals along x vector numbers (0; 1) specifying quantiles explicitly. na.rm logical, whether NA removed calculating quantiles, passed na.rm quantile. Default set TRUE. marginal logical, parametrize spline, see Details names character, vector names constructed variables","code":""},{"path":"/reference/qlsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"qlspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/qlsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment. Function qlspline wraps lspline calculates knot positions quantiles x. q numerical scalar greater equal 2, quantiles computed seq(0, 1, length.= q + 1)[-c(1, q+1)], .e. knots q-tiles distribution x. Alternatively, q can vector values [0; 1] specifying quantile probabilities directly (vector passed argument probs quantile).","code":""},{"path":"/reference/qlsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/quantileMeanDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"probabilities 5 used compute corresponding quantiles.","code":""},{"path":"/reference/quantileMeanDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"","code":"quantileMeanDS(x)"},{"path":"/reference/quantileMeanDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/quantileMeanDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"list, quantiles, numeric vector represents sample quantiles, class, class input object client-side consistency checking","code":""},{"path":"/reference/quantileMeanDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"Burton, P.; Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rBinomDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rBinomDS serverside assign function — rBinomDS","title":"rBinomDS serverside assign function — rBinomDS","text":"primary serverside assign function called ds.rBinom","code":""},{"path":"/reference/rBinomDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rBinomDS serverside assign function — rBinomDS","text":"","code":"rBinomDS(n, size = 1, prob = 0.5)"},{"path":"/reference/rBinomDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rBinomDS serverside assign function — rBinomDS","text":"n length pseudorandom number vector generated specified argument function ds.rBinom size scalar must positive integer. Value set directly argument ds.rBinom - details see help ds.rBinom. May scalar vector allowing size vary observation observation. prob numeric scalar range 0 > prob > 1 specifies probability positive response. Value set directly argument ds.rBinom - details see help ds.rBinom May scalar vector allowing size vary observation observation.","code":""},{"path":"/reference/rBinomDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rBinomDS serverside assign function — rBinomDS","text":"vector pseudorandom numbers binomial distribution, written serverside object named argument ds.rBinom.","code":""},{"path":"/reference/rBinomDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rBinomDS serverside assign function — rBinomDS","text":"Generates vector pseudorandom numbers binomial distribution data source specified arguments ds.rBinom. serverside function effectively function rbinom() native R arguments .","code":""},{"path":"/reference/rBinomDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rBinomDS serverside assign function — rBinomDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rNormDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rNormDS serverside assign function — rNormDS","title":"rNormDS serverside assign function — rNormDS","text":"primary serverside assign function called ds.rNorm","code":""},{"path":"/reference/rNormDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rNormDS serverside assign function — rNormDS","text":"","code":"rNormDS(n, mean = 0, sd = 1, force.output.to.k.decimal.places = 9)"},{"path":"/reference/rNormDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rNormDS serverside assign function — rNormDS","text":"n length pseudorandom number vector generated specified argument function ds.rNorm mean specifies mean pseudorandom number vector generated specified argument function ds.rNorm. May scalar vector allowing mean vary observation observation. sd specifies standard deviation pseudorandom number vector generated specified argument function ds.rNorm May scalar vector allowing sd vary observation observation. force.output..k.decimal.places scalar integer. Forces output random number vector k decimal places. 0 rounds coerces decimal random number output integer, k range 1-8 forces output k decimal places. k = 9, rounding occurs native output. Default=9. Value specified argument ds.rNorm","code":""},{"path":"/reference/rNormDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rNormDS serverside assign function — rNormDS","text":"numeric vector pseudorandom numbers normal distribution, rounded decimal places less 9, written serverside object named argument ds.rNorm.","code":""},{"path":"/reference/rNormDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rNormDS serverside assign function — rNormDS","text":"Generates vector pseudorandom numbers normal distribution data source specified arguments ds.rNorm. serverside function effectively function rnorm() native R arguments .","code":""},{"path":"/reference/rNormDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rNormDS serverside assign function — rNormDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rPoisDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rPoisDS serverside assign function — rPoisDS","title":"rPoisDS serverside assign function — rPoisDS","text":"primary serverside assign function called ds.rPois","code":""},{"path":"/reference/rPoisDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rPoisDS serverside assign function — rPoisDS","text":"","code":"rPoisDS(n, lambda = 1)"},{"path":"/reference/rPoisDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rPoisDS serverside assign function — rPoisDS","text":"n length pseudorandom number vector generated specified argument function ds.rPois lambda numeric scalar specifying expected count Poisson distribution used generate random counts. Specified directly lambda argument ds.rPois. May scalar vector allowing lambda vary observation observation.","code":""},{"path":"/reference/rPoisDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rPoisDS serverside assign function — rPoisDS","text":"vector pseudorandom non-negative integers Poisson distribution, written serverside object named argument ds.rPois.","code":""},{"path":"/reference/rPoisDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rPoisDS serverside assign function — rPoisDS","text":"Generates vector pseudorandom numbers (non-negative integers) Poisson distribution data source specified arguments ds.rPois. serverside function effectively function rpois() native R arguments .","code":""},{"path":"/reference/rPoisDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rPoisDS serverside assign function — rPoisDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rUnifDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rUnifDS serverside assign function — rUnifDS","title":"rUnifDS serverside assign function — rUnifDS","text":"primary serverside assign function called ds.rUnif","code":""},{"path":"/reference/rUnifDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rUnifDS serverside assign function — rUnifDS","text":"","code":"rUnifDS(n, min = 0, max = 1, force.output.to.k.decimal.places = 9)"},{"path":"/reference/rUnifDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rUnifDS serverside assign function — rUnifDS","text":"n length pseudorandom number vector generated specified argument function ds.rUnif min numeric scalar specifying minimum range across random numbers generated source. Specified directly min argument ds.rUnif. May scalar vector allowing min vary observation observation. max numeric scalar specifying maximum range across random numbers generated source. Specified directly max argument ds.rUnif. May scalar vector allowing min vary observation observation. force.output..k.decimal.places scalar integer. Forces output random number vector k decimal places. 0 rounds coerces decimal random number output integer, k range 1-8 forces output k decimal places. k = 9, rounding occurs native output. Default=9. Value specified argument ds.rUnif","code":""},{"path":"/reference/rUnifDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rUnifDS serverside assign function — rUnifDS","text":"numeric vector pseudorandom numbers uniform distribution, rounded decimal places less 9, written serverside object named argument ds.rUnif.","code":""},{"path":"/reference/rUnifDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rUnifDS serverside assign function — rUnifDS","text":"Generates vector pseudorandom numbers uniform distribution data source specified arguments ds.rUnif. serverside function effectively function runif() native R arguments .","code":""},{"path":"/reference/rUnifDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rUnifDS serverside assign function — rUnifDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rangeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"returns the minimum and maximum of a numeric vector — rangeDS","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"function similar R function range instead return real minimum maximum, computed values multiplied small random number.","code":""},{"path":"/reference/rangeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"","code":"rangeDS(x)"},{"path":"/reference/rangeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/rangeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"numeric vector contains minimum maximum values vector","code":""},{"path":"/reference/rangeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rbindDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rbindDS called by ds.rbind — rbindDS","title":"rbindDS called by ds.rbind — rbindDS","text":"serverside assign function takes sequence vector, matrix data-frame arguments combines row produce matrix.","code":""},{"path":"/reference/rbindDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rbindDS called by ds.rbind — rbindDS","text":"","code":"rbindDS(x.names.transmit = NULL, colnames.transmit = NULL)"},{"path":"/reference/rbindDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rbindDS called by ds.rbind — rbindDS","text":"x.names.transmit vector character strings representing names elemental components combined converted transmittable format. argument fully specified argument ds.rbind colnames.transmit NULL vector character strings representing forced column names output object converted transmittable format. argument fully specified argument ds.cbind.","code":""},{"path":"/reference/rbindDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rbindDS called by ds.rbind — rbindDS","text":"object specified argument ds.rbind(default name ) written serverside. well writing output object serverside, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.cbind() also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/rbindDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rbindDS called by ds.rbind — rbindDS","text":"sequence vector, matrix data-frame arguments combined row row produce matrix written serverside. details see help ds.rbind native R function rbind.","code":""},{"path":"/reference/rbindDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rbindDS called by ds.rbind — rbindDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/reShapeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"reShapeDS (assign function) called by ds.reShape — reShapeDS","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"Reshapes data frame containing longitudinal otherwise grouped data 'wide' 'long' format vice-versa","code":""},{"path":"/reference/reShapeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"","code":"reShapeDS( data.name, varying.transmit, v.names.transmit, timevar.name, idvar.name, drop.transmit, direction, sep )"},{"path":"/reference/reShapeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"data.name, name data.frame reshaped. Specified via argument ds.reShape function varying.transmit, names sets variables wide format correspond single variables long format (typically may called 'time-varying' 'time-dependent' variables). Specified via argument ds.reShape function. v.names.transmit, names variables long format correspond multiple variables wide format - example, sbp7, sbp11, sbp15 (measured systolic blood pressure ages 7, 11 15 years). Specified via argument ds.reShape function timevar.name, variable long format differentiates multiple records group individual. Specified via argument ds.reShape function idvar.name, names one variables long format identify multiple records group/individual. /variable(s) may also present wide format. Specified via argument ds.reShape function drop.transmit, vector names variables drop reshaping. Specified via argument ds.reShape function direction, character string, partially matched either \"wide\" reshape long wide format, \"long\" reshape wide long format. Specified via argument ds.reShape function sep, character vector length 1, indicating separating character variable names wide format. Specified via argument ds.reShape function","code":""},{"path":"/reference/reShapeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"reshaped data.frame converted long wide format wide long format written serverside given name provided argument ds.reShape 'newObject' name specified.","code":""},{"path":"/reference/reShapeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"function based native R function reshape. reshapes data frame containing longitudinal otherwise grouped data 'wide' format repeated measurements separate columns record 'long' format repeated measurements separate records. reshaping can either direction","code":""},{"path":"/reference/reShapeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"Demetris Avraam, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/recodeValuesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"function recodes specified values elements vector matched set alternative specified values.","code":""},{"path":"/reference/recodeValuesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"","code":"recodeValuesDS( var.name.text = NULL, values2replace.text = NULL, new.values.text = NULL, missing = NULL )"},{"path":"/reference/recodeValuesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"var.name.text character string providing name vector representing variable recoded. argument generated passed directly recodeValuesDS ds.recodeValues values2replace.text character string specifying values vector specified argument replaced new values specified new.values.vector. argument generated passed directly recodeValuesDS ds.recodeValues. effect, argument ds.recodeValues function converted character string format acceptable DataSHIELD R parser data repository can accepted recodeValuesDS new.values.text character string specifying new values specified values vector converted. argument generated passed directly recodeValuesDS ds.recodeValues. effect, argument ds.recodeValues function converted character string format acceptable DataSHIELD R parser data repository can used call recodeValuesDS. missing supplied, missing values variable referred var.name.text replaced value.","code":""},{"path":"/reference/recodeValuesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"object specified argument (default name '_recoded') initially specified calling ds.recodeValues. output object (required recoded variable called written serverside.","code":""},{"path":"/reference/recodeValuesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"details see help header ds.recodeValues","code":""},{"path":"/reference/recodeValuesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/repDS.html","id":null,"dir":"Reference","previous_headings":"","what":"repDS called by ds.rep — repDS","title":"repDS called by ds.rep — repDS","text":"assign function creates repetitive sequence repeating identified scalar, specified elements vector list. analogous rep function native R. sequence written new object serverside","code":""},{"path":"/reference/repDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"repDS called by ds.rep — repDS","text":"","code":"repDS( x1.transmit, times.transmit, length.out.transmit, each.transmit, x1.includes.characters, source.x1, source.times, source.length.out, source.each )"},{"path":"/reference/repDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"repDS called by ds.rep — repDS","text":"x1.transmit argument determines input scalar, vector list. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. times.transmit argument determines number replications pattern replications input scalar/vector construct output repetitive sequence. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. length..transmit argument fixes length output repetitive sequence vector behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. .transmit argument specifies number replications individual elements rather replications full sequence. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument <> call ds.rep calls repDS. x1.includes.characters Boolean parameter determining whether coerce final output sequence numeric. Defaults FALSE output coerced numeric. detailed behaviour see help ds.rep. parameter usually fully defined argument call ds.rep calls repDS. source.x1 defines source scalar vector defined argument. Four character strings allowed: \"clientside\" \"c\" serverside \"s\". behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. source.times see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS. source.length.see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS. source.see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS.","code":""},{"path":"/reference/repDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"repDS called by ds.rep — repDS","text":"vector containing specified repetitive sequence write output object defined argument (default name seq.vect) written serverside source. addition, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.matrixDiag also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/repDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"repDS called by ds.rep — repDS","text":"details can found help details ds.rep following aspects help function rep native R also apply (explained detail exceptions identified help ds.rep): addition Details R help : default behaviour call rep(x, times = 1, length.= NA, = 1) Normally just one additional arguments specified, '' specified either two, replication performed first, followed replication implied times length.. times consists single integer, result consists whole input repeated many times. times vector length x (replication ), result consists x[1] repeated times[1] times, x[2] repeated times[2] times . ***Note exception 1 . length.may given place times, case x repeated many times necessary create vector length. given, length.takes priority times ignored. ***Note exception 3 . Non-integer values times truncated towards zero. times computed quantity prudent add small fuzz use round. analogously .","code":""},{"path":"/reference/repDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"repDS called by ds.rep — repDS","text":"Paul Burton DataSHIELD Development Team, 14/10/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/replaceNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Replaces the missing values in a vector — replaceNaDS","title":"Replaces the missing values in a vector — replaceNaDS","text":"function identifies missing values replaces value values specified analyst.","code":""},{"path":"/reference/replaceNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replaces the missing values in a vector — replaceNaDS","text":"","code":"replaceNaDS(x, replacements)"},{"path":"/reference/replaceNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replaces the missing values in a vector — replaceNaDS","text":"x character, name vector process. replacements vector contains replacement value(s), vector one values study.","code":""},{"path":"/reference/replaceNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replaces the missing values in a vector — replaceNaDS","text":"new vector without missing values","code":""},{"path":"/reference/replaceNaDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Replaces the missing values in a vector — replaceNaDS","text":"function used analyst prefer requires complete vectors. possible specify one value missing value first returning number missing values using function numNaDS cases might sensible replace missing values one specific value e.g. replace missing values vector mean median value. missing values replaced new vector created.","code":""},{"path":"/reference/replaceNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Replaces the missing values in a vector — replaceNaDS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rmDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rmDS an aggregate function called by ds.rm — rmDS","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"deletes R object serverside","code":""},{"path":"/reference/rmDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"","code":"rmDS(x.names.transmit)"},{"path":"/reference/rmDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"x.names.transmit, names objects deleted converted transmissible form, comma separated list character string. argument specified via argument ds.rm","code":""},{"path":"/reference/rmDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"specified object deleted serverside. successful message \"Object successfully deleted\" returned clientside (x.names names object deleted). objects deleted already absent given source, source return message: \"Object deleted, .e. , exist need deleting\".","code":""},{"path":"/reference/rmDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"serverside function based rm() function native R. aggregate function may surprising modifies object serverside, therefore expected assign function. However, assign function last step running write modified object newobj. fail effect function delete object impossible write anywhere.","code":""},{"path":"/reference/rmDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"Paul Burton DataSHIELD Development Team","code":""},{"path":"/reference/rowColCalcDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"function similar R base functions 'rowSums', 'colSums', 'rowMeans' 'colMeans'.","code":""},{"path":"/reference/rowColCalcDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"","code":"rowColCalcDS(dataset.name, operation)"},{"path":"/reference/rowColCalcDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"dataset.name character string providing name server-side array two dimensions. operation integer indicates operation carry : 1 'rowSums', 2 'colSums', 3 'rowMeans' 4 'colMeans'","code":""},{"path":"/reference/rowColCalcDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"numeric vector","code":""},{"path":"/reference/rowColCalcDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"output returned user number entries output vector greater equal allowed size.","code":""},{"path":"/reference/rowColCalcDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/sampleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"draws pseudorandom sample vector, dataframe matrix serverside - special case - randomly permutes vector, dataframe matrix.","code":""},{"path":"/reference/sampleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"","code":"sampleDS( x.transmit, size.transmit, replace.transmit = NULL, prob.transmit = NULL )"},{"path":"/reference/sampleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"x.transmit Either character string providing name serverside vector, matrix data.frame sampled permuted, integer/numeric scalar (e.g. 923) indicating one create new vector serverside randomly permuted sample vector 1:923. x.transmit fully specified [x] argument ds.sample. details see help ds.sample native R help sample(). size.transmit numeric/integer scalar indicating size sample drawn. size.transmit fully specified [size] argument ds.sample. details see help ds.sample native R help sample(). replace.transmit Boolean indicator (TRUE FALSE) specifying whether sample drawn without replacement. Default FALSE sample drawn without replacement. replace.transmit fully specified [replace] argument ds.sample. details see help ds.sample native R help sample(). prob.transmit character string containing name numeric vector probability weights serverside associated elements vector sampled enabling drawing sample elements given higher probability drawn others. prob.transmit fully specified [prob] argument ds.sample. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"object specified argument (default name 'newobj.sample') written serverside. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"Serverside assign function sampleDS called clientside function ds.sample. Based native R function sample() deals slightly differently data.frames matrices. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"Paul Burton, DataSHIELD Development Team, 15/4/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/scatterPlotDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the coordinates of the data to be plot — scatterPlotDS","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"function uses two disclosure control methods generate non-disclosive coordinates returned client generates non-disclosive scatter plots.","code":""},{"path":"/reference/scatterPlotDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"","code":"scatterPlotDS(x.name, y.name, method.indicator, k, noise)"},{"path":"/reference/scatterPlotDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"x.name character string providing name server-side numeric vector, x-variable. y.name character string providing name server-side numeric vector, y-variable. method.indicator integer either 1 2. user selects deterministic method client side function method.indicator set 1 user selects probabilistic method argument set 2. k number nearest neighbours centroid calculated deterministic method selected. noise percentage initial variance used variance embedded noise probabilistic method selected.","code":""},{"path":"/reference/scatterPlotDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"list x y coordinates data plot, along classes x y inputs (class.x class.y)","code":""},{"path":"/reference/scatterPlotDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"user chooses deterministic approach, function finds k-1 nearest neighbours data point 2-dimensional space. nearest neighbours data points minimum Euclidean distances point interest. point interest k-1 nearest neighbours used calculation coordinates centroid k points. Centroid referred centre mass, .e. x-coordinate centroid average value x-coordinates k nearest neighbours y-coordinate centroid average y-coordinates k nearest neighbours. user chooses probabilistic approach, function adds random noise $x$ $y$ separately. random noise follows normal distribution zero mean variance equal 10 disclosure fix random number generator value specified input variables. Thus function returns always noisy data given pair variables.","code":""},{"path":"/reference/scatterPlotDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/seqDS.html","id":null,"dir":"Reference","previous_headings":"","what":"seqDS a serverside assign function called by ds.seq — seqDS","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"assign function seqDS called ds.seq","code":""},{"path":"/reference/seqDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"","code":"seqDS( FROM.value.char, TO.value.char, BY.value.char, LENGTH.OUT.value.char, ALONG.WITH.name )"},{"path":"/reference/seqDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":".value.char starting value sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. .value.char terminal value sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. .value.char value increment step sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. LENGTH..value.char length sequence point extension stopped, expressed integer real number decimal point character form. Fully specified argument ds.seq. ALONG..name convenience, rather specifying value LENGTH.can often better specify variable name argument. Fully specified argument ds.seq.","code":""},{"path":"/reference/seqDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"object specified argument ds.seq (default name newObj) written serverside. well writing output object serverside, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.seq() also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/seqDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"assign function uses native R function seq() create one flexible range sequence vectors can used help manage analyse data. assign function resultant vector written new object specified data source servers. Please see \"details\" ds.seq information allowable combinations arguments etc.","code":""},{"path":"/reference/seqDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"Paul Burton DataSHIELD Development Team, 17/9/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/setSeedDS.html","id":null,"dir":"Reference","previous_headings":"","what":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"aggregate serverside function primes pseudorandom number generator data source","code":""},{"path":"/reference/setSeedDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"","code":"setSeedDS(seedtext = NULL, kind = NULL, normal.kind = NULL)"},{"path":"/reference/setSeedDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"seedtext simply value argument ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois ds.rBinom coerced character format. done clientside functions require DataSHIELD user anything. Please see help clientside functions, particular, information argument details. kind see help set.seed() function native R normal.kind see help set.seed() function native R","code":""},{"path":"/reference/setSeedDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"Sets values vector integers length 626 known .Random.seed data source true current state random seed source.","code":""},{"path":"/reference/setSeedDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"setSeedDS effectively equivalent native R function set.seed() help function can provide many additional details. minor difference first argument setSeedDS, takes integer priming seed character format. However, user integer still specified directly integer argument one clientside functions ds.setSeed, ds.rNorm ..... clientside functions coerces integer character format calls setSeedDS first active line code setSeedDS converts character string back integer treats first argument native R function set.seed(). two arguments set.seed() native R, defaulted specifying NULL. defaulting hard wired setSeedDS function changed analyst means setSeedDS much less flexible native R's set.seed() function. DataSHIELD user requires aspect flexibility returned development team can approached, unless actually theoretical work random number generators likely ","code":""},{"path":"/reference/setSeedDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/skewness1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the skewness of a numeric variable — skewness1DS","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"function calculates skewness numeric variable study separately.","code":""},{"path":"/reference/skewness1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"","code":"skewness1DS(x, method)"},{"path":"/reference/skewness1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"x string character, name numeric variable. method integer 1 3 selecting one algorithms computing skewness detailed headers client-side ds.skewness function.","code":""},{"path":"/reference/skewness1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"list including skewness input numeric variable, number valid observations class, class input object client-side consistency checking.","code":""},{"path":"/reference/skewness1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"function calculates skewness input variable x three different methods. method specified argument method client-side ds.skewness function.","code":""},{"path":"/reference/skewness1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/skewness2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the skewness of a numeric variable — skewness2DS","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"function calculates summary statistics returned client-side used estimation combined skewness numeric variable across studies.","code":""},{"path":"/reference/skewness2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"","code":"skewness2DS(x, global.mean)"},{"path":"/reference/skewness2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"x string character, name numeric variable. global.mean numeric, combined mean input variable across studies.","code":""},{"path":"/reference/skewness2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"list including sum cubed differences values x global mean x across studies, sum squared differences values x global mean x across studies, number valid observations (.e. length x excluding missing values), class, class input object client-side consistency checking.","code":""},{"path":"/reference/skewness2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"function calculates sum squared differences values x global mean x across studies, sum cubed differences values x global mean x across studies number valid observations input variable x.","code":""},{"path":"/reference/skewness2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/sqrtDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the square root values of the input variable — sqrtDS","title":"Computes the square root values of the input variable — sqrtDS","text":"function similar R function sqrt.","code":""},{"path":"/reference/sqrtDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the square root values of the input variable — sqrtDS","text":"","code":"sqrtDS(x)"},{"path":"/reference/sqrtDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the square root values of the input variable — sqrtDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/sqrtDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the square root values of the input variable — sqrtDS","text":"object specified newobj argument ds.sqrt (default name sqrt.newobj) written server-side. output object class numeric integer.","code":""},{"path":"/reference/sqrtDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the square root values of the input variable — sqrtDS","text":"function computes square root values input numeric integer vector.","code":""},{"path":"/reference/sqrtDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the square root values of the input variable — sqrtDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/table1DDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates 1-dimensional contingency tables — table1DDS","title":"Creates 1-dimensional contingency tables — table1DDS","text":"function generates 1-dimensional table potentially disclosive cells. (based set threshold) replaced missing value ('NA').","code":""},{"path":"/reference/table1DDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates 1-dimensional contingency tables — table1DDS","text":"","code":"table1DDS(xvect)"},{"path":"/reference/table1DDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates 1-dimensional contingency tables — table1DDS","text":"xvect numerical vector discrete values - usually factor.","code":""},{"path":"/reference/table1DDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates 1-dimensional contingency tables — table1DDS","text":"list contains two elements: 'table', 1-dimensional table 'message' message informs validity table.","code":""},{"path":"/reference/table1DDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates 1-dimensional contingency tables — table1DDS","text":"generates 1-dimensional tables valid (non-disclosive) 1-dimensional tables defined data sources table cells counts 1 set threshold. output table invalid cells total count replaced missing values. total count visible table returned client side. message also returned 1-dimensional; message says \"invalid table - invalid counts present\" table invalid 'valid table' otherwise.","code":""},{"path":"/reference/table1DDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Creates 1-dimensional contingency tables — table1DDS","text":"Gaye .","code":""},{"path":"/reference/table2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"Helps creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/table2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"","code":"table2DS(newobj, rvar.transmit, cvar.transmit, stvar.transmit)"},{"path":"/reference/table2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"newobj character string providing name output table object written serverside TRUE. explicit name table object specified, nevertheless TRUE, name serverside table object defaults 'newObj'. Fully specified argument ds.table. information see help ds.table rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table","code":""},{"path":"/reference/table2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"information see help ds.table","code":""},{"path":"/reference/table2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":" argument ds.table set TRUE, aggregate function returns non-disclosive information table object written serverside tableDS.assign. information see help ds.table, tableDS.assign tableDS DataSHIELD table function native R.","code":""},{"path":"/reference/table2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tableDS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"helps creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/tableDS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"","code":"tableDS.assign( rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, cvar.all.unique.levels.transmit, stvar.all.unique.levels.transmit, exclude.transmit, useNA.transmit )"},{"path":"/reference/tableDS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table rvar..unique.levels.transmit character string containing unique level rvar, across studies, separated ','. cvar..unique.levels.transmit character string containing unique level cvar, across studies, separated ','. stvar..unique.levels.transmit character string containing unique level stvar, across studies, separated ','. exclude.transmit information see help argument ds.table. Fully specified argument ds.table useNA.transmit information see help argument ds.table. Fully specified argument ds.table","code":""},{"path":"/reference/tableDS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"information see help ds.table","code":""},{"path":"/reference/tableDS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":" argument ds.table set TRUE, assign function writes table requested format specified ds.table function object named argument ds.table. information see help ds.table DataSHIELD table function native R.","code":""},{"path":"/reference/tableDS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tableDS.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/tableDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"","code":"tableDS( rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, cvar.all.unique.levels.transmit, stvar.all.unique.levels.transmit, exclude.transmit, useNA.transmit, force.nfilter.transmit )"},{"path":"/reference/tableDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table rvar..unique.levels.transmit character string containing unique level rvar, across studies, separated ','. cvar..unique.levels.transmit character string containing unique level cvar, across studies, separated ','. stvar..unique.levels.transmit character string containing unique level stvar, across studies, separated ','. exclude.transmit information see help argument ds.table. Fully specified argument ds.table useNA.transmit information see help argument ds.table. Fully specified argument ds.table force.nfilter.transmit information see help argument ds.table. Fully specified argument ds.table","code":""},{"path":"/reference/tableDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"information see help ds.table","code":""},{"path":"/reference/tableDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"serverside function workhorse ds.table - creating table requested format specified ds.table. information see help ds.table DataSHIELD table function native R.","code":""},{"path":"/reference/tableDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tapplyDS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"Apply one selected range functions summarize outcome variable one indexing factors write resultant summary newobj serverside","code":""},{"path":"/reference/tapplyDS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"","code":"tapplyDS.assign(X.name, INDEX.names.transmit, FUN.name)"},{"path":"/reference/tapplyDS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"X.name, name variable summarized. Specified via argument ds.tapply.assign function INDEX.names.transmit, name single factor vector names factors index variable summarized. Specified via argument ds.tapply.assign function FUN.name, name one allowable summarizing functions applied. Specified via argument ds.tapply.assign function.","code":""},{"path":"/reference/tapplyDS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"array summarized values created tapplyDS.assign function. array written newobj serverside. number dimensions INDEX.","code":""},{"path":"/reference/tapplyDS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"see details ds.tapply.assign function","code":""},{"path":"/reference/tapplyDS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tapplyDS.html","id":null,"dir":"Reference","previous_headings":"","what":"tapplyDS called by ds.tapply — tapplyDS","title":"tapplyDS called by ds.tapply — tapplyDS","text":"Apply one selected range functions summarize outcome variable one indexing factors write resultant summary clientside","code":""},{"path":"/reference/tapplyDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tapplyDS called by ds.tapply — tapplyDS","text":"","code":"tapplyDS(X.name, INDEX.names.transmit, FUN.name)"},{"path":"/reference/tapplyDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tapplyDS called by ds.tapply — tapplyDS","text":"X.name, name variable summarized. Specified via argument ds.tapply function INDEX.names.transmit, name single factor vector names factors index variable summarized. Specified via argument ds.tapply function FUN.name, name one allowable summarizing functions applied. Specified via argument ds.tapply function.","code":""},{"path":"/reference/tapplyDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tapplyDS called by ds.tapply — tapplyDS","text":"array summarized values created tapplyDS function. array returned clientside. number dimensions INDEX.","code":""},{"path":"/reference/tapplyDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tapplyDS called by ds.tapply — tapplyDS","text":"see details ds.tapply function","code":""},{"path":"/reference/tapplyDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tapplyDS called by ds.tapply — tapplyDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/unListDS.html","id":null,"dir":"Reference","previous_headings":"","what":"unListDS a serverside assign function called by ds.unList — unListDS","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"function based native R function unlist coerces object list class back class coerced list","code":""},{"path":"/reference/unListDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"","code":"unListDS(x.name)"},{"path":"/reference/unListDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"x.name name input object unlisted. must specified inverted commas e.g. x.name=\"input.object.name\". Fully specified x.name argument ds.unList","code":""},{"path":"/reference/unListDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"object specified newobj argument ds.unList function (default \"unlist.newobj\" newobj argument NULL). written serverside. well writing output object newobj serverside, two validity messages returned indicating whether newobj created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.seq also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating newobj studysideMessage saved. outcome object ds.unList typically list object names, errors creating message returned ds.message(\"\") study read \"Outcome object list without names. studysideMessage may hidden. Please check output OK\". suggests - case specific function - one check far one can nature output call ds.unList - e.g. ds.class, ds.length etc","code":""},{"path":"/reference/unListDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"See details native R function unlist. function represents substantive restructuring earlier version created Amadou Gaye. details working please see 'details' help ds.unList.","code":""},{"path":"/reference/unListDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"Amadou Gaye (2016), Paul Burton (19/09/2019) DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/uniqueDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Applies the unique method to a server-side variable. — uniqueDS","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"function similar R function unique.","code":""},{"path":"/reference/uniqueDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"","code":"uniqueDS(x.name.transmit = NULL)"},{"path":"/reference/uniqueDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"x.name.transmit name variable upon unique method applied","code":""},{"path":"/reference/uniqueDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"object specified newobj argument written server-side.","code":""},{"path":"/reference/uniqueDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"function computes uniques values variable.","code":""},{"path":"/reference/uniqueDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"Stuart Wheater DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/varDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the variance of vector — varDS","title":"Computes the variance of vector — varDS","text":"Calculates variance.","code":""},{"path":"/reference/varDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the variance of vector — varDS","text":"","code":"varDS(x)"},{"path":"/reference/varDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the variance of vector — varDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/varDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the variance of vector — varDS","text":"list, sum input variable, sum squares input variable, number missing values, number valid values, number total length variable, class, class input object client-side consistency checking","code":""},{"path":"/reference/varDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the variance of vector — varDS","text":"length input vector less set filter missing value returned.","code":""},{"path":"/reference/varDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the variance of vector — varDS","text":"Amadou Gaye, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/vectorDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates a vector on the server-side. — vectorDS","title":"Creates a vector on the server-side. — vectorDS","text":"function similar R function c.","code":""},{"path":"/reference/vectorDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates a vector on the server-side. — vectorDS","text":"","code":"vectorDS(...)"},{"path":"/reference/vectorDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates a vector on the server-side. — vectorDS","text":"... parameter used form vector.","code":""},{"path":"/reference/vectorDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates a vector on the server-side. — vectorDS","text":"object specified newobj argument written server-side.","code":""},{"path":"/reference/vectorDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates a vector on the server-side. — vectorDS","text":"function computes vectors values.","code":""},{"path":"/reference/vectorDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Creates a vector on the server-side. — vectorDS","text":"Stuart Wheater DataSHIELD Development Team","code":""}] +[{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Paul Burton. Author. Rebecca Wilson. Author. Olly Butters. Author. Patricia Ryser-Welch. Author. Alex Westerberg. Author. Leire Abarrategui. Author. Roberto Villegas-Diaz. Author. Demetris Avraam. Author. Yannick Marcon. Author. Tom Bishop. Author. Amadou Gaye. Author. Xavier Escribà-Montagut. Author. Stuart Wheater. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg , Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye , Escribà-Montagut X, Wheater S (????). dsBase: 'DataSHIELD' Server Side Base Functions. R package version 7.0.0.9000. Gaye , Marcon Y, Isaeva J, LaFlamme P, Turner , Jones E, Minion J, Boyd , Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir , Doiron D, Giepmans L, Wallace S, Budin-Ljøsne , Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry , Peters , Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier , Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking analysis data, data analysis.” International Journal Epidemiology, 43(6), 1929–1944. doi:10.1093/ije/dyu188. Wilson R, Butters O, Avraam D, Baker J, Tedds J, Turner , Murtagh M, Burton P (2017). “DataSHIELD – New Directions Dimensions.” Data Science Journal, 16(21), 1–21. doi:10.5334/dsj-2017-021. Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan , Murtagh M, Nestor M, Nybo Andersen , Parker S, Pinot de Moira , Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1–21. doi:10.1093/bioadv/vbaf046.","code":"@Manual{, title = {dsBase: 'DataSHIELD' Server Side Base Functions}, author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater}, note = {R package version 7.0.0.9000}, } @Article{, title = {{DataSHIELD: taking the analysis to the data, not the data to the analysis}}, author = {Amadou Gaye and Yannick Marcon and Julia Isaeva and Philippe {LaFlamme} and Andrew Turner and Elinor M Jones and Joel Minion and Andrew W Boyd and Christopher J Newby and Marja-Liisa Nuotio and Rebecca Wilson and Oliver Butters and Barnaby Murtagh and Ipek Demir and Dany Doiron and Lisette Giepmans and Susan E Wallace and Isabelle Budin-Lj{\\o}sne and Carsten O. Schmidt and Paolo Boffetta and Mathieu Boniol and Maria Bota and Kim W Carter and Nick {deKlerk} and Chris Dibben and Richard W Francis and Tero Hiekkalinna and Kristian Hveem and Kirsti Kval{\\o}y and Sean Millar and Ivan J Perry and Annette Peters and Catherine M Phillips and Frank Popham and Gillian Raab and Eva Reischl and Nuala Sheehan and Melanie Waldenberger and Markus Perola and Edwin {{van den Heuvel}} and John Macleod and Bartha M Knoppers and Ronald P Stolk and Isabel Fortier and Jennifer R Harris and Bruce H R Woffenbuttel and Madeleine J Murtagh and Vincent Ferretti and Paul R Burton}, journal = {International Journal of Epidemiology}, year = {2014}, volume = {43}, number = {6}, pages = {1929--1944}, doi = {10.1093/ije/dyu188}, } @Article{, title = {{DataSHIELD – New Directions and Dimensions}}, author = {Rebecca C. Wilson and Oliver W. Butters and Demetris Avraam and James Baker and Jonathan A. Tedds and Andrew Turner and Madeleine Murtagh and Paul R. Burton}, journal = {Data Science Journal}, year = {2017}, volume = {16}, number = {21}, pages = {1--21}, doi = {10.5334/dsj-2017-021}, } @Article{, title = {{DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform}}, author = {Demetris Avraam and Rebecca C Wilson and Noemi {{Aguirre Chan}} and Soumya Banerjee and Tom R P Bishop and Olly Butters and Tim Cadman and Luise Cederkvist and Liesbeth Duijts and Xavier {{Escrib{\\a`a} Montagut}} and Hugh Garner and Gon{\\c c}alo {Gon{\\c c}alves} and Juan R Gonz{\\a'a}lez and Sido Haakma and Mette Hartlev and Jan Hasenauer and Manuel Huth and Eleanor Hyde and Vincent W V Jaddoe and Yannick Marcon and Michaela Th Mayrhofer and Fruzsina Molnar-Gabor and Andrei Scott Morgan and Madeleine Murtagh and Marc Nestor and Anne-Marie {{Nybo Andersen}} and Simon Parker and Angela {{Pinot de Moira}} and Florian Schwarz and Katrine Strandberg-Larsen and Morris A Swertz and Marieke Welten and Stuart Wheater and Paul R Burton}, journal = {Bioinformatics Advances}, year = {2024}, volume = {5}, number = {1}, pages = {1--21}, doi = {10.1093/bioadv/vbaf046}, editor = {Thomas Lengauer}, publisher = {Oxford University Press (OUP)}, }"},{"path":[]},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"DataSHIELD Server Side Base Functions","text":"can install released version dsBase CRAN : development version GitHub : full list development branches, checkout https://github.com/datashield/dsBase/branches","code":"install.packages(\"dsBase\") install.packages(\"remotes\") remotes::install_github(\"datashield/dsBase\", \"\") # Install v6.3.6 with the following remotes::install_github(\"datashield/dsBase\", \"6.3.6\")"},{"path":"/index.html","id":"about","dir":"","previous_headings":"","what":"About","title":"DataSHIELD Server Side Base Functions","text":"DataSHIELD software package allows non-disclosive federated analysis sensitive data. website (https://www.datashield.org) depth descriptions , works install . key point highlight DataSHIELD client-server infrastructure, dsBase package (https://github.com/datashield/dsBase) needs used conjunction dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying use one without makes sense. Detailed instructions install DataSHIELD https://wiki.datashield.org/. code organised :","code":""},{"path":"/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"DataSHIELD Server Side Base Functions","text":"[1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg , Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye , Escribà Montagut X, Wheater S (2025). dsBase: ‘DataSHIELD’ Server Side Base Functions. R package version 6.3.4. https://doi.org/10.32614/CRAN.package.dsBase. [2] Gaye , Marcon Y, Isaeva J, LaFlamme P, Turner , Jones E, Minion J, Boyd , Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir , Doiron D, Giepmans L, Wallace S, Budin-Ljøsne , Oliver Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry , Peters , Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier , Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking analysis data, data analysis.” International Journal Epidemiology, 43(6), 1929-1944. https://doi.org/10.1093/ije/dyu188. [3] Wilson R, W. Butters O, Avraam D, Baker J, Tedds J, Turner , Murtagh M, R. Burton P (2017). “DataSHIELD – New Directions Dimensions.” Data Science Journal, 16(21), 1-21. https://doi.org/10.5334/dsj-2017-021. [4] Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan , Murtagh M, Nestor M, Nybo Andersen , Parker S, Pinot de Moira , Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1-21. https://doi.org/10.1093/bioadv/vbaf046. Note: Apple Mx architecture users, please aware numerical limitations platform, leads unexpected results using base R packages, like stats​. x <- c(0, 3, 7) 1 - cor(x, x)​ result value zero. Also See: details see https://cran.r-project.org/doc/FAQ/R-FAQ.html#-doesn_0027t-R-think--numbers--equal_003f bug report: https://bugs.r-project.org/show_bug.cgi?id=18941","code":""},{"path":"/reference/BooleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"BooleDS — BooleDS","title":"BooleDS — BooleDS","text":"Converts individual elements vector object Boolean indicators.","code":""},{"path":"/reference/BooleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BooleDS — BooleDS","text":"","code":"BooleDS( V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, na.assign.text, numeric.output = TRUE )"},{"path":"/reference/BooleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BooleDS — BooleDS","text":"V1.name character string specifying name vector Boolean operator applied V2.name character string specifying name vector scalar compared. Boolean.operator.n integer value (1 6) providing numeric coding character string specifying one six possible Boolean operators: '==', '!=', '>', '>=','<', '<=' legally passed client server via DataSHIELD parser na.assign.text character string taking values 'NA', '1' '0'. 'NA' NA values input vector remain NAs output vector. '1' '0' NA values input vector converted 1 0 respectively. numeric.output TRUE/FALSE indicator defaulting TRUE determining whether final output variable class numeric (1/0) class logical (TRUE/FALSE).","code":""},{"path":"/reference/BooleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"BooleDS — BooleDS","text":"levels input variable.","code":""},{"path":"/reference/BooleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"BooleDS — BooleDS","text":"function converts input vector Boolean indicators.","code":""},{"path":"/reference/BooleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"BooleDS — BooleDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/absDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the absolute values of the input variable — absDS","title":"Computes the absolute values of the input variable — absDS","text":"function similar R function abs.","code":""},{"path":"/reference/absDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the absolute values of the input variable — absDS","text":"","code":"absDS(x)"},{"path":"/reference/absDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the absolute values of the input variable — absDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/absDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the absolute values of the input variable — absDS","text":"object specified newobj argument ds.abs (default name abs.newobj) written serverside. output object class numeric integer.","code":""},{"path":"/reference/absDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the absolute values of the input variable — absDS","text":"function computes absolute values input numeric integer vector.","code":""},{"path":"/reference/absDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the absolute values of the input variable — absDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asCharacterDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class character — asCharacterDS","title":"Coerces an R object into class character — asCharacterDS","text":"function based native R function .character","code":""},{"path":"/reference/asCharacterDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class character — asCharacterDS","text":"","code":"asCharacterDS(x.name)"},{"path":"/reference/asCharacterDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class character — asCharacterDS","text":"x.name name input object coerced class character. Must specified inverted commas. argument usually specified directly x.name argument clientside function ds.asCharacter","code":""},{"path":"/reference/asCharacterDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class character — asCharacterDS","text":"object specified newobj argument (default name \"ascharacter.newobj\") written serverside. details see help clientside function ds.asCharacter","code":""},{"path":"/reference/asCharacterDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class character — asCharacterDS","text":"See help function .character native R","code":""},{"path":"/reference/asCharacterDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class character — asCharacterDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asDataMatrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"Coerces R object matrix maintaining original class columns data.frames.","code":""},{"path":"/reference/asDataMatrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"","code":"asDataMatrixDS(x.name)"},{"path":"/reference/asDataMatrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"x.name name input object coerced class data.matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asDataMatrix","code":""},{"path":"/reference/asDataMatrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"object specified argument (default name \"asdatamatrix.newobj\") written serverside. details see help clientside function ds.asDataMatrix","code":""},{"path":"/reference/asDataMatrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"assign function based native R function data.matrix applied data.frame, native R function .matrix converts columns character class. contrast, applied data.frame native R function data.matrix converts data.frame matrix maintains data columns original class","code":""},{"path":"/reference/asDataMatrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"asDataMatrixDS a serverside assign function called by ds.asDataMatrix — asDataMatrixDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactor1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Determines the levels of the input variable in each single study — asFactor1DS","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"function aggregate DataSHIELD function returns levels input variable single study client-side function.","code":""},{"path":"/reference/asFactor1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"","code":"asFactor1DS(input.var.name = NULL)"},{"path":"/reference/asFactor1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"input.var.name name variable converted factor.","code":""},{"path":"/reference/asFactor1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"levels input variable.","code":""},{"path":"/reference/asFactor1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"function encodes input vector factor returns levels ascending order levels numerical alphabetical order levels type character.","code":""},{"path":"/reference/asFactor1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Determines the levels of the input variable in each single study — asFactor1DS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactor2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts a numeric vector into a factor — asFactor2DS","title":"Converts a numeric vector into a factor — asFactor2DS","text":"function assign DataSHIELD function converts numeric vector factor type presented vector matrix dummy variables.","code":""},{"path":"/reference/asFactor2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts a numeric vector into a factor — asFactor2DS","text":"","code":"asFactor2DS( input.var.name = NULL, all.unique.levels.transmit = NULL, fixed.dummy.vars = NULL, baseline.level = NULL )"},{"path":"/reference/asFactor2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts a numeric vector into a factor — asFactor2DS","text":"input.var.name name variable converted factor. .unique.levels.transmit levels variable transmitted . fixed.dummy.vars boolean determines whether new object represented vector matrix dummy variables indicating factor level data point. argument set FALSE (default) input variable converted factor assigned vector. set TRUE input variable converted factor assigned matrix dummy variables. baseline.level number indicating baseline level used creation matrix dummy variables.","code":""},{"path":"/reference/asFactor2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts a numeric vector into a factor — asFactor2DS","text":"object class factor","code":""},{"path":"/reference/asFactor2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Converts a numeric vector into a factor — asFactor2DS","text":"functions converts input variable factor presented vector fixed.dummy.vars set FALSE matrix dummy variables fixed.dummy.vars set TRUE (see help file ds.asFactor.b details).","code":""},{"path":"/reference/asFactor2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts a numeric vector into a factor — asFactor2DS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asFactorSimpleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts a numeric vector into a factor — asFactorSimpleDS","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"function assign DataSHIELD function coerces numeric character vector factor","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"","code":"asFactorSimpleDS(input.var.name = NULL)"},{"path":"/reference/asFactorSimpleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"input.var.name name variable converted factor.","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"object class factor","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"functions converts input variable factor. Unlike ds.asFactor serverside functions, ds.asFactorSimple coerce class variable factor study. check enforce consistency factor levels across sources allow force arbitrary set levels unless levels actually exist sources. addition, allow create array binary dummy variables equivalent factor. need things use ds.asFactor function.","code":""},{"path":"/reference/asFactorSimpleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts a numeric vector into a factor — asFactorSimpleDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asIntegerDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class integer — asIntegerDS","title":"Coerces an R object into class integer — asIntegerDS","text":"function based native R function .integer.","code":""},{"path":"/reference/asIntegerDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class integer — asIntegerDS","text":"","code":"asIntegerDS(x.name)"},{"path":"/reference/asIntegerDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class integer — asIntegerDS","text":"x.name name input object coerced class integer. Must specified inverted commas. argument usually specified directly argument clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class integer — asIntegerDS","text":"object specified argument (default name \"asinteger.newobj\") written serverside. details see help clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class integer — asIntegerDS","text":"See help function .integer native R, details section help file clientside function ds.asInteger.","code":""},{"path":"/reference/asIntegerDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class integer — asIntegerDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asListDS.html","id":null,"dir":"Reference","previous_headings":"","what":"asListDS a serverside assign function called by ds.asList — asListDS","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"Coerces R object list","code":""},{"path":"/reference/asListDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"","code":"asListDS(x.name)"},{"path":"/reference/asListDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"x.name name input object coerced class data.matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asList","code":""},{"path":"/reference/asListDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"input object coerced list, ds.asList writes serverside. way .list coerces objects list depends class object","code":""},{"path":"/reference/asListDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"assign function based native R function .list additional information can found help .list","code":""},{"path":"/reference/asListDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"asListDS a serverside assign function called by ds.asList — asListDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asLogicalDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class logical — asLogicalDS","title":"Coerces an R object into class logical — asLogicalDS","text":"function based native R function .logical","code":""},{"path":"/reference/asLogicalDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class logical — asLogicalDS","text":"","code":"asLogicalDS(x.name)"},{"path":"/reference/asLogicalDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class logical — asLogicalDS","text":"x.name name input object coerced class logical. Must specified inverted commas. argument usually specified directly argument clientside function ds.asLogical","code":""},{"path":"/reference/asLogicalDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class logical — asLogicalDS","text":"object specified argument (default name .logic) written serverside. details see help clientside function ds.asLogical","code":""},{"path":"/reference/asLogicalDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class logical — asLogicalDS","text":"See help function .logical native R","code":""},{"path":"/reference/asLogicalDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class logical — asLogicalDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asMatrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into a matrix — asMatrixDS","title":"Coerces an R object into a matrix — asMatrixDS","text":"function based native R function .matrix","code":""},{"path":"/reference/asMatrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into a matrix — asMatrixDS","text":"","code":"asMatrixDS(x.name)"},{"path":"/reference/asMatrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into a matrix — asMatrixDS","text":"x.name name input object coerced class matrix. Must specified inverted commas. argument usually specified directly argument clientside function ds.asMatrix","code":""},{"path":"/reference/asMatrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into a matrix — asMatrixDS","text":"object specified argument (default name .mat) written serverside. details see help clientside function ds.asMatrix","code":""},{"path":"/reference/asMatrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into a matrix — asMatrixDS","text":"See help function .matrix native R","code":""},{"path":"/reference/asMatrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into a matrix — asMatrixDS","text":"Amadou Gaye, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/asNumericDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerces an R object into class numeric — asNumericDS","title":"Coerces an R object into class numeric — asNumericDS","text":"function based native R function .numeric.","code":""},{"path":"/reference/asNumericDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerces an R object into class numeric — asNumericDS","text":"","code":"asNumericDS(x.name)"},{"path":"/reference/asNumericDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerces an R object into class numeric — asNumericDS","text":"x.name name input object coerced class numeric. Must specified inverted commas. argument usually specified directly argument clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerces an R object into class numeric — asNumericDS","text":"object specified argument (default name .num) written serverside. details see help clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerces an R object into class numeric — asNumericDS","text":"See help function .numeric native R, details section help file clientside function ds.asNumeric.","code":""},{"path":"/reference/asNumericDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerces an R object into class numeric — asNumericDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/aucDS.html","id":null,"dir":"Reference","previous_headings":"","what":"aucDS an aggregate function called by ds.auc — aucDS","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"function calculates C-statistic AUC logistic regression models.","code":""},{"path":"/reference/aucDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"","code":"aucDS(pred = pred, y = y)"},{"path":"/reference/aucDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"pred name vector predicted values y name outcome variable. Note variable include complete cases used regression model.","code":""},{"path":"/reference/aucDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"returns AUC standard error","code":""},{"path":"/reference/aucDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"AUC determines discriminative ability model.","code":""},{"path":"/reference/aucDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"aucDS an aggregate function called by ds.auc — aucDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/booleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"booleDS — booleDS","title":"booleDS — booleDS","text":"Converts individual elements vector object Boolean indicators.","code":""},{"path":"/reference/booleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"booleDS — booleDS","text":"","code":"booleDS( V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, na.assign.text, numeric.output = TRUE )"},{"path":"/reference/booleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"booleDS — booleDS","text":"V1.name character string specifying name vector Boolean operator applied V2.name character string specifying name vector scalar compared. Boolean.operator.n integer value (1 6) providing numeric coding character string specifying one six possible Boolean operators: '==', '!=', '>', '>=','<', '<=' legally passed client server via DataSHIELD parser na.assign.text character string taking values 'NA', '1' '0'. 'NA' NA values input vector remain NAs output vector. '1' '0' NA values input vector converted 1 0 respectively. numeric.output TRUE/FALSE indicator defaulting TRUE determining whether final output variable class numeric (1/0) class logical (TRUE/FALSE).","code":""},{"path":"/reference/booleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"booleDS — booleDS","text":"levels input variable.","code":""},{"path":"/reference/booleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"booleDS — booleDS","text":"function converts input vector Boolean indicators.","code":""},{"path":"/reference/booleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"booleDS — booleDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGGDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"order create non disclosive box plot, data passed client purely geometrical aspects plot, ggplot object contains data inside, graphical parameters passed. three different cases depending grouping variables. outliers also removed graphical parameters.","code":""},{"path":"/reference/boxPlotGGDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"","code":"boxPlotGGDS(data_table.name, group = NULL, group2 = NULL)"},{"path":"/reference/boxPlotGGDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"data_table.name character Name server-side data frame holds information plotted, arranged : Column 'x': Names X axis boxplot, aka variables plot Column 'value': Values variable (raw data columns rbinded) Column 'group': (Optional) Values grouping variable Column 'group2': (Optional) Values second grouping variable group character (default NULL) Name first grouping variable. group2 character (default NULL) Name second grouping variable.","code":""},{"path":"/reference/boxPlotGGDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"list : -data frame Geometrical parameters (identity stats ggplot) -character Type plot (single_group, double_group no_group)","code":""},{"path":"/reference/boxPlotGGDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create the identity stats and necessary data to draw a plot on the client — boxPlotGGDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"Arrange data frame pass boxplot function","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"","code":"boxPlotGG_data_TreatmentDS(table.name, variables, group = NULL, group2 = NULL)"},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"table.name character Name server-side data frame holds information plotted later variables character vector Name column(s) data frame include boxplot group character (default NULL) Name first grouping variable. group2 character (default NULL) Name second grouping variable.","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"data frame following structure: Column 'x': Names X axis boxplot, aka variables plot Column 'value': Values variable (raw data columns rbinded) Column 'group': (Optional) Values grouping variable Column 'group2': (Optional) Values second grouping variable","code":""},{"path":"/reference/boxPlotGG_data_TreatmentDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Arrange data frame to pass it to the boxplot function — boxPlotGG_data_TreatmentDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"Arrange vector pass boxplot function","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"","code":"boxPlotGG_data_Treatment_numericDS(vector.name)"},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"vector.name character Name server-side numeric vector arrange plotted later","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"data frame following structure: Column 'x': Names X axis boxplot, aka name vector (vector.name argument) Column 'value': Values variable","code":""},{"path":"/reference/boxPlotGG_data_Treatment_numericDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Arrange vector to pass it to the boxplot function — boxPlotGG_data_Treatment_numericDS","text":"Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/bp_standardsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates Blood pressure z-scores — bp_standardsDS","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"function calculates blood pressure z-scores two steps: Step 1. Calculates z-score height according CDC growth chart (growth chart!). Step 2. Calculates z-score BP according fourth report BP management, USA","code":""},{"path":"/reference/bp_standardsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"","code":"bp_standardsDS( sex = sex, age = age, height = height, bp = bp, systolic = systolic )"},{"path":"/reference/bp_standardsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"sex name sex variable. variable coded 1 males 2 females. coded differently (e.g. 0/1), can use ds.recodeValues function recode categories 1/2 use ds.bp_standards age name age variable years. height name height variable cm bp name blood pressure variable. systolic logical. TRUE (default) function assumes conversion systolic blood pressure. FALSE function assumes conversion diastolic blood pressure.","code":""},{"path":"/reference/bp_standardsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"assigns new object server-side. assigned object list two elements: 'Zbp' zscores blood pressure 'perc' percentiles BP zscores.","code":""},{"path":"/reference/bp_standardsDS.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"z-scores height based CDC growth charts calculated sds function childsds R package.","code":""},{"path":"/reference/bp_standardsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates Blood pressure z-scores — bp_standardsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/cDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenates objects into a vector or list — cDS","title":"Concatenates objects into a vector or list — cDS","text":"function similar R base function 'c'.","code":""},{"path":"/reference/cDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenates objects into a vector or list — cDS","text":"","code":"cDS(x.names)"},{"path":"/reference/cDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenates objects into a vector or list — cDS","text":"x.names character vector object names concatenate.","code":""},{"path":"/reference/cDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenates objects into a vector or list — cDS","text":"vector list","code":""},{"path":"/reference/cDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Concatenates objects into a vector or list — cDS","text":"Unlike R base function 'c' vector list certain length allowed output","code":""},{"path":"/reference/cDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Concatenates objects into a vector or list — cDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/cbindDS.html","id":null,"dir":"Reference","previous_headings":"","what":"cbindDS called by ds.cbind — cbindDS","title":"cbindDS called by ds.cbind — cbindDS","text":"serverside assign function takes sequence vector, matrix data-frame arguments combines column produce data-frame.","code":""},{"path":"/reference/cbindDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cbindDS called by ds.cbind — cbindDS","text":"","code":"cbindDS(x.names.transmit = NULL, colnames.transmit = NULL)"},{"path":"/reference/cbindDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"cbindDS called by ds.cbind — cbindDS","text":"x.names.transmit vector character strings representing names elemental components combined converted transmittable format. argument fully specified x argument client-side ds.cbind function. colnames.transmit vector character strings representing column names output object converted transmittable format.","code":""},{"path":"/reference/cbindDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"cbindDS called by ds.cbind — cbindDS","text":"object specified newobj argument ds.cbind (default name cbind.newobj) written serverside. output object class data.frame.","code":""},{"path":"/reference/cbindDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"cbindDS called by ds.cbind — cbindDS","text":"sequence vector, matrix data-frame arguments combined column column produce data-frame written serverside. critical requirement length component variables, number rows component data.frames matrices must . output data.frame number rows. details see help ds.cbind native R function cbind.","code":""},{"path":"/reference/cbindDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"cbindDS called by ds.cbind — cbindDS","text":"Paul Burton Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/changeRefGroupDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Changes a reference level of a factor — changeRefGroupDS","title":"Changes a reference level of a factor — changeRefGroupDS","text":"function similar R function relevel,","code":""},{"path":"/reference/changeRefGroupDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Changes a reference level of a factor — changeRefGroupDS","text":"","code":"changeRefGroupDS(x, ref = NULL, reorderByRef = NULL)"},{"path":"/reference/changeRefGroupDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Changes a reference level of a factor — changeRefGroupDS","text":"x character string, name factor vector. ref character, reference level reorderByRef boolean tells whether new vector ordered reference group.","code":""},{"path":"/reference/changeRefGroupDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Changes a reference level of a factor — changeRefGroupDS","text":"factor length input vector","code":""},{"path":"/reference/changeRefGroupDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Changes a reference level of a factor — changeRefGroupDS","text":"addition R function , function allows user re-order vector, putting reference group first. user chooses re-order warning issued can introduce mismatch values vector put back table reordered way. mismatch can render results operations table invalid.","code":""},{"path":"/reference/changeRefGroupDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Changes a reference level of a factor — changeRefGroupDS","text":"Isaeva, J., Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/checkNegValueDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if a numeric variable has negative values — checkNegValueDS","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"function called client function ds.glm.","code":""},{"path":"/reference/checkNegValueDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"","code":"checkNegValueDS(weights)"},{"path":"/reference/checkNegValueDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"weights numeric vector","code":""},{"path":"/reference/checkNegValueDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"boolean; TRUE vector one negative values FALSE otherwise","code":""},{"path":"/reference/checkNegValueDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"user sets parameter 'weights' client side function ds.glm server side function called verify 'weights' vector negative values negative allowed weights.","code":""},{"path":"/reference/checkNegValueDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if a numeric variable has negative values — checkNegValueDS","text":"Gaye, .","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":null,"dir":"Reference","previous_headings":"","what":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"server-side function check server running \"permissive\" privacy control level.","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"","code":"checkPermissivePrivacyControlLevel(privacyControlLevels)"},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"privacyControlLevels vector strings contains privacy control level names permitted calling method.","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"return value, called side effects","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"Tests whether R option \"datashield.privacyControlLevel\" set \"permissive\", cause call stop() message \"BLOCKED: server running 'non-permissive' mode caused method blocked\".","code":""},{"path":"/reference/checkPermissivePrivacyControlLevel.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"checkPermissivePrivacyControlLevel — checkPermissivePrivacyControlLevel","text":"Wheater, Dr SM., DataSHIELD Development Team.","code":""},{"path":"/reference/classDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the class of an object — classDS","title":"Returns the class of an object — classDS","text":"function similar R function class.","code":""},{"path":"/reference/classDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the class of an object — classDS","text":"","code":"classDS(x)"},{"path":"/reference/classDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the class of an object — classDS","text":"x string character, name object","code":""},{"path":"/reference/classDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the class of an object — classDS","text":"class input object","code":""},{"path":"/reference/classDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the class of an object — classDS","text":"function returns class object","code":""},{"path":"/reference/classDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the class of an object — classDS","text":"Stuart Wheater, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/colnamesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the column names of a data frame or matrix — colnamesDS","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"function similar R function colnames.","code":""},{"path":"/reference/colnamesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"","code":"colnamesDS(x)"},{"path":"/reference/colnamesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"x string character, name dataframe matrix","code":""},{"path":"/reference/colnamesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"column names input object","code":""},{"path":"/reference/colnamesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"function returns column names input dataframe matrix","code":""},{"path":"/reference/colnamesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the column names of a data frame or matrix — colnamesDS","text":"Demetris Avraam, DataSHIELD Development Team","code":""},{"path":"/reference/completeCasesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"Identifies strips rows data.frame, matrix vector contain NAs.","code":""},{"path":"/reference/completeCasesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"","code":"completeCasesDS(x1.transmit)"},{"path":"/reference/completeCasesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"x1.transmit argument determines input data.frame, matrix vector rows NAs stripped. argument fully specified argument ds.completeCases function.","code":""},{"path":"/reference/completeCasesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"modified data.frame, matrix vector rows containing least one NA deleted. modified object written serverside source. addition, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.completeCases also returns studysideMessages can help explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/completeCasesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"case data.frame matrix, completeCasesDS identifies rows containing one NAs deletes rows altogether. one variable NA given row lead deletion whole row. case vector, completeCasesDS acts equivalent manner equivalent 'row' simply strips observations recorded NA. ds.completeCASES analogous complete.cases function native R. Limited additional information can therefore found help(\"complete.cases\") native R.","code":""},{"path":"/reference/completeCasesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"completeCasesDS: an assign function called by ds.completeCases — completeCasesDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/corDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"function computes sum vector variable sum products two variables (.e. scalar product two vectors).","code":""},{"path":"/reference/corDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"","code":"corDS(x = NULL, y = NULL)"},{"path":"/reference/corDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"x character, name vector, matrix dataframe variables(s) correlation(s) () going calculated . y NULL (default) name vector, matrix dataframe compatible dimensions x.","code":""},{"path":"/reference/corDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"list includes matrix elements sum products two variables, matrix elements sum values variable, matrix elements number complete cases pair variables, list number missing values variable separately (columnwise) number missing values casewise, vector elements sum squares variable. first disclosure control checks number variables bigger percentage individual-level records (allowed percentage pre-specified 'nfilter.glm'). second disclosure control checks none dichotomous level fewer counts pre-specified 'nfilter.tab' threshold. list also includes class, class input object client-side consistency checking.","code":""},{"path":"/reference/corDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"computes sum vector variable sum products two variables","code":""},{"path":"/reference/corDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the sum of each variable and the sum of products for each pair of variables — corDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/corTestDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests for correlation between paired samples — corTestDS","title":"Tests for correlation between paired samples — corTestDS","text":"function similar R function cor.test.","code":""},{"path":"/reference/corTestDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests for correlation between paired samples — corTestDS","text":"","code":"corTestDS(x, y, method, exact, conf.level)"},{"path":"/reference/corTestDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests for correlation between paired samples — corTestDS","text":"x character string providing name numerical vector. y character string providing name numerical vector. method character string indicating correlation coefficient used test. One \"pearson\", \"kendall\", \"spearman\", can abbreviated. exact logical indicating whether exact p-value computed. Used Kendall's tau Spearman's rho. conf.level confidence level returned confidence interval. Currently used Pearson product moment correlation coefficient least 4 complete pairs observations.","code":""},{"path":"/reference/corTestDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tests for correlation between paired samples — corTestDS","text":"list results correlation test class, class input object client-side consistency checking.","code":""},{"path":"/reference/corTestDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tests for correlation between paired samples — corTestDS","text":"function runs two-sided correlation test","code":""},{"path":"/reference/corTestDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Tests for correlation between paired samples — corTestDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/covDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"function computes sum vector variable sum products two variables (.e. scalar product two vectors).","code":""},{"path":"/reference/covDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"","code":"covDS(x = NULL, y = NULL, use = NULL)"},{"path":"/reference/covDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"x character, name vector, matrix dataframe variable(s) covariance(s) correlation(s) () going calculated . y NULL (default) name vector, matrix dataframe compatible dimensions x. use character string giving method computing covariances presence missing values. must one strings \"casewise.complete\" \"pairwise.complete\". use set 'casewise.complete' rows missing values omitted vector, matrix dataframe calculations sums. use set 'pairwise.complete' (default case set client-side), sums products computed two variables using complete pairs observations two variables.","code":""},{"path":"/reference/covDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"list includes matrix elements sum products two variables, matrix elements sum values variable, matrix elements number complete cases pair variables, list number missing values variable separately (columnwise) number missing values casewise pairwise depending argument use, error message indicates whether input variables pass disclosure controls. first disclosure control checks number variables bigger percentage individual-level records (allowed percentage pre-specified 'nfilter.glm'). second disclosure control checks none dichotomous level fewer counts pre-specified 'nfilter.tab' threshold. input variables pass disclosure controls output values replaced NAs. list also includes class, class input object client-side consistency checking.","code":""},{"path":"/reference/covDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"computes sum vector variable sum products two variables","code":""},{"path":"/reference/covDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the sum of each variable and the sum of products for each pair of variables — covDS","text":"Amadou Gaye, Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameDS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameDS called by ds.dataFrame — dataFrameDS","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"serverside function creates data frame elemental components. : pre-existing data frames; single variables; /matrices","code":""},{"path":"/reference/dataFrameDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"","code":"dataFrameDS( vectors = NULL, r.names = NULL, ch.rows = FALSE, ch.names = TRUE, clnames = NULL, strAsFactors = TRUE, completeCases = FALSE )"},{"path":"/reference/dataFrameDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"vectors list contains elemental components combine. correspond vector character strings specified argument x clientside function ds.dataFrame() r.names NULL character vector specifying names rows. Default NULL. ch.rows logical, TRUE rows checked consistency length names. Default FALSE. ch.names logical, TRUE names variables data frame checked ensure syntactically valid variable names duplicated. Default TRUE. fact, clientside function ensures duplicated names can presented dataFrameDS argument kept check forms syntactic validity. clnames list characters, column names output data frame. generated clientside function names vectors, column names data.frames matrices combined producing output data.frame strAsFactors logical, TRUE determines whether character vectors automatically converted factors? Default TRUE. completeCases logical. TRUE indicates complete cases included: rows missing values component excluded. Default FALSE.","code":""},{"path":"/reference/dataFrameDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"dataframe composed specified elemental components created serverside named according argument clientside function ds.dataFrame()","code":""},{"path":"/reference/dataFrameDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"data frame list variables number rows unique row names, class 'data.frame'. ds.dataFrame create data frame combining series elemental components may pre-existing data.frames, matrices variables. critical requirement length component variables, number rows component data.frames matrices must . output data.frame number rows. serverside function dataFrameDS() calls native R function data.frame() several arguments precisely data.frame(). consequence, additional information can sought help() data.frame().","code":""},{"path":"/reference/dataFrameDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameDS called by ds.dataFrame — dataFrameDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSortDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Sorts data frame using specified alphanumeric numeric sort key","code":""},{"path":"/reference/dataFrameSortDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"","code":"dataFrameSortDS( df.name = NULL, sort.key.name = NULL, sort.descending, sort.method )"},{"path":"/reference/dataFrameSortDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"df.name character string providing name serverside data.frame sorted. parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.key.name character string providing name sort key. serverside vector may sit inside data frame sorted independently serverside analysis environment. , sits outside data frame must length data frame. parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.descending logical, TRUE data.frame sorted sort key descending order. Default = FALSE (sort order ascending). parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\"). sort.method character string taking one values: \"default\", \"d\", \"alphabetic\", \"\", \"numeric\", \"n\", NULL. Default value \"default\". parameter fully specified equivalent argument ds.dataFrameShort details can found help(\"ds.dataFrameSort\").","code":""},{"path":"/reference/dataFrameSortDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"appropriately re-sorted data.frame written serverside R environment data.frame named according argument(default name 'dataframesort.newobj') name specified","code":""},{"path":"/reference/dataFrameSortDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Serverside assign function dataFrameSortDS called clientside function ds.dataFrameSort. vector matrix can added , coerced , data frame (using function [ds.dataFrame]) means can sorted/reordered using ds.dataFrameSort. Fundamentally, function [ds.dataFrameSort] sort specified data frame serverside using sort key also serverside. details see help clientside function: [ds.dataFrameShort]","code":""},{"path":"/reference/dataFrameSortDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Sorting and reordering data frames, vectors or matrices — dataFrameSortDS","text":"Paul Burton, critical error identification Leire Abarrategui-Martinez, DataSHIELD Development Team, 2/4/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"First serverside function subsetting data frame row column.","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"","code":"dataFrameSubset1DS( df.name = NULL, V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, keep.cols = NULL, rm.cols = NULL, keep.NAs = NULL )"},{"path":"/reference/dataFrameSubset1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"df.name character string providing name data.frame sorted. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset V1.name character string specifying name subsetting vector Boolean operator applied define subset created. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset V2.name character string specifying name vector scalar values vector specified argument compared. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset Boolean.operator.n character string specifying one six possible Boolean operators: '==', '!=', '>', '>=', '<', '<=' argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset keep.cols numeric vector specifying numbers columns kept final subset subsetting column. example: keep.cols=c(2:5,7,12) keep columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset rm.cols numeric vector specifying numbers columns removed creating final subset subsetting column. example: rm.cols=c(2:5,7,12) remove columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset keep.NAs logical, TRUE NAs vector holding final Boolean vector indicating whether given row included subset converted 1s included subset. NAs caused NAs either . FALSE NULL NAs final Boolean vector converted 0s corresponding row therefore excluded subset. argument generated passed directly dataFrameSubset1DS ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"first serverside function called ds.dataFrameSubset provides first level traps comprehensive series disclosure risks can returned directly clientside dataFrameSubset1DS aggregate function. second serverside function called ds.dataFrameSubset (dataFrameSubset2DS) carries disclosure tests, assign function writes subsetted data.frame serverside. consequence, records error messages studysideMessages can retrieved using ds.message","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"data frame list variables number rows, class 'data.frame'. details see help header ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameSubset1DS an aggregate function called by ds.dataFrameSubset — dataFrameSubset1DS","text":"Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"Second serverside function subsetting data frame row column.","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"","code":"dataFrameSubset2DS( df.name = NULL, V1.name = NULL, V2.name = NULL, Boolean.operator.n = NULL, keep.cols = NULL, rm.cols = NULL, keep.NAs = NULL )"},{"path":"/reference/dataFrameSubset2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"df.name character string providing name data.frame sorted. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset V1.name character string specifying name subsetting vector Boolean operator applied define subset created. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset V2.name character string specifying name vector scalar values vector specified argument compared. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset Boolean.operator.n character string specifying one six possible Boolean operators: '==', '!=', '>', '>=', '<', '<=' argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset keep.cols numeric vector specifying numbers columns kept final subset subsetting column. example: keep.cols=c(2:5,7,12) keep columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset rm.cols numeric vector specifying numbers columns removed creating final subset subsetting column. example: rm.cols=c(2:5,7,12) remove columns 2,3,4,5,7 12. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset keep.NAs logical, TRUE NAs vector holding final Boolean vector indicating whether given row included subset converted 1s included subset. NAs caused NAs either . FALSE NULL NAs final Boolean vector converted 0s corresponding row therefore excluded subset. argument generated passed directly dataFrameSubset2DS ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"object specified argument (default name '_subset') initially specified calling ds.dataFrameSubset. output object (required subsetted data.frame called written serverside. addition, two validity messages returned via ds.dataFrameSubset indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - dataFrameSubset2DS (via ds.dataFrame()) also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"data frame list variables number rows, class 'data.frame'. details see help header ds.dataFrameSubset","code":""},{"path":"/reference/dataFrameSubset2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dataFrameSubset2DS an assign function called by ds.dataFrameSubset — dataFrameSubset2DS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/densityGridDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates a density grid with or without a priori defined limits — densityGridDS","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Generates density grid can used heatmap contour plots.","code":""},{"path":"/reference/densityGridDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"","code":"densityGridDS( x, y, limits = FALSE, x.min = NULL, x.max = NULL, y.min = NULL, y.max = NULL, numints = 20 )"},{"path":"/reference/densityGridDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"x character string providing name server-side numerical vector y character string providing name server-side numerical vector limits logical expression whether limits density grid defined user. limits set \"FALSE\", min max x y used range. limits set \"TRUE\", limits defined x.min, x.max, y.min y.max used. x.min minimum value x axis grid density object, needed x.max maximum value x axis grid density object, needed y.min minimum value y axis grid density object, needed y.max maximum value y axis grid density object, needed numints number intervals grid density object, default 20","code":""},{"path":"/reference/densityGridDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"list grid density matrix (grid) classes x y inputs (class.x class.y)","code":""},{"path":"/reference/densityGridDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Invalid cells (cells count < set filter value minimum allowed counts table cells) turn 0.","code":""},{"path":"/reference/densityGridDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generates a density grid with or without a priori defined limits — densityGridDS","text":"Julia Isaeva, Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dimDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the dimension of a data frame or matrix — dimDS","title":"Returns the dimension of a data frame or matrix — dimDS","text":"function similar R function dim.","code":""},{"path":"/reference/dimDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the dimension of a data frame or matrix — dimDS","text":"","code":"dimDS(x)"},{"path":"/reference/dimDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the dimension of a data frame or matrix — dimDS","text":"x string character, name dataframe matrix","code":""},{"path":"/reference/dimDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the dimension of a data frame or matrix — dimDS","text":"list two elements: dim (dimension input object) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/dimDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the dimension of a data frame or matrix — dimDS","text":"function returns dimension input dataframe matrix","code":""},{"path":"/reference/dimDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the dimension of a data frame or matrix — dimDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/dmtC2SDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"Creates data.frame, matrix tibble serverside equivalent data.frame, matrix tibble (DMT) clientside.","code":""},{"path":"/reference/dmtC2SDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"","code":"dmtC2SDS( dfdata.mat.transmit, inout.object.transmit, from, nrows.transmit, ncols.transmit, colnames.transmit, colclass.transmit, byrow )"},{"path":"/reference/dmtC2SDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"dfdata.mat.transmit character string format can pass DataSHIELD R parser specifies name DMT copied clientside serverside. Value fully specified argument ds.dmtC2S. inout.object.transmit character string taking values \"DF\", \"MAT\" \"TBL\". value argument automatically set ds.dmtC2S depending whether clientside DMT data.frame, matrix tibble. Correspondingly, value determines whether object created serverside data.frame, matrix tibble. unlikely always work (class misspecifications may occur) works test cases. character string specifying source . Fixed clientside function \"clientside.matdftbl\". nrows.transmit specifies number rows matrix created. Fixed clientside function equal number rows clientside DMT transferred. ncols.transmit specifies number columns matrix created. Fixed clientside function equal number columns clientside DMT transferred. colnames.transmit parser-transmissible vector specifying name column DMT transferred clientside serverside. Generated automatically clientside function colnames clientside DMT. colclass.transmit parser-transmissible vector specifying class vector representing individual column DMT transferred. Generated automatically clientside function. allows transmission DMTs containing columns different classes.something going go wrong class misspecification (see inout.object.transmit) DMT complex combination data/column types likely cause. suggests always check class serverside DMT individual columns (latter important). situation arises class columns crucial function needed please contact DataSHIELD forum can try remedy problem. byrow logical value specifying whether DMT created serverside filled row row column column. fixed clientside function FALSE (fill column column).","code":""},{"path":"/reference/dmtC2SDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"object specified argument (default name \"matdftbl.copied.C2S\") written data.frame, matrix tibble serverside.","code":""},{"path":"/reference/dmtC2SDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"dmtC2SDS serverside assign function called ds.dmtC2S. information works see help ds.dmtC2S","code":""},{"path":"/reference/dmtC2SDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Copy a clientside data.frame, matrix or tibble (DMT) to the serverside. — dmtC2SDS","text":"Paul Burton DataSHIELD Development Team - 3rd June, 2021","code":""},{"path":"/reference/dsBase-package.html","id":null,"dir":"Reference","previous_headings":"","what":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","title":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","text":"Base 'DataSHIELD' functions server side. 'DataSHIELD' software package allows non-disclosive federated analysis sensitive data. 'DataSHIELD' analytic functions designed share non disclosive summary statistics, built automated output checking based statistical disclosure control. data sites setting threshold values automated output checks. details, see 'citation(\"dsBase\")'.","code":""},{"path":"/reference/dsBase-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dsBase: 'DataSHIELD' Server Side Base Functions — dsBase-package","text":"Maintainer: Stuart Wheater stuart.wheater@arjuna.com (ORCID) Authors: Stuart Wheater stuart.wheater@arjuna.com (ORCID) Paul Burton (ORCID) Rebecca Wilson (ORCID) Olly Butters (ORCID) Patricia Ryser-Welch (ORCID) Alex Westerberg Leire Abarrategui Roberto Villegas-Diaz (ORCID) Demetris Avraam (ORCID) Yannick Marcon yannick.marcon@obiba.org (ORCID) Tom Bishop Amadou Gaye (ORCID) Xavier Escribà-Montagut (ORCID)","code":""},{"path":"/reference/elsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"function based native R function elspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/elsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"","code":"elsplineDS(x = x, n = n, marginal = FALSE, names = NULL)"},{"path":"/reference/elsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"x name input numeric variable n integer greater 2, knots computed cut n equally-spaced intervals along range x marginal logical, parametrize spline, see Details names character, vector names constructed variables","code":""},{"path":"/reference/elsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"elspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/elsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment. Function elspline wraps lspline computes knot positions cut range x n equal-width intervals.","code":""},{"path":"/reference/elsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — elsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/expDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the exponential values of the input variable — expDS","title":"Computes the exponential values of the input variable — expDS","text":"function similar R function exp.","code":""},{"path":"/reference/expDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the exponential values of the input variable — expDS","text":"","code":"expDS(x)"},{"path":"/reference/expDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the exponential values of the input variable — expDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/expDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the exponential values of the input variable — expDS","text":"object specified newobj argument ds.exp (default name exp.newobj) written serverside. output object class numeric.","code":""},{"path":"/reference/expDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the exponential values of the input variable — expDS","text":"function computes exponential values input numeric integer vector.","code":""},{"path":"/reference/expDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the exponential values of the input variable — expDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/fixClassDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Change Class of Target Variables in a Data Frame — fixClassDS","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"Change Class Target Variables Data Frame","code":""},{"path":"/reference/fixClassDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"","code":"fixClassDS(df.name, target_vars, target_class)"},{"path":"/reference/fixClassDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"df.name string representing name data frame. target_vars character vector specifying columns modified. target_class character vector specifying new classes column (1 = factor, 2 = integer, 3 = numeric, 4 = character, 5 = logical).","code":""},{"path":"/reference/fixClassDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change Class of Target Variables in a Data Frame — fixClassDS","text":"modified data frame specified columns converted target classes.","code":""},{"path":"/reference/fixColsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Missing Columns with NA Values — fixColsDS","title":"Add Missing Columns with NA Values — fixColsDS","text":"Add Missing Columns NA Values","code":""},{"path":"/reference/fixColsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Missing Columns with NA Values — fixColsDS","text":"","code":"fixColsDS(.data, cols)"},{"path":"/reference/fixColsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Missing Columns with NA Values — fixColsDS","text":".data string representing name data frame. cols character vector specifying columns added missing.","code":""},{"path":"/reference/fixColsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Missing Columns with NA Values — fixColsDS","text":"modified data frame missing columns added filled NA.","code":""},{"path":"/reference/fixLevelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"Set Factor Levels Specific Columns Data Frame","code":""},{"path":"/reference/fixLevelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"","code":"fixLevelsDS(df.name, vars, levels)"},{"path":"/reference/fixLevelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"df.name string representing name data frame modify. vars character vector specifying columns modified. levels named list element contains levels corresponding factor variable.","code":""},{"path":"/reference/fixLevelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Factor Levels for Specific Columns in a Data Frame — fixLevelsDS","text":"modified data frame specified columns converted factors provided levels.","code":""},{"path":"/reference/gamlssDS.html","id":null,"dir":"Reference","previous_headings":"","what":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"function calls gamlssDS wrapper function gamlss R package. function returns object class \"gamlss\", generalized additive model location, scale shape (GAMLSS). function also saves residuals object server-side name specified newobj argument. addition, argument centiles set TRUE, function calls centiles function gamlss package returns sample percentages centile curve.","code":""},{"path":"/reference/gamlssDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"","code":"gamlssDS( formula = formula, sigma.formula = sigma.formula, nu.formula = nu.formula, tau.formula = tau.formula, family = family, data = data, method = method, mu.fix = mu.fix, sigma.fix = sigma.fix, nu.fix = nu.fix, tau.fix = tau.fix, control = control, i.control = i.control, centiles = centiles, xvar = xvar, newobj = newobj )"},{"path":"/reference/gamlssDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"formula formula object, response left ~ operator, terms, separated + operators, right. Nonparametric smoothing terms indicated pb() penalised beta splines, cs smoothing splines, lo loess smooth terms random ra random terms, e.g. y~cs(x,df=5)+x1+x2*x3. sigma.formula formula object fitting model sigma parameter, formula , e.g. sigma.formula=~cs(x,df=5). nu.formula formula object fitting model nu parameter, e.g. nu.formula=~x tau.formula formula object fitting model tau parameter, e.g. tau.formula=~cs(x,df=2) family gamlss.family object, used define distribution link functions various parameters. distribution families supported gamlss() can found gamlss.family. Functions BI() (binomial) produce family object. Also can given without parentheses .e. BI. Family functions can take arguments, BI(mu.link=probit). data data frame containing variables occurring formula. missing, variables parent environment. method character indicating algorithm GAMLSS. Can either 'RS', 'CG' 'mixed'. method='RS' function use Rigby Stasinopoulos algorithm, method='CG' function use Cole Green algorithm, method='mixed' function use RS algorithm twice switching Cole Green algorithm 10 extra iterations. mu.fix logical, indicate whether mu parameter kept fixed fitting processes. sigma.fix logical, indicate whether sigma parameter kept fixed fitting processes. nu.fix logical, indicate whether nu parameter kept fixed fitting processes. tau.fix logical, indicate whether tau parameter kept fixed fitting processes. control sets control parameters outer iterations algorithm using gamlss.control function. vector 7 numeric values: () c.crit (convergence criterion algorithm), (ii) n.cyc (number cycles algorithm), (iii) mu.step (step length parameter mu), (iv) sigma.step (step length parameter sigma), (v) nu.step (step length parameter nu), (vi) tau.step (step length parameter tau), (vii) gd.tol (global deviance tolerance level). default values 7 parameters set c(0.001, 20, 1, 1, 1, 1, Inf). .control sets control parameters inner iterations RS algorithm using glim.control function. vector 4 numeric values: () cc (convergence criterion algorithm), (ii) cyc (number cycles algorithm), (iii) bf.cyc (number cycles backfitting algorithm), (iv) bf.tol (convergence criterion (tolerance level) backfitting algorithm). default values 4 parameters set c(0.001, 50, 30, 0.001). centiles logical, indicating whether function centiles() used tabulate sample percentages centile curve. Default set FALSE. xvar unique explanatory variable used centiles() function. variable used centiles argument set TRUE. restriction centiles function applies models one explanatory variable . newobj character string provides name output object stored data servers. Default gamlss_residuals.","code":""},{"path":"/reference/gamlssDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"gamlss object components native R gamlss function. Individual-level information like components y (response response) residuals (normalised quantile residuals model) disclosed client-side.","code":""},{"path":"/reference/gamlssDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"additional details see help header gamlss centiles functions native R gamlss package.","code":""},{"path":"/reference/gamlssDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gamlssDS an aggregate function called by ds.gamlss — gamlssDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/getAllLevelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"Retrieve Factor Levels Specific Columns","code":""},{"path":"/reference/getAllLevelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"","code":"getAllLevelsDS(df.name, factor_vars)"},{"path":"/reference/getAllLevelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"df.name string representing name data frame. factor_vars character vector specifying factor columns.","code":""},{"path":"/reference/getAllLevelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Factor Levels for Specific Columns — getAllLevelsDS","text":"list factor levels specified columns.","code":""},{"path":"/reference/getClassAllColsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"Get Class Columns Data Frame","code":""},{"path":"/reference/getClassAllColsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"","code":"getClassAllColsDS(df.name)"},{"path":"/reference/getClassAllColsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"df.name string representing name data frame.","code":""},{"path":"/reference/getClassAllColsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the Class of All Columns in a Data Frame — getClassAllColsDS","text":"tibble class column data frame.","code":""},{"path":"/reference/getWGSRDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"Calculate Growth Reference z-score given anthropometric measurement function similar R function getWGSR zscorer package.","code":""},{"path":"/reference/getWGSRDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"","code":"getWGSRDS(sex, firstPart, secondPart, index, standing = NA, thirdPart = NA)"},{"path":"/reference/getWGSRDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"sex name binary variable indicates sex subject. must coded 1 = male 2 = female. project variable sex different levels, recode levels 1 males 2 females using ds.recodeValues DataSHIELD function use ds.getWGSR. firstPart Name variable specifying: Weight (kg) BMI/, W/, W/H, W/L Head circumference (cm) HC/Height (cm) H/Length (cm) L/MUAC (cm) MUAC/Sub-scapular skinfold (mm) SSF/Triceps skinfold (mm) TSF/Give quoted variable name (e.g.) \"weight\". careful units (weight kg; height, length, head circumference, MUAC cm, skinfolds mm). secondPart Name variable specifying: Age (days) H/, HC/, L/, MUAC/, SSF/, TSF/Height (cm) BMI/, W/H Length (cm) W/L Give quoted variable name (e.g.) \"age\". careful units (age days; height length cm). index index calculated added data. One : bfa BMI age hca Head circumference age hfa Height age lfa Length age mfa MUAC age ssa Sub-scapular skinfold age tsa Triceps skinfold age wfa Weight age wfh Weight height wfl Weight length Give quoted index name (e.g.) \"wfh\". standing Variable specifying stature measured. NA (default) age (\"hfa\" \"lfa\") height rules (\"wfh\" \"wfl\") applied. must coded 1 = Standing; 2 = Supine; 3 = Unknown. Missing values recoded 3 = Unknown. Give single value (e.g.\"1\"). value specified height age rules applied. thirdPart Name variable specifying age (days) BMI/. Give quoted variable name (e.g.) \"age\". careful units (age days).","code":""},{"path":"/reference/getWGSRDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"ds.getWGSR assigns numeric vector includes z-scores specified index.","code":""},{"path":"/reference/getWGSRDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"function computes Growth Reference z-scores anthropometric data weight, height length, MUAC, head circumference, sub-scapular skinfold triceps skinfold. Note function might fail return NAs variables outside ranges given WGS (Child Growth Standards) reference (.e. 45 120 cm height 0 60 months age). user check ranges units data.","code":""},{"path":"/reference/getWGSRDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the WHO Growth Reference z-scores of anthropometric data — getWGSRDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glm1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"glm1DS called by ds.glm — glm1DS","title":"glm1DS called by ds.glm — glm1DS","text":"first server-side aggregate function called ds.glm","code":""},{"path":"/reference/glm1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"glm1DS called by ds.glm — glm1DS","text":"","code":"glm1DS(formula, family, weights, offset, data)"},{"path":"/reference/glm1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"glm1DS called by ds.glm — glm1DS","text":"formula glm() formula consistent R syntax eg U~x+y+Z regress variables U x,y Z family glm() family consistent R syntax eg \"gaussian\", \"poisson\", \"binomial\" weights optional variable providing regression weights offset offset data optional character string specifying data.frame object holding data analysed specified model","code":""},{"path":"/reference/glm1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"glm1DS called by ds.glm — glm1DS","text":"List values GLM model.","code":""},{"path":"/reference/glm1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"glm1DS called by ds.glm — glm1DS","text":"aggregation function sets model structure creates starting beta.vector feeds, via ds.glm, glm2DS enable iterative fitting generalized linear model specified. details please see extensive header ds.glm.","code":""},{"path":"/reference/glm1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"glm1DS called by ds.glm — glm1DS","text":"Burton PR DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glm2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"glm2DS called by ds.glm — glm2DS","title":"glm2DS called by ds.glm — glm2DS","text":"second server-side aggregate function called ds.glm.","code":""},{"path":"/reference/glm2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"glm2DS called by ds.glm — glm2DS","text":"","code":"glm2DS(formula, family, beta.vect, offset, weights, dataName)"},{"path":"/reference/glm2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"glm2DS called by ds.glm — glm2DS","text":"formula glm() formula consistent R syntax eg U~x+y+Z regress variables U x, y Z family glm() family consistent R syntax eg \"gaussian\", \"poisson\", \"binomial\" beta.vect numeric vector created clientside function specifying vector regression coefficients current iteration offset optional variable providing regression offset weights optional variable providing regression weights dataName optional character string specifying data.frame object holding data analysed specified model ","code":""},{"path":"/reference/glm2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"glm2DS called by ds.glm — glm2DS","text":"List values GLM model","code":""},{"path":"/reference/glm2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"glm2DS called by ds.glm — glm2DS","text":"aggregate function uses model structure starting beta.vector constructed glm1DS iteratively fit generalized linear model specified. function glm2DS also carries series disclosure checks arguments data fail tests, model construction blocked appropriate serverside error message created returned ds.glm clientside. details please see extensive header ds.glm.","code":""},{"path":"/reference/glm2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"glm2DS called by ds.glm — glm2DS","text":"Paul Burton, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmPredictDS.ag.html","id":null,"dir":"Reference","previous_headings":"","what":"predict regression responses from a glm object — glmPredictDS.ag","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"identify return key components/summaries serverside glm_predict object can safely returned clientside without disclosure risk","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"","code":"glmPredictDS.ag( glmname.transmit, newdataname.transmit, output.type, se.fit, dispersion, terms.transmit, na.action )"},{"path":"/reference/glmPredictDS.ag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"glmname.transmit character string specifying name glm object serverside used prediction. Fully specified glmname argument ds.glmPredict newdataname.transmit character string specifying (optional) dataframe serverside look (potentially) new covariate values base predictions. Fully specified newdataname argument ds.glmPredict. output.type character string taking values 'response', 'link' 'terms'. Fully specified corresponding argument ds.glmPredict. se.fit logical standard errors fitted predictions required. Fully specified corresponding argument ds.glmPredict. dispersion numeric value specifying dispersion GLM fit assumed computing standard errors. Fully specified corresponding argument ds.glmPredict. terms.transmit character vector specifying subset terms return prediction. Fully specified 'terms' argument ds.glmPredict. na.action character string determining done missing values data.frame identified . Fully specified na.action argument ds.glmPredict.","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"components/summarising statistics serverside predict_glm object can safely transmitted clientside without risk disclosure. details see DataSHIELD help ds.glmPredict glmPredict.help native R predict.glm predict.glm native R","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"Serverside aggregate function called ds.glmPredict. called immediately assign function glmPredict.created predict_glm object serverside applying equivalent predict.glm() native R glm object serverside. aggregate function, glmPredict.ag, identifies returns components predict_glm object can safely returned clientside without risk disclosure. details see DataSHIELD help ds.glmPredict glmPredict.help native R predict.glm","code":""},{"path":"/reference/glmPredictDS.ag.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"predict regression responses from a glm object — glmPredictDS.ag","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmPredictDS.as.html","id":null,"dir":"Reference","previous_headings":"","what":"predict regression responses from a glm object — glmPredictDS.as","title":"predict regression responses from a glm object — glmPredictDS.as","text":"create predict_glm object serverside applying equivalent predict.glm() native R glm object serverside. Identify return components predict_glm object can safely sent clientside without risk disclosure","code":""},{"path":"/reference/glmPredictDS.as.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"predict regression responses from a glm object — glmPredictDS.as","text":"","code":"glmPredictDS.as( glmname.transmit, newdataname.transmit, output.type, se.fit, dispersion, terms.transmit, na.action )"},{"path":"/reference/glmPredictDS.as.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"predict regression responses from a glm object — glmPredictDS.as","text":"glmname.transmit character string specifying name glm object serverside used prediction. Fully specified glmname argument ds.glmPredict newdataname.transmit character string specifying (optional) dataframe serverside look (potentially) new covariate values base predictions. Fully specified newdataname argument ds.glmPredict. output.type character string taking values 'response', 'link' 'terms'. Fully specified corresponding argument ds.glmPredict. se.fit logical standard errors fitted predictions required. Fully specified corresponding argument ds.glmPredict. dispersion numeric value specifying dispersion GLM fit assumed computing standard errors. Fully specified corresponding argument ds.glmPredict. terms.transmit character vector specifying subset terms return prediction. Fully specified 'terms' argument ds.glmPredict. na.action character string determining done missing values data.frame identified . Fully specified na.action argument ds.glmPredict.","code":""},{"path":"/reference/glmPredictDS.as.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"predict regression responses from a glm object — glmPredictDS.as","text":"glmPredict.writes new object serverside containing output precisely equivalent output predict.glm native R. details see DataSHIELD help ds.glmPredict help predict.glm native R","code":""},{"path":"/reference/glmPredictDS.as.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"predict regression responses from a glm object — glmPredictDS.as","text":"Serverside assign function called ds.glmPredict makes predictions regression responses based serverside glm object already created serverside ds.glmSLMA writes predict_glm object serverside. details see help ds.glmPredict help native R predict.glm","code":""},{"path":"/reference/glmPredictDS.as.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"predict regression responses from a glm object — glmPredictDS.as","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMA11DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMA11DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"","code":"glmSLMA11DS(formula, family, weights, offset, data)"},{"path":"/reference/glmSLMA11DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA weights character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. offset character string specifying variable used offset. Specified call ds.glmSLMA. data character string specifying name data.frame holding data model. Specified dataName call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"assesses returns information failure pass disclosure traps test model complexity (saturation). detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"glmSLMADS.assign aggregate function called clientside function ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS assign function glmSLMADS.assign detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA11DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA11DS","text":"Paul Burton DataSHIELD Development Team (14/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMA1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA1DS","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA1DS","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMA1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA1DS","text":"","code":"glmSLMA1DS(formula, family, weights, offset, data)"},{"path":"/reference/glmSLMA1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA1DS","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA weights character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. offset character string specifying variable used offset. Specified call ds.glmSLMA. data character string specifying name data.frame holding data model. Specified dataName call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA1DS","text":"assesses returns information failure pass disclosure traps test model complexity (saturation). detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA1DS","text":"glmSLMADS.assign aggregate function called clientside function ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS assign function glmSLMADS.assign detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA1DS","text":"Paul Burton DataSHIELD Development Team (14/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"","code":"glmSLMA2DS(formula, family, offset, weights, newobj, dataName)"},{"path":"/reference/glmSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA offset character string specifying variable used offset. Specified call ds.glmSLMA. weights character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. newobj character string specifying name glm object written serverside glmSLMADS.assign. either name specified newobj argument ds.glmSLMA newobj unspecified NULL called new.glm.obj. dataName character string specifying name data.frame holding data model. Specified call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"quantitative, Boolean, character objects required enable SLMA pooling separate glm models fitted study - particular including study-specific regression coefficients corresponding standard errors.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"glmSLMADS.assign aggregate function called clientside function ds.glmSLMA. ds.glmSLMA also calls another aggregate function glmSLMA2DS assign function glmSLMADS.assign detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMA2DS","text":"Paul Burton DataSHIELD Development Team (14/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"Fits generalized linear model (GLM) data single multiple sources pooled co-analysis across studies based SLMA (Study Level Meta Analysis).","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"","code":"glmSLMADS.assign(formula, family, offsetName, weightsName, dataName)"},{"path":"/reference/glmSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"formula glm formula, specified call ds.glmSLMA family glm family, specified call ds.glmSLMA offsetName character string specifying variable used offset. Specified call ds.glmSLMA. weightsName character string specifying variable used regression weights. Specified call ds.glmSLMA. Specified call ds.glmSLMA. dataName character string specifying name data.frame holding data model. Specified call ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"writes glm object summarising fitted model serverside. detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"glmSLMADS.assign assign function called clientside function ds.glmSLMA. ds.glmSLMA also calls two aggregate functions glmSLMA1DS glmSLMA2DS. detailed information see help ds.glmSLMA.","code":""},{"path":"/reference/glmSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — glmSLMADS.assign","text":"Paul Burton DataSHIELD Development Team (14/7/20)","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize a glm object on the serverside — glmSummaryDS.ag","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"returns non-disclosive elements clientside glm object corresponding object holding output summary(glm object) serverside.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"","code":"glmSummaryDS.ag(x.transmit)"},{"path":"/reference/glmSummaryDS.ag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"x.transmit character string specifying name glm object serverside summarised. specified x.name argument ds.glmSummary","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"returns clientside non-disclosive elements (non-disclosive elements) specified serverside glm corresponding summary_glm object.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"Serverside aggregate function called ds.glmSummary. ds.glmSummary first calls glmSummaryDS.ag create glm_summary object serverside based applying native R's summary.glm() serverside glm object previously created ds.glmSLMA. calls glmSummaryDS.ag return clientside non-disclosive elements (non-disclosive elements) serverside glm corresponding summary_glm object.","code":""},{"path":"/reference/glmSummaryDS.ag.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"summarize a glm object on the serverside — glmSummaryDS.ag","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmSummaryDS.as.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize a glm object on the serverside — glmSummaryDS.as","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"summarize glm object serverside create summary_glm object. Also identify return components glm object summary_glm object can safely sent clientside without risk disclosure","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"","code":"glmSummaryDS.as(x.transmit)"},{"path":"/reference/glmSummaryDS.as.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"x.transmit character string specifying name glm object serverside summarised. specified x.name argument ds.glmSummary","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"writes object serverside precisely equivalent summary(glm object) native R","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"Serverside assign function called ds.glmSummary summarises glm object already created serverside fitting ds.glmSLMA writes summary_glm object serverside. details see help ds.glmSLMA help native R glm() summary.glm","code":""},{"path":"/reference/glmSummaryDS.as.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"summarize a glm object on the serverside — glmSummaryDS.as","text":"Paul Burton DataSHIELD Development Team (20/7/20) Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmerSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"glmerSLMA2DS fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data one multiple sources pooling via SLMA (study level meta-analysis)","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"","code":"glmerSLMA2DS( formula, offset, weights, dataName, family, control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL )"},{"path":"/reference/glmerSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"formula see help ds.glmerSLMA offset see help ds.glmerSLMA weights see help ds.glmerSLMA dataName see help ds.glmerSLMA family see help ds.glmerSLMA control_type see help ds.glmerSLMA control_value.transmit see help argument function ds.glmerSLMA nAGQ integer scalar, defaulting 1L. PRACTICE, MAY NECESSARY SET nAGQ 0L model appears converge perfectly well (e.g. verbose=2 demonstrates good initial convergence log-likelihood regression coefficients) formal convergence get declared - output produced - despite running model many iterations. nAGQ argument set nAGQ argument ds.glmerSLMA details can found help(ds.glmerSLMA) native R help glmer() verbose see help ds.glmerSLMA theta see help argument function ds.glmerSLMA fixef see help argument function ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"key model components see help ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"glmerSLMA2DS serverside function called ds.glmerSLMA clientside. analytic work engine glmer function R sits lme4 package. ds.glmerSLMA fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data single multiple sources. multiple data sources, glme fitted convergence data source independently estimates standard errors returned client thereby enabling cross-study pooling using study level meta-analysis (SLMA). default SLMA undertaken using metafor package, SLMA occurs clientside , far user concerned just standard R environment, user can choose use approach meta-analysis choose. Additional information fitting glmes using glmer engine can obtained using R help glmer lme4 package","code":""},{"path":"/reference/glmerSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMA2DS","text":"Tom Bishop, additions Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"glmerSLMADS.assign glmerSLMA2DS fits generalized linear mixed effects model (glme) per study saves outcomes study","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"","code":"glmerSLMADS.assign( formula, offset, weights, dataName, family, control_type = NULL, control_value.transmit = NULL, nAGQ = 1L, verbose = 0, theta = NULL, fixef = NULL )"},{"path":"/reference/glmerSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"formula see help ds.glmerSLMA offset see help ds.glmerSLMA weights see help ds.glmerSLMA dataName see help ds.glmerSLMA family see help ds.glmerSLMA control_type see help ds.glmerSLMA control_value.transmit see help argument function ds.glmerSLMA nAGQ integer scalar, defaulting 1L. PRACTICE, MAY NECESSARY SET nAGQ 0L model appears converge perfectly well (e.g. verbose=2 demonstrates good initial convergence log-likelihood regression coefficients) formal convergence get declared - output produced - despite running model many iterations. nAGQ argument set nAGQ argument ds.glmerSLMA details can found help(ds.glmerSLMA) native R help glmer() verbose see help ds.glmerSLMA theta see help argument function ds.glmerSLMA fixef see help argument function ds.glmerSLMA","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"writes glmerMod object summarising fitted model serverside. detailed information see help ds.glmerSLMA.","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"glmerSLMADS.assign serverside function called ds.glmerSLMA clientside. analytic work engine glmer function R sits lme4 package. glmerSLMADS.assign fits generalized linear mixed effects model (glme) - e.g. logistic Poisson regression model including fixed random effects - data single data source saves regression outcomes serverside.","code":""},{"path":"/reference/glmerSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting generalized linear mixed effect models - serverside function — glmerSLMADS.assign","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/heatmapPlotDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"function calculates coordinates centroids n nearest neighbours.","code":""},{"path":"/reference/heatmapPlotDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"","code":"heatmapPlotDS(x.name, y.name, k, noise, method.indicator)"},{"path":"/reference/heatmapPlotDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"x.name character string providing name server-side numeric vector, x-variable. y.name character string providing name server-side numeric vector, y-variable. k number nearest neighbours centroid calculated method.indicator equal 1 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 2 (.e. probabilistic method). method.indicator number equal either 1 2. value equal 1 'deterministic' method used. value set 2 'probabilistic' method used.","code":""},{"path":"/reference/heatmapPlotDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"list x y coordinates centroids deterministic method used x y coordinated noisy data probabilistic method used, along classes x y inputs (class.x class.y)","code":""},{"path":"/reference/heatmapPlotDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"function finds n-1 nearest neighbours data point 2-dimensional space. nearest neighbours data points minimum Euclidean distances point interest. point interest n-1 nearest neighbours used calculation coordinates centroid n points. Centroid referred centre mass, .e. x-coordinate centroid average value x-coordinates n nearest neighbours y-coordinate centroid average y-coordinates n nearest neighbours. coordinates centroids return client side function can used plot non-disclosive graphs (e.g. scatter plots, heatmap plots, contour plots, etc).","code":""},{"path":"/reference/heatmapPlotDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the coordinates of the centroid of each n nearest neighbours — heatmapPlotDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/hetcorDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Heterogeneous Correlation Matrix — hetcorDS","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"function based hetcor function R package polycor.","code":""},{"path":"/reference/hetcorDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"","code":"hetcorDS(data, ML, std.err, bins, pd, use)"},{"path":"/reference/hetcorDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"data name data frame consisting factors, ordered factors, logical variables, character variables, /numeric variables, first several variables. ML TRUE, compute maximum-likelihood estimates; FALSE (default), compute quick two-step estimates. std.err TRUE (default), compute standard errors. bins number bins use continuous variables testing bivariate normality; default 4. pd TRUE (default) correlation matrix positive-definite, attempt made adjust positive-definite matrix, using nearPD function Matrix package. Note default arguments nearPD used (except corr=TRUE); control call nearPD directly. use \"complete.obs\", remove observations missing data; \"pairwise.complete.obs\", compute correlation using observations valid data pair variables.","code":""},{"path":"/reference/hetcorDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Returns object class \"hetcor\" following components: correlation matrix; type correlation: \"Pearson\", \"Polychoric\", \"Polyserial\"; standard errors correlations, requested; number (numbers) observations correlations based; p-values tests bivariate normality pair variables; method missing data handled: \"complete.obs\" \"pairwise.complete.obs\"; TRUE ML estimates, FALSE two-step estimates.","code":""},{"path":"/reference/hetcorDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Computes heterogeneous correlation matrix, consisting Pearson product-moment correlations numeric variables, polyserial correlations numeric ordinal variables, polychoric correlations ordinal variables.","code":""},{"path":"/reference/hetcorDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Heterogeneous Correlation Matrix — hetcorDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/histogram1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"returns the minimum and the maximum of the input numeric vector — histogram1DS","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"function returns minimum maximum input numeric vector depends argument method.indicator. method.indicator set 1 (.e. 'smallCellsRule' used) computed minimum maximum values multiplied small random number. method.indicator set 2 (.e. 'deterministic' method used) function returns minimum maximum values vector scaled centroids. method.indicator set 3 (.e. 'probabilistic' method used) function returns minimum maximum values generated 'noisy' vector.","code":""},{"path":"/reference/histogram1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"","code":"histogram1DS(x, method.indicator, k, noise)"},{"path":"/reference/histogram1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"x character string providing name server-side numeric vector histogram desired. method.indicator number equal either 1, 2 3 indicating method disclosure control used generation histogram. value equal 1 'smallCellsRule' used. value equal 2 'deterministic' method used. value set 3 'probabilistic' method used. k number nearest neighbours centroid calculated method.indicator equal 2 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 3 (.e. probabilistic method).","code":""},{"path":"/reference/histogram1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"list numeric vector containing minimum maximum values vector (range) class input vector (class)","code":""},{"path":"/reference/histogram1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"returns the minimum and the maximum of the input numeric vector — histogram1DS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/histogram2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes a histogram of the input variable without plotting. — histogram2DS","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"function produces information required plot histogram. done without allowing bins (cells) number counts less pre-specified disclosure control set minimum cell size table. bin less counts threshold counts density replaced 0 value.","code":""},{"path":"/reference/histogram2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"","code":"histogram2DS(x, num.breaks, min, max, method.indicator, k, noise)"},{"path":"/reference/histogram2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"x character string providing name server-side numeric vector histogram desired. num.breaks number breaks range variable divided. min numeric, lower limit distribution. max numeric, upper limit distribution. method.indicator number equal either 1, 2 3 indicating method disclosure control used generation histogram. value equal 1 'smallCellsRule' used. value equal 2 'deterministic' method used. value set 3 'probabilistic' method used. k number nearest neighbours centroid calculated method.indicator equal 2 (.e. deterministic method). noise percentage initial variance used variance embedded noise method.indicator equal 3 (.e. probabilistic method).","code":""},{"path":"/reference/histogram2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"list object class histogram number invalid cells","code":""},{"path":"/reference/histogram2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"Please find details documentation clientside ds.histogram function.","code":""},{"path":"/reference/histogram2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes a histogram of the input variable without plotting. — histogram2DS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/igb_standardsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"Converts birth measurements INTERGROWTH z-scores/centiles (generic)","code":""},{"path":"/reference/igb_standardsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"","code":"igb_standardsDS( gagebrth = gagebrth, z = z, p = p, val = val, var = var, sex = sex, fun = fun )"},{"path":"/reference/igb_standardsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"gagebrth name \"gestational age birth days\" variable. z z-score(s) convert (must 0 1). Default value 0. value used fun set \"igb_zscore2value\". p centile(s) convert (must 0 100). Default value p=50. value used fun set \"igb_centile2value\". val name anthropometric variable convert. var name measurement convert (\"lencm\", \"wtkg\", \"hcircm\", \"wlr\") sex name sex factor variable. variable coded Male/Female. coded differently (e.g. 0/1), can use ds.recodeValues function recode categories Male/Female use ds.igb_standards fun name function used. can one : \"igb_centile2value\", \"igb_zscore2value\", \"igb_value2zscore\" (default), \"igb_value2centile\".","code":""},{"path":"/reference/igb_standardsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"assigns converted measurement new object server-side","code":""},{"path":"/reference/igb_standardsDS.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"gestational ages 24 33 weeks, INTERGROWTH early preterm standard used.","code":""},{"path":"/reference/igb_standardsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts birth measurements to intergrowth z-scores/centiles — igb_standardsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/isNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if a vector is empty — isNaDS","title":"Checks if a vector is empty — isNaDS","text":"function similar R function .na instead vector booleans returns just one boolean tell element missing values.","code":""},{"path":"/reference/isNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if a vector is empty — isNaDS","text":"","code":"isNaDS(x)"},{"path":"/reference/isNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if a vector is empty — isNaDS","text":"x character string, name server-side vector","code":""},{"path":"/reference/isNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if a vector is empty — isNaDS","text":"list two elements: .na (TRUE vector contains NAs, FALSE otherwise) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/isNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if a vector is empty — isNaDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/isValidDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if an input is valid — isValidDS","title":"Checks if an input is valid — isValidDS","text":"Tells object server side valid.","code":""},{"path":"/reference/isValidDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if an input is valid — isValidDS","text":"","code":"isValidDS(x)"},{"path":"/reference/isValidDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if an input is valid — isValidDS","text":"x character string, name vector (numeric, integer, factor, character, logical), data.frame matrix","code":""},{"path":"/reference/isValidDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if an input is valid — isValidDS","text":"list valid, boolean TRUE input valid FALSE , class, class input object client-side consistency checking","code":""},{"path":"/reference/isValidDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Checks if an input is valid — isValidDS","text":"function checks object valid.","code":""},{"path":"/reference/isValidDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Checks if an input is valid — isValidDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/kurtosis1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the kurtosis of a numeric variable — kurtosis1DS","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"function calculates kurtosis numeric variable study separately.","code":""},{"path":"/reference/kurtosis1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"","code":"kurtosis1DS(x, method)"},{"path":"/reference/kurtosis1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"x string character, name numeric variable. method integer 1 3 selecting one algorithms computing kurtosis detailed headers client-side ds.kurtosis function.","code":""},{"path":"/reference/kurtosis1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"list including kurtosis input numeric variable, number valid observations class, class input object client-side consistency checking.","code":""},{"path":"/reference/kurtosis1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"function calculates kurtosis input variable x three different methods. method specified argument method client-side ds.kurtosis function.","code":""},{"path":"/reference/kurtosis1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the kurtosis of a numeric variable — kurtosis1DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/kurtosis2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the kurtosis of a numeric variable — kurtosis2DS","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"function calculates summary statistics returned client-side used estimation combined kurtosis numeric variable across studies.","code":""},{"path":"/reference/kurtosis2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"","code":"kurtosis2DS(x, global.mean)"},{"path":"/reference/kurtosis2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"x string character, name numeric variable. global.mean numeric, combined mean input variable across studies.","code":""},{"path":"/reference/kurtosis2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"list including sum quartic differences values x global mean x across studies, sum squared differences values x global mean x across studies, number valid observations (.e. length x excluding missing values), class, class input object client-side consistency checking.","code":""},{"path":"/reference/kurtosis2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"function calculates sum squared differences values x global mean x across studies, sum quatric differences values x global mean x across studies number valid observations input variable x.","code":""},{"path":"/reference/kurtosis2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the kurtosis of a numeric variable — kurtosis2DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lengthDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the length of a vector or list — lengthDS","title":"Returns the length of a vector or list — lengthDS","text":"function similar R function length.","code":""},{"path":"/reference/lengthDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the length of a vector or list — lengthDS","text":"","code":"lengthDS(x)"},{"path":"/reference/lengthDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the length of a vector or list — lengthDS","text":"x string character, name vector list","code":""},{"path":"/reference/lengthDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the length of a vector or list — lengthDS","text":"list two elements: length (number elements input vector list) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/lengthDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the length of a vector or list — lengthDS","text":"function returns length input vector list.","code":""},{"path":"/reference/lengthDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the length of a vector or list — lengthDS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/levelsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the levels of a factor vector — levelsDS","title":"Returns the levels of a factor vector — levelsDS","text":"function similar R function levels.","code":""},{"path":"/reference/levelsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the levels of a factor vector — levelsDS","text":"","code":"levelsDS(x)"},{"path":"/reference/levelsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the levels of a factor vector — levelsDS","text":"x character string, name factor vector","code":""},{"path":"/reference/levelsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the levels of a factor vector — levelsDS","text":"list one element: Levels (factor levels present vector)","code":""},{"path":"/reference/levelsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the levels of a factor vector — levelsDS","text":"function returns levels input vector list.","code":""},{"path":"/reference/levelsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the levels of a factor vector — levelsDS","text":"Alex Westerberg, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"lexis1DS — lexis1DS","title":"lexis1DS — lexis1DS","text":"first server-side function called ds.lexis.","code":""},{"path":"/reference/lexis1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lexis1DS — lexis1DS","text":"","code":"lexis1DS(exitCol = NULL)"},{"path":"/reference/lexis1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lexis1DS — lexis1DS","text":"exitCol character string specifying variable holding time individual censored fails","code":""},{"path":"/reference/lexis1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lexis1DS — lexis1DS","text":"List `max.time`","code":""},{"path":"/reference/lexis1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lexis1DS — lexis1DS","text":"aggregate function. details see extensive header ds.lexis.","code":""},{"path":"/reference/lexis1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lexis1DS — lexis1DS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"lexis2DS — lexis2DS","title":"lexis2DS — lexis2DS","text":"second serverside function called ds.lexis.","code":""},{"path":"/reference/lexis2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lexis2DS — lexis2DS","text":"","code":"lexis2DS( datatext = NULL, intervalWidth, maxmaxtime, idCol, entryCol, exitCol, statusCol, vartext = NULL )"},{"path":"/reference/lexis2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lexis2DS — lexis2DS","text":"datatext clientside provided character string specifying data.frame holding data set expanded intervalWidth clientside generated character string specifying width survival epochs expanded data maxmaxtime clientside generated object specifying maximum follow time sources idCol clientside generated character string specifying variable holding IDs individuals data set expanded entryCol clientside specified character string identifying variable holding time individual starts follow exitCol clientside specified character string identifying variable holding time individual ends follow (censored fails) statusCol clientside specified character string identifying variable holding final censoring status (failed/censored) vartext clientside provided vector character strings denoting column names additional variables include final expanded table. 'variables' argument set (null) 'data' argument set full data.frame expanded carried forward","code":""},{"path":"/reference/lexis2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lexis2DS — lexis2DS","text":"List `expanded.table`","code":""},{"path":"/reference/lexis2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lexis2DS — lexis2DS","text":"assign function actually creates expanded dataframe containing survival data piecewise exponential regression. lexis2DS also carries series disclosure checks arguments data fail tests, creation expanded dataframe blocked appropriate serverside error message stored. details see extensive header ds.lexis.","code":""},{"path":"/reference/lexis2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lexis2DS — lexis2DS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lexis3DS.html","id":null,"dir":"Reference","previous_headings":"","what":"@title lexis3DS — lexis3DS","title":"@title lexis3DS — lexis3DS","text":"third serverside function called ds.lexis.","code":""},{"path":"/reference/lexis3DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"@title lexis3DS — lexis3DS","text":"","code":"lexis3DS()"},{"path":"/reference/lexis3DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"@title lexis3DS — lexis3DS","text":"Data frame `messageobj` object","code":""},{"path":"/reference/lexis3DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"@title lexis3DS — lexis3DS","text":"assign function simplifies returned output ds.lexis. Specifically, without lexis3DS output consists table within list, lexis3DS converts directly dataframe. details see extensive header ds.lexis.","code":""},{"path":"/reference/listDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce objects into a list — listDS","title":"Coerce objects into a list — listDS","text":"function similar R function 'list'","code":""},{"path":"/reference/listDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce objects into a list — listDS","text":"","code":"listDS(x.names = NULL, eltnames = NULL)"},{"path":"/reference/listDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce objects into a list — listDS","text":"x.names character vector object names coerce list. eltnames character vector, names elements list.","code":""},{"path":"/reference/listDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce objects into a list — listDS","text":"list","code":""},{"path":"/reference/listDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerce objects into a list — listDS","text":"Unlike R function 'list' takes also vector characters, names elements output list.","code":""},{"path":"/reference/listDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerce objects into a list — listDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"listDisclosureSettingsDS — listDisclosureSettingsDS","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"serverside function aggregate function called ds.listDisclosureSettings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"","code":"listDisclosureSettingsDS()"},{"path":"/reference/listDisclosureSettingsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"List DataSHIELD disclosure settings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"details see extensive header ds.listDisclosureSettings","code":""},{"path":"/reference/listDisclosureSettingsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"listDisclosureSettingsDS — listDisclosureSettingsDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team","code":""},{"path":"/reference/lmerSLMA2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"lmerSLMA2DS serverside function fits linear mixed effects model (lme) - .e. can include fixed random effects - data one multiple sources pooling via SLMA (study level meta-analysis)","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"","code":"lmerSLMA2DS( formula, offset, weights, dataName, REML = TRUE, control_type, control_value.transmit, optimizer, verbose = 0 )"},{"path":"/reference/lmerSLMA2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"formula see help ds.lmerSLMA offset see help ds.lmerSLMA weights see help ds.lmerSLMA dataName see help ds.lmerSLMA REML see help ds.lmerSLMA control_type see help ds.lmerSLMA control_value.transmit see help argument function ds.lmerSLMA optimizer see help ds.lmerSLMA verbose see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"key model components see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"lmerSLMA2DS serverside function called ds.lmerSLMA clientside. analytic work engine lmer function R sits lme4 package. ds.lmerSLMA fits linear mixed effects model (lme) - can include fixed random effects - data single multiple sources. multiple data sources, lme fitted convergence data source independently estimates standard errors returned client thereby enabling cross-study pooling using study level meta-analysis (SLMA). default SLMA undertaken using metafor package, SLMA occurs clientside , far user concerned just standard R environment, user can choose use approach meta-analysis choose. detailed help aspect lmerSLM2DS please see extensive help ds.lmerSLMA. Additional information fitting lmes using lmer engine can obtained using R help lmer lme4 package","code":""},{"path":"/reference/lmerSLMA2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting linear mixed effect models - serverside function — lmerSLMA2DS","text":"Tom Bishop, additions Paul Burton Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"lmerSLMADS.assign lmerSLMA2DS fits linear mixed effects model (lme) per study saves outcomes study","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"","code":"lmerSLMADS.assign( formula, offset, weights, dataName, REML = TRUE, control_type, control_value.transmit, optimizer, verbose = 0 )"},{"path":"/reference/lmerSLMADS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"formula see help ds.lmerSLMA offset see help ds.lmerSLMA weights see help ds.lmerSLMA dataName see help ds.lmerSLMA REML see help ds.lmerSLMA control_type see help ds.lmerSLMA control_value.transmit see help argument function ds.lmerSLMA optimizer see help ds.lmerSLMA verbose see help ds.lmerSLMA","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"writes lmerMod object summarising fitted model serverside. detailed information see help ds.lmerSLMA.","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"lmerSLMADS.assign serverside function called ds.lmerSLMA clientside. analytic work engine lmer function R sits lme4 package. lmerSLMADS.assign fits linear mixed effects model (lme) including fixed random effects - data single data source saves regression outcomes serverside.","code":""},{"path":"/reference/lmerSLMADS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fitting linear mixed effect models - serverside function — lmerSLMADS.assign","text":"TDemetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/logDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the logarithm values of the input variable — logDS","title":"Computes the logarithm values of the input variable — logDS","text":"function similar R function log.","code":""},{"path":"/reference/logDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the logarithm values of the input variable — logDS","text":"","code":"logDS(x, base = exp(1))"},{"path":"/reference/logDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the logarithm values of the input variable — logDS","text":"x string character, name numeric integer vector base positive number, base logarithms computed. Default exp(1).","code":""},{"path":"/reference/logDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the logarithm values of the input variable — logDS","text":"object specified newobj argument ds.log (default name log.newobj) written serverside. output object class numeric.","code":""},{"path":"/reference/logDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the logarithm values of the input variable — logDS","text":"function computes logarithm values input numeric integer vector. default natural logarithms computed.","code":""},{"path":"/reference/logDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the logarithm values of the input variable — logDS","text":"DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/lsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"lists all objects on a serverside environment — lsDS","title":"lists all objects on a serverside environment — lsDS","text":"creates list names objects specified serverside environment","code":""},{"path":"/reference/lsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lists all objects on a serverside environment — lsDS","text":"","code":"lsDS(search.filter = NULL, env.to.search)"},{"path":"/reference/lsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lists all objects on a serverside environment — lsDS","text":"search.filter either NULL character string (potentially including '*' wildcards) specifying required search criteria. argument fully specified corresponding argument clientside function. env..search integer (e.g. format '2' '5L' format) specifying position search path environment explored. argument fully specified corresponding argument clientside function.","code":""},{"path":"/reference/lsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lists all objects on a serverside environment — lsDS","text":"list containing: (1) name/details serverside R environment ds.ls searched; (2) vector character strings giving names objects meeting naming criteria specified argument specified R serverside environment; (3) nature search filter string actually applied","code":""},{"path":"/reference/lsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"lists all objects on a serverside environment — lsDS","text":"Serverside aggregate function lsDS called clientside function ds.ls. running analyses one may want know objects already generated. request disclosive returns names objects contents. default, objects current 'active analytic environment' (\".GlobalEnv\") displayed. environment contains objects serverside DataSHIELD using main analysis written serverside process managing undertaking analysis (variables, scalars, matrices, data.frames etc). details see help ds.ls function native R function ls","code":""},{"path":"/reference/lsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"lists all objects on a serverside environment — lsDS","text":"Gaye, (2015). Updated extended Paul Burton (2020).","code":""},{"path":"/reference/lsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"function based native R function lspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/lsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"","code":"lsplineDS(x = x, knots = NULL, marginal = FALSE, names = NULL)"},{"path":"/reference/lsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"x name input numeric variable knots numeric vector knot positions marginal logical, parametrize spline, see Details names, character, vector names constructed variables","code":""},{"path":"/reference/lsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"lspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/lsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment.","code":""},{"path":"/reference/lsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — lsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDS assign function called by ds.matrix — matrixDS","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Creates matrix serverside","code":""},{"path":"/reference/matrixDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"","code":"matrixDS(mdata.transmit, from, nrows.transmit, ncols.transmit, byrow, dimnames)"},{"path":"/reference/matrixDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"mdata.transmit specifies elements matrix created. Fully specified argument ds.matrix character string specifying source nature . Fully specified <> argument ds.matrix nrows.transmit specifies number rows matrix created. Fully specified argument ds.matrix ncols.transmit specifies number columns matrix created. Fully specified argument ds.matrix byrow logical value specifying whether, vector, matrix created filled row row column column. Fully specified argument ds.matrix dimnames dimnames attribute matrix: NULL list length 2 giving row column names respectively. empty list treated NULL, list length one row names . Fully specified argument ds.matrix","code":""},{"path":"/reference/matrixDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Output matrix written serverside. details see help ds.matrix","code":""},{"path":"/reference/matrixDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Similar matrix() function native R. Creates matrix dimensions specified arguments assigns values elements based argument","code":""},{"path":"/reference/matrixDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDS assign function called by ds.matrix — matrixDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDet1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Calculates determinant square matrix returns output clientside","code":""},{"path":"/reference/matrixDet1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"","code":"matrixDet1DS(M1.name = NULL, logarithm)"},{"path":"/reference/matrixDet1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"M1.name character string specifying name matrix determinant calculated logarithm logical. Default FALSE, returns determinant , TRUE returns logarithm modulus determinant.","code":""},{"path":"/reference/matrixDet1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Output determinant matrix identified argument returned clientside. details see help ds.matrixDet","code":""},{"path":"/reference/matrixDet1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Calculates determinant square matrix (additional information see help det function native R). operation possible number columns rows .","code":""},{"path":"/reference/matrixDet1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDetDS aggregate function called by ds.matrixDet.report — matrixDet1DS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDet2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Calculates determinant square matrix writes output serverside","code":""},{"path":"/reference/matrixDet2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"","code":"matrixDet2DS(M1.name = NULL, logarithm)"},{"path":"/reference/matrixDet2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"M1.name character string specifying name matrix determinant calculated logarithm logical. Default FALSE, returns determinant , TRUE returns logarithm modulus determinant.","code":""},{"path":"/reference/matrixDet2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Output determinant matrix identified argument written serverside. details see help ds.matrixDet","code":""},{"path":"/reference/matrixDet2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Calculates determinant square matrix (additional information see help det function native R). operation possible number columns rows .","code":""},{"path":"/reference/matrixDet2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDetDS assign function called by ds.matrixDet — matrixDet2DS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDiagDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Extracts diagonal vector square matrix creates diagonal matrix based vector scalar value writes output serverside","code":""},{"path":"/reference/matrixDiagDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"","code":"matrixDiagDS(x1.transmit, aim, nrows.transmit)"},{"path":"/reference/matrixDiagDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"x1.transmit identifies input matrix vector. Fully specified argument ds.matrixDiag. details see help ds.matrixDiag. aim character string specifying behaviour required function. Fully specified argument ds.matrixDiag. details see help ds.matrixDiag. nrows.transmit scalar value forcing number rows columns output matrix.Fully specified argument ds.matrixDiag. details see help ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Output matrix vector specified argument (default name diag_) written serverside. details see help ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"details see help function ds.matrixDiag.","code":""},{"path":"/reference/matrixDiagDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDiagDS assign function called by ds.matrixDiag — matrixDiagDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixDimnamesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Adds dimnames (row names, column names ) matrix serverside.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"","code":"matrixDimnamesDS(M1.name = NULL, dimnames)"},{"path":"/reference/matrixDimnamesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"M1.name Specifies name serverside matrix dimnames added. Fully specified argument function ds.matrixDimnames. details see help ds.matrixDimnames. dimnames dimnames attribute matrix: NULL list length 2 giving row column names respectively. Fully specified argument function ds.matrixDimnames. details see help ds.matrixDimnames.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Output serverside matrix specified argument (default name diag_) specified dimnames (row column names) written serverside.","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Adds dimnames (row names, column names ) matrix serverside. Similar dimnames function native R. details see help function ds.matrixDimnames","code":""},{"path":"/reference/matrixDimnamesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixDimnamesDS assign function called by ds.matrixDimnames — matrixDimnamesDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixInvertDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Inverts square matrix writes output serverside","code":""},{"path":"/reference/matrixInvertDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"","code":"matrixInvertDS(M1.name = NULL)"},{"path":"/reference/matrixInvertDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"M1.name character string specifying name matrix inverted","code":""},{"path":"/reference/matrixInvertDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Output matrix representing inverse written serverside. details see help ds.matrixInvert","code":""},{"path":"/reference/matrixInvertDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Undertakes standard matrix inversion. operation possible number columns rows matrix non-singular - positive definite (eg row column zeros)","code":""},{"path":"/reference/matrixInvertDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixInvertDS serverside assign function called by ds.matrixInvert — matrixInvertDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixMultDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Calculates matrix product two matrices writes output serverside","code":""},{"path":"/reference/matrixMultDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"","code":"matrixMultDS(M1.name = NULL, M2.name = NULL)"},{"path":"/reference/matrixMultDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"M1.name character string specifying name first matrix (M1) argument specified M1 argument original call ds.matrixMult M2.name character string specifying name second matrix (M2) argument specified M1 argument original call ds.matrixMult","code":""},{"path":"/reference/matrixMultDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Output matrix representing product M1 M2 written serverside. details see help ds.matrixMult","code":""},{"path":"/reference/matrixMultDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Undertakes standard matrix multiplication input matrices B dimensions : mxn B: nxp output C dimensions mxp element C[,j] value equal dot product row column j B dot product obtained sum([,1]*B[1,j] + [,2]*B[2,j] + .... + [,n]*B[n,j]). calculation valid number columns number rows B","code":""},{"path":"/reference/matrixMultDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixMultDS serverside assign function called by ds.matrixMult — matrixMultDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/matrixTransposeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Transposes matrix writes output serverside","code":""},{"path":"/reference/matrixTransposeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"","code":"matrixTransposeDS(M1.name = NULL)"},{"path":"/reference/matrixTransposeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"M1.name character string specifying name matrix transposed","code":""},{"path":"/reference/matrixTransposeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Output matrix representing transpose written serverside. details see help ds.matrixTranspose","code":""},{"path":"/reference/matrixTransposeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Undertakes standard matrix transposition. operation converts matrix matrix C element C[,j] matrix C equals element [j,] matrix . Matrix therefore number rows matrix C columns vice versa.","code":""},{"path":"/reference/matrixTransposeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"matrixTransposeDS serverside assign function called by ds.matrixTranspose — matrixTransposeDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/mdPatternDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Missing data pattern with disclosure control — mdPatternDS","title":"Missing data pattern with disclosure control — mdPatternDS","text":"function serverside aggregate function computes missing data pattern using mice::md.pattern applies disclosure control prevent revealing small cell counts.","code":""},{"path":"/reference/mdPatternDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Missing data pattern with disclosure control — mdPatternDS","text":"","code":"mdPatternDS(x)"},{"path":"/reference/mdPatternDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Missing data pattern with disclosure control — mdPatternDS","text":"x character string specifying name data frame matrix containing data analyze missing patterns.","code":""},{"path":"/reference/mdPatternDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Missing data pattern with disclosure control — mdPatternDS","text":"list containing: pattern missing data pattern matrix disclosure control applied valid Logical indicating patterns meet disclosure requirements message message describing validity status class class input object, client-side consistency checking","code":""},{"path":"/reference/mdPatternDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Missing data pattern with disclosure control — mdPatternDS","text":"function calls mice::md.pattern function generate matrix showing missing data patterns input data. ensure disclosure control, pattern counts threshold (nfilter.tab, default=3) suppressed. Suppression Method: pattern count threshold: - Row name changed \"suppressed()\" N threshold - pattern values row set NA - Summary row also set NA (prevents back-calculation) Output Matrix Structure: - Rows represent different missing data patterns (plus summary row bottom) - Row names contain pattern counts (\"suppressed()\" invalid patterns) - Columns show 1 variable observed, 0 missing - Last column shows total number missing values per pattern - Last row shows total number missing values per variable Note Pooling: function called ds.mdPattern type='combine', suppressed patterns excluded pooling prevent disclosure subtraction. means pooled counts may underestimate true total patterns suppressed studies.","code":""},{"path":"/reference/mdPatternDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Missing data pattern with disclosure control — mdPatternDS","text":"Xavier Escribà montagut DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/meanDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes statistical mean of a vector — meanDS","title":"Computes statistical mean of a vector — meanDS","text":"Calculates mean value.","code":""},{"path":"/reference/meanDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes statistical mean of a vector — meanDS","text":"","code":"meanDS(x)"},{"path":"/reference/meanDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes statistical mean of a vector — meanDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/meanDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes statistical mean of a vector — meanDS","text":"list, estimated mean, number missing values, number valid values, total number values, class, class input object client-side consistency checking","code":""},{"path":"/reference/meanDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes statistical mean of a vector — meanDS","text":"length input vector less set filter missing value returned.","code":""},{"path":"/reference/meanDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes statistical mean of a vector — meanDS","text":"Gaye , Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/meanSdGpDS.html","id":null,"dir":"Reference","previous_headings":"","what":"MeanSdGpDS — meanSdGpDS","title":"MeanSdGpDS — meanSdGpDS","text":"Server-side function called ds.meanSdGp","code":""},{"path":"/reference/meanSdGpDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MeanSdGpDS — meanSdGpDS","text":"","code":"meanSdGpDS(x, index)"},{"path":"/reference/meanSdGpDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MeanSdGpDS — meanSdGpDS","text":"x client-side supplied character string identifying variable means/SDs calculated index client-side supplied character string identifying factor across means/SDs calculated","code":""},{"path":"/reference/meanSdGpDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MeanSdGpDS — meanSdGpDS","text":"List results group statistics","code":""},{"path":"/reference/meanSdGpDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MeanSdGpDS — meanSdGpDS","text":"Computes mean standard deviation across groups defined one factor","code":""},{"path":"/reference/meanSdGpDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MeanSdGpDS — meanSdGpDS","text":"Burton PR Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/mergeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"mergeDS (assign function) called by ds.merge — mergeDS","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"merges (links) two data.frames together based common values defined vectors data.frame","code":""},{"path":"/reference/mergeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"","code":"mergeDS( x.name, y.name, by.x.names.transmit, by.y.names.transmit, all.x, all.y, sort, suffixes.transmit, no.dups, incomparables )"},{"path":"/reference/mergeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"x.name, name first data.frame merged specified inverted commas. Specified via argument ds.merge function y.name, name second data.frame merged specified inverted commas. Specified via argument ds.merge function .x.names.transmit name single variable vector names multiple variables (transmittable form) containing IDs data data.frame x merged/linked data.frame y. Specified via argument <.x.names> ds.merge function .y.names.transmit name single variable vector names multiple variables (transmittable form) containing IDs data data.frame y merged/linked data.frame x. Specified via argument <.y.names> ds.merge function .x logical, TRUE, extra rows added output, one row x matching row y. Specified via argument <.x> ds.merge function. Default = FALSE. .y logical, TRUE, extra rows added output, one row y matching row x. Specified via argument <.y> ds.merge function. Default = FALSE. sort logical, TRUE merged result sorted elements .x.names .y.names columns. Specified via argument ds.merge function. Default = TRUE. suffixes.transmit character vector length 2 (transmittable form) specifying suffixes used making unique common column names two input data.frames appear merged data.frame. Specified via argument ds.merge function. Default '.x' '.y'. .dups logical, TRUE suffixes appended cases rigorously avoid duplicated column names merged data.frame. Specified via argument <.dups> ds.merge function. Default TRUE apparently implicitly FALSE R version 3.5.0. incomparables, values intended merging one column matched. See 'match' help Native R merge function. Specified via argument ds.merge","code":""},{"path":"/reference/mergeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"merged data.frame specified argument ds.merge (default 'x.name_y.name' argument NULL) written serverside. addition, two validity messages returned clientside indicating whether created data source whether valid form. form valid least one study may studysideMessage can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message() print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message() return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/mergeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"information see details native R function merge DataSHIELD clientside function ds.merge.","code":""},{"path":"/reference/mergeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"mergeDS (assign function) called by ds.merge — mergeDS","text":"Paul Burton, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/metadataDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the metadata, if any, about the specified variable — metadataDS","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"function returns metadata, , specified variable.","code":""},{"path":"/reference/metadataDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"","code":"metadataDS(x)"},{"path":"/reference/metadataDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"x string character, containing name specified variable","code":""},{"path":"/reference/metadataDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"list containing metadata. elements list depend metadata available.","code":""},{"path":"/reference/metadataDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"function returns metadata, obtained attributes function.","code":""},{"path":"/reference/metadataDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Returns the metadata, if any, about the specified variable — metadataDS","text":"Stuart Wheater, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/miceDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Aggregate function called by ds.mice — miceDS","title":"Aggregate function called by ds.mice — miceDS","text":"function wrapper function mice mice R package. function creates multiple imputations (replacement values) multivariate missing data. method based Fully Conditional Specification, incomplete variable imputed separate model. MICE algorithm can impute mixes continuous, binary, unordered categorical ordered categorical data. addition, MICE can impute continuous two-level data, maintain consistency imputations means passive imputation.","code":""},{"path":"/reference/miceDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Aggregate function called by ds.mice — miceDS","text":"","code":"miceDS( data = data, m = m, maxit = maxit, method = method, post = post, seed = seed, predictorMatrix = predictorMatrix, ncol.pred.mat = ncol.pred.mat, newobj_mids = newobj_mids, newobj_df = newobj_df )"},{"path":"/reference/miceDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Aggregate function called by ds.mice — miceDS","text":"data data frame matrix containing incomplete data. m Number multiple imputations. default m=5. maximum allowed number DataSHIELD m=20. maxit scalar giving number iterations. default 5. maximum allowed number DataSHIELD maxit=30. method Can either single string, vector strings length ncol(data), specifying imputation method used column data. specified single string, method used blocks. default imputation method (argument specified) depends measurement level target column, regulated defaultMethod argument native R mice function. Columns need imputed empty method \"\". post vector strings length ncol(data) specifying expressions strings. string parsed executed within sampler() function post-process imputed values iterations. default vector empty strings, indicating post-processing. Multivariate (block) imputation methods ignore post parameter. seed either NA (default) \"fixed\". seed set \"fixed\" fixed seed random number generator study-specific used. predictorMatrix numeric matrix ncol(data) rows ncol(data) columns, containing 0/1 data specifying set predictors used target column. row corresponds variable imputed. value 1 means column variable used predictor target variables (rows). default, predictorMatrix square matrix ncol(data) rows columns 1's, except diagonal. ncol.pred.mat number columns predictorMatrix. newobj_mids character string provides name output mids object stored data servers. Default mids_object. newobj_df character string provides name output dataframes stored data servers. Default imputationSet. example, m=5, newobj_df=\"imputationSet\", five imputed dataframes saved servers names imputationSet.1, imputationSet.2, imputationSet.3, imputationSet.4, imputationSet.5.","code":""},{"path":"/reference/miceDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Aggregate function called by ds.mice — miceDS","text":"list three elements: method, predictorMatrix post. function also saves server mids object completed datasets dataframes.","code":""},{"path":"/reference/miceDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Aggregate function called by ds.mice — miceDS","text":"additional details see help header mice function native R mice package.","code":""},{"path":"/reference/miceDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Aggregate function called by ds.mice — miceDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/namesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the names of a list object — namesDS","title":"Return the names of a list object — namesDS","text":"Returns names designated server-side list","code":""},{"path":"/reference/namesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the names of a list object — namesDS","text":"","code":"namesDS(xname.transmit)"},{"path":"/reference/namesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the names of a list object — namesDS","text":"xname.transmit character string specifying name list.","code":""},{"path":"/reference/namesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the names of a list object — namesDS","text":"namesDS returns client-side names list object stored server-side.","code":""},{"path":"/reference/namesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Return the names of a list object — namesDS","text":"namesDS aggregate function called ds.names. function similar native R function names subsume functionality, example, works extract names already exist, create new names objects. function restricted objects type list, includes objects primary class list return TRUE native R function .list. example, includes multi-component object created fitting generalized linear model using ds.glmSLMA. resultant object saved separate server formally double class \"glm\" \"ls\" responds TRUE .list(),","code":""},{"path":"/reference/namesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Return the names of a list object — namesDS","text":"Amadou Gaye, updated Paul Burton 25/06/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/nsDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"function based native R function ns splines package. function generate B-spline basis matrix natural cubic spline.","code":""},{"path":"/reference/nsDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"","code":"nsDS(x, df, knots, intercept, Boundary.knots)"},{"path":"/reference/nsDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"x predictor variable. Missing values allowed. df degrees freedom. One can supply df rather knots; ns() chooses df - 1 - intercept knots suitably chosen quantiles x (ignore missing values). default, df = NULL, sets number inner knots length(knots). knots breakpoints define spline. default knots; together natural boundary conditions results basis linear regression x. Typical values mean median one knot, quantiles knots. See also Boundary.knots. intercept TRUE, intercept included basis; default FALSE. Boundary.knots boundary points impose natural boundary conditions anchor B-spline basis (default range data). knots Boundary.knots supplied, basis parameters depend x. Data can extend beyond Boundary.knots","code":""},{"path":"/reference/nsDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"matrix dimension length(x) * df either df supplied knots supplied, df = length(knots) + 1 + intercept. Attributes returned correspond arguments ns, explicitly give knots, Boundary.knots etc use predict.ns(). object assigned serverside.","code":""},{"path":"/reference/nsDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"ns native R based function splineDesign. generates basis matrix representing family piecewise-cubic splines specified sequence interior knots, natural boundary conditions. enforce constraint function linear beyond boundary knots, can either supplied default extremes data. primary use modeling formula directly specify natural spline term model.","code":""},{"path":"/reference/nsDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generate a Basis Matrix for Natural Cubic Splines — nsDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/numNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Counts the number of missing values — numNaDS","title":"Counts the number of missing values — numNaDS","text":"function just counts number missing entries vector.","code":""},{"path":"/reference/numNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Counts the number of missing values — numNaDS","text":"","code":"numNaDS(x)"},{"path":"/reference/numNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Counts the number of missing values — numNaDS","text":"x character string, name server-side vector","code":""},{"path":"/reference/numNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Counts the number of missing values — numNaDS","text":"list two elements: numNA (integer, number missing values) class (class input object, client-side consistency checking)","code":""},{"path":"/reference/numNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Counts the number of missing values — numNaDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/qlsplineDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"function based native R function qlspline lspline package. function computes basis piecewise-linear spline , depending argument marginal, coefficients can interpreted (1) slopes consecutive spline segments, (2) slope change consecutive knots.","code":""},{"path":"/reference/qlsplineDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"","code":"qlsplineDS(x = x, q = q, na.rm = TRUE, marginal = FALSE, names = NULL)"},{"path":"/reference/qlsplineDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"x name input numeric variable q numeric, single scalar greater equal 2 number equal-frequency intervals along x vector numbers (0; 1) specifying quantiles explicitly. na.rm logical, whether NA removed calculating quantiles, passed na.rm quantile. Default set TRUE. marginal logical, parametrize spline, see Details names character, vector names constructed variables","code":""},{"path":"/reference/qlsplineDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"object class \"lspline\" \"matrix\", name specified newobj argument (default name \"qlspline.newobj\"), assigned serverside.","code":""},{"path":"/reference/qlsplineDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"marginal FALSE (default) coefficients spline correspond slopes consecutive segments. TRUE first coefficient correspond slope first segment. consecutive coefficients correspond change slope compared previous segment. Function qlspline wraps lspline calculates knot positions quantiles x. q numerical scalar greater equal 2, quantiles computed seq(0, 1, length.= q + 1)[-c(1, q+1)], .e. knots q-tiles distribution x. Alternatively, q can vector values [0; 1] specifying quantile probabilities directly (vector passed argument probs quantile).","code":""},{"path":"/reference/qlsplineDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Basis for a piecewise linear spline with meaningful coefficients — qlsplineDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/quantileMeanDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"probabilities 5 used compute corresponding quantiles.","code":""},{"path":"/reference/quantileMeanDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"","code":"quantileMeanDS(x)"},{"path":"/reference/quantileMeanDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/quantileMeanDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"list, quantiles, numeric vector represents sample quantiles, class, class input object client-side consistency checking","code":""},{"path":"/reference/quantileMeanDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Generates quantiles and mean information without maximum and minimum — quantileMeanDS","text":"Burton, P.; Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rBinomDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rBinomDS serverside assign function — rBinomDS","title":"rBinomDS serverside assign function — rBinomDS","text":"primary serverside assign function called ds.rBinom","code":""},{"path":"/reference/rBinomDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rBinomDS serverside assign function — rBinomDS","text":"","code":"rBinomDS(n, size = 1, prob = 0.5)"},{"path":"/reference/rBinomDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rBinomDS serverside assign function — rBinomDS","text":"n length pseudorandom number vector generated specified argument function ds.rBinom size scalar must positive integer. Value set directly argument ds.rBinom - details see help ds.rBinom. May scalar vector allowing size vary observation observation. prob numeric scalar range 0 > prob > 1 specifies probability positive response. Value set directly argument ds.rBinom - details see help ds.rBinom May scalar vector allowing size vary observation observation.","code":""},{"path":"/reference/rBinomDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rBinomDS serverside assign function — rBinomDS","text":"vector pseudorandom numbers binomial distribution, written serverside object named argument ds.rBinom.","code":""},{"path":"/reference/rBinomDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rBinomDS serverside assign function — rBinomDS","text":"Generates vector pseudorandom numbers binomial distribution data source specified arguments ds.rBinom. serverside function effectively function rbinom() native R arguments .","code":""},{"path":"/reference/rBinomDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rBinomDS serverside assign function — rBinomDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rNormDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rNormDS serverside assign function — rNormDS","title":"rNormDS serverside assign function — rNormDS","text":"primary serverside assign function called ds.rNorm","code":""},{"path":"/reference/rNormDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rNormDS serverside assign function — rNormDS","text":"","code":"rNormDS(n, mean = 0, sd = 1, force.output.to.k.decimal.places = 9)"},{"path":"/reference/rNormDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rNormDS serverside assign function — rNormDS","text":"n length pseudorandom number vector generated specified argument function ds.rNorm mean specifies mean pseudorandom number vector generated specified argument function ds.rNorm. May scalar vector allowing mean vary observation observation. sd specifies standard deviation pseudorandom number vector generated specified argument function ds.rNorm May scalar vector allowing sd vary observation observation. force.output..k.decimal.places scalar integer. Forces output random number vector k decimal places. 0 rounds coerces decimal random number output integer, k range 1-8 forces output k decimal places. k = 9, rounding occurs native output. Default=9. Value specified argument ds.rNorm","code":""},{"path":"/reference/rNormDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rNormDS serverside assign function — rNormDS","text":"numeric vector pseudorandom numbers normal distribution, rounded decimal places less 9, written serverside object named argument ds.rNorm.","code":""},{"path":"/reference/rNormDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rNormDS serverside assign function — rNormDS","text":"Generates vector pseudorandom numbers normal distribution data source specified arguments ds.rNorm. serverside function effectively function rnorm() native R arguments .","code":""},{"path":"/reference/rNormDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rNormDS serverside assign function — rNormDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rPoisDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rPoisDS serverside assign function — rPoisDS","title":"rPoisDS serverside assign function — rPoisDS","text":"primary serverside assign function called ds.rPois","code":""},{"path":"/reference/rPoisDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rPoisDS serverside assign function — rPoisDS","text":"","code":"rPoisDS(n, lambda = 1)"},{"path":"/reference/rPoisDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rPoisDS serverside assign function — rPoisDS","text":"n length pseudorandom number vector generated specified argument function ds.rPois lambda numeric scalar specifying expected count Poisson distribution used generate random counts. Specified directly lambda argument ds.rPois. May scalar vector allowing lambda vary observation observation.","code":""},{"path":"/reference/rPoisDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rPoisDS serverside assign function — rPoisDS","text":"vector pseudorandom non-negative integers Poisson distribution, written serverside object named argument ds.rPois.","code":""},{"path":"/reference/rPoisDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rPoisDS serverside assign function — rPoisDS","text":"Generates vector pseudorandom numbers (non-negative integers) Poisson distribution data source specified arguments ds.rPois. serverside function effectively function rpois() native R arguments .","code":""},{"path":"/reference/rPoisDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rPoisDS serverside assign function — rPoisDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rUnifDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rUnifDS serverside assign function — rUnifDS","title":"rUnifDS serverside assign function — rUnifDS","text":"primary serverside assign function called ds.rUnif","code":""},{"path":"/reference/rUnifDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rUnifDS serverside assign function — rUnifDS","text":"","code":"rUnifDS(n, min = 0, max = 1, force.output.to.k.decimal.places = 9)"},{"path":"/reference/rUnifDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rUnifDS serverside assign function — rUnifDS","text":"n length pseudorandom number vector generated specified argument function ds.rUnif min numeric scalar specifying minimum range across random numbers generated source. Specified directly min argument ds.rUnif. May scalar vector allowing min vary observation observation. max numeric scalar specifying maximum range across random numbers generated source. Specified directly max argument ds.rUnif. May scalar vector allowing min vary observation observation. force.output..k.decimal.places scalar integer. Forces output random number vector k decimal places. 0 rounds coerces decimal random number output integer, k range 1-8 forces output k decimal places. k = 9, rounding occurs native output. Default=9. Value specified argument ds.rUnif","code":""},{"path":"/reference/rUnifDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rUnifDS serverside assign function — rUnifDS","text":"numeric vector pseudorandom numbers uniform distribution, rounded decimal places less 9, written serverside object named argument ds.rUnif.","code":""},{"path":"/reference/rUnifDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rUnifDS serverside assign function — rUnifDS","text":"Generates vector pseudorandom numbers uniform distribution data source specified arguments ds.rUnif. serverside function effectively function runif() native R arguments .","code":""},{"path":"/reference/rUnifDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rUnifDS serverside assign function — rUnifDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rangeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"returns the minimum and maximum of a numeric vector — rangeDS","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"function similar R function range instead return real minimum maximum, computed values multiplied small random number.","code":""},{"path":"/reference/rangeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"","code":"rangeDS(x)"},{"path":"/reference/rangeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/rangeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"numeric vector contains minimum maximum values vector","code":""},{"path":"/reference/rangeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"returns the minimum and maximum of a numeric vector — rangeDS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rbindDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rbindDS called by ds.rbind — rbindDS","title":"rbindDS called by ds.rbind — rbindDS","text":"serverside assign function takes sequence vector, matrix data-frame arguments combines row produce matrix.","code":""},{"path":"/reference/rbindDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rbindDS called by ds.rbind — rbindDS","text":"","code":"rbindDS(x.names.transmit = NULL, colnames.transmit = NULL)"},{"path":"/reference/rbindDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rbindDS called by ds.rbind — rbindDS","text":"x.names.transmit vector character strings representing names elemental components combined converted transmittable format. argument fully specified argument ds.rbind colnames.transmit NULL vector character strings representing forced column names output object converted transmittable format. argument fully specified argument ds.cbind.","code":""},{"path":"/reference/rbindDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rbindDS called by ds.rbind — rbindDS","text":"object specified argument ds.rbind(default name ) written serverside. well writing output object serverside, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.cbind() also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/rbindDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rbindDS called by ds.rbind — rbindDS","text":"sequence vector, matrix data-frame arguments combined row row produce matrix written serverside. details see help ds.rbind native R function rbind.","code":""},{"path":"/reference/rbindDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rbindDS called by ds.rbind — rbindDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/reShapeDS.html","id":null,"dir":"Reference","previous_headings":"","what":"reShapeDS (assign function) called by ds.reShape — reShapeDS","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"Reshapes data frame containing longitudinal otherwise grouped data 'wide' 'long' format vice-versa","code":""},{"path":"/reference/reShapeDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"","code":"reShapeDS( data.name, varying.transmit, v.names.transmit, timevar.name, idvar.name, drop.transmit, direction, sep )"},{"path":"/reference/reShapeDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"data.name, name data.frame reshaped. Specified via argument ds.reShape function varying.transmit, names sets variables wide format correspond single variables long format (typically may called 'time-varying' 'time-dependent' variables). Specified via argument ds.reShape function. v.names.transmit, names variables long format correspond multiple variables wide format - example, sbp7, sbp11, sbp15 (measured systolic blood pressure ages 7, 11 15 years). Specified via argument ds.reShape function timevar.name, variable long format differentiates multiple records group individual. Specified via argument ds.reShape function idvar.name, names one variables long format identify multiple records group/individual. /variable(s) may also present wide format. Specified via argument ds.reShape function drop.transmit, vector names variables drop reshaping. Specified via argument ds.reShape function direction, character string, partially matched either \"wide\" reshape long wide format, \"long\" reshape wide long format. Specified via argument ds.reShape function sep, character vector length 1, indicating separating character variable names wide format. Specified via argument ds.reShape function","code":""},{"path":"/reference/reShapeDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"reshaped data.frame converted long wide format wide long format written serverside given name provided argument ds.reShape 'newObject' name specified.","code":""},{"path":"/reference/reShapeDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"function based native R function reshape. reshapes data frame containing longitudinal otherwise grouped data 'wide' format repeated measurements separate columns record 'long' format repeated measurements separate records. reshaping can either direction","code":""},{"path":"/reference/reShapeDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"reShapeDS (assign function) called by ds.reShape — reShapeDS","text":"Demetris Avraam, Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/recodeValuesDS.html","id":null,"dir":"Reference","previous_headings":"","what":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"function recodes specified values elements vector matched set alternative specified values.","code":""},{"path":"/reference/recodeValuesDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"","code":"recodeValuesDS( var.name.text = NULL, values2replace.text = NULL, new.values.text = NULL, missing = NULL )"},{"path":"/reference/recodeValuesDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"var.name.text character string providing name vector representing variable recoded. argument generated passed directly recodeValuesDS ds.recodeValues values2replace.text character string specifying values vector specified argument replaced new values specified new.values.vector. argument generated passed directly recodeValuesDS ds.recodeValues. effect, argument ds.recodeValues function converted character string format acceptable DataSHIELD R parser data repository can accepted recodeValuesDS new.values.text character string specifying new values specified values vector converted. argument generated passed directly recodeValuesDS ds.recodeValues. effect, argument ds.recodeValues function converted character string format acceptable DataSHIELD R parser data repository can used call recodeValuesDS. missing supplied, missing values variable referred var.name.text replaced value.","code":""},{"path":"/reference/recodeValuesDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"object specified argument (default name '_recoded') initially specified calling ds.recodeValues. output object (required recoded variable called written serverside.","code":""},{"path":"/reference/recodeValuesDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"details see help header ds.recodeValues","code":""},{"path":"/reference/recodeValuesDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"recodeValuesDS an assign function called by ds.recodeValues — recodeValuesDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/repDS.html","id":null,"dir":"Reference","previous_headings":"","what":"repDS called by ds.rep — repDS","title":"repDS called by ds.rep — repDS","text":"assign function creates repetitive sequence repeating identified scalar, specified elements vector list. analogous rep function native R. sequence written new object serverside","code":""},{"path":"/reference/repDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"repDS called by ds.rep — repDS","text":"","code":"repDS( x1.transmit, times.transmit, length.out.transmit, each.transmit, x1.includes.characters, source.x1, source.times, source.length.out, source.each )"},{"path":"/reference/repDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"repDS called by ds.rep — repDS","text":"x1.transmit argument determines input scalar, vector list. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. times.transmit argument determines number replications pattern replications input scalar/vector construct output repetitive sequence. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. length..transmit argument fixes length output repetitive sequence vector behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. .transmit argument specifies number replications individual elements rather replications full sequence. behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument <> call ds.rep calls repDS. x1.includes.characters Boolean parameter determining whether coerce final output sequence numeric. Defaults FALSE output coerced numeric. detailed behaviour see help ds.rep. parameter usually fully defined argument call ds.rep calls repDS. source.x1 defines source scalar vector defined argument. Four character strings allowed: \"clientside\" \"c\" serverside \"s\". behaviour see help ds.rep \"details native R help \" (see ). parameter usually fully defined argument call ds.rep calls repDS. source.times see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS. source.length.see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS. source.see \"param source.x1\" parameter usually fully defined argument call ds.rep calls repDS.","code":""},{"path":"/reference/repDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"repDS called by ds.rep — repDS","text":"vector containing specified repetitive sequence write output object defined argument (default name seq.vect) written serverside source. addition, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.matrixDiag also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"newobj\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"newobj\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/repDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"repDS called by ds.rep — repDS","text":"details can found help details ds.rep following aspects help function rep native R also apply (explained detail exceptions identified help ds.rep): addition Details R help : default behaviour call rep(x, times = 1, length.= NA, = 1) Normally just one additional arguments specified, '' specified either two, replication performed first, followed replication implied times length.. times consists single integer, result consists whole input repeated many times. times vector length x (replication ), result consists x[1] repeated times[1] times, x[2] repeated times[2] times . ***Note exception 1 . length.may given place times, case x repeated many times necessary create vector length. given, length.takes priority times ignored. ***Note exception 3 . Non-integer values times truncated towards zero. times computed quantity prudent add small fuzz use round. analogously .","code":""},{"path":"/reference/repDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"repDS called by ds.rep — repDS","text":"Paul Burton DataSHIELD Development Team, 14/10/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/replaceNaDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Replaces the missing values in a vector — replaceNaDS","title":"Replaces the missing values in a vector — replaceNaDS","text":"function identifies missing values replaces value values specified analyst.","code":""},{"path":"/reference/replaceNaDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replaces the missing values in a vector — replaceNaDS","text":"","code":"replaceNaDS(x, replacements)"},{"path":"/reference/replaceNaDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replaces the missing values in a vector — replaceNaDS","text":"x character, name vector process. replacements vector contains replacement value(s), vector one values study.","code":""},{"path":"/reference/replaceNaDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replaces the missing values in a vector — replaceNaDS","text":"new vector without missing values","code":""},{"path":"/reference/replaceNaDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Replaces the missing values in a vector — replaceNaDS","text":"function used analyst prefer requires complete vectors. possible specify one value missing value first returning number missing values using function numNaDS cases might sensible replace missing values one specific value e.g. replace missing values vector mean median value. missing values replaced new vector created.","code":""},{"path":"/reference/replaceNaDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Replaces the missing values in a vector — replaceNaDS","text":"Amadou Gaye, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/rmDS.html","id":null,"dir":"Reference","previous_headings":"","what":"rmDS an aggregate function called by ds.rm — rmDS","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"deletes R object serverside","code":""},{"path":"/reference/rmDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"","code":"rmDS(x.names.transmit)"},{"path":"/reference/rmDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"x.names.transmit, names objects deleted converted transmissible form, comma separated list character string. argument specified via argument ds.rm","code":""},{"path":"/reference/rmDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"specified object deleted serverside. successful message \"Object successfully deleted\" returned clientside (x.names names object deleted). objects deleted already absent given source, source return message: \"Object deleted, .e. , exist need deleting\".","code":""},{"path":"/reference/rmDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"serverside function based rm() function native R. aggregate function may surprising modifies object serverside, therefore expected assign function. However, assign function last step running write modified object newobj. fail effect function delete object impossible write anywhere.","code":""},{"path":"/reference/rmDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rmDS an aggregate function called by ds.rm — rmDS","text":"Paul Burton DataSHIELD Development Team","code":""},{"path":"/reference/rowColCalcDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"function similar R base functions 'rowSums', 'colSums', 'rowMeans' 'colMeans'.","code":""},{"path":"/reference/rowColCalcDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"","code":"rowColCalcDS(dataset.name, operation)"},{"path":"/reference/rowColCalcDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"dataset.name character string providing name server-side array two dimensions. operation integer indicates operation carry : 1 'rowSums', 2 'colSums', 3 'rowMeans' 4 'colMeans'","code":""},{"path":"/reference/rowColCalcDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"numeric vector","code":""},{"path":"/reference/rowColCalcDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"output returned user number entries output vector greater equal allowed size.","code":""},{"path":"/reference/rowColCalcDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes sums and means of rows or columns of numeric arrays — rowColCalcDS","text":"Gaye, . Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/sampleDS.html","id":null,"dir":"Reference","previous_headings":"","what":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"draws pseudorandom sample vector, dataframe matrix serverside - special case - randomly permutes vector, dataframe matrix.","code":""},{"path":"/reference/sampleDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"","code":"sampleDS( x.transmit, size.transmit, replace.transmit = NULL, prob.transmit = NULL )"},{"path":"/reference/sampleDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"x.transmit Either character string providing name serverside vector, matrix data.frame sampled permuted, integer/numeric scalar (e.g. 923) indicating one create new vector serverside randomly permuted sample vector 1:923. x.transmit fully specified [x] argument ds.sample. details see help ds.sample native R help sample(). size.transmit numeric/integer scalar indicating size sample drawn. size.transmit fully specified [size] argument ds.sample. details see help ds.sample native R help sample(). replace.transmit Boolean indicator (TRUE FALSE) specifying whether sample drawn without replacement. Default FALSE sample drawn without replacement. replace.transmit fully specified [replace] argument ds.sample. details see help ds.sample native R help sample(). prob.transmit character string containing name numeric vector probability weights serverside associated elements vector sampled enabling drawing sample elements given higher probability drawn others. prob.transmit fully specified [prob] argument ds.sample. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"object specified argument (default name 'newobj.sample') written serverside. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"Serverside assign function sampleDS called clientside function ds.sample. Based native R function sample() deals slightly differently data.frames matrices. details see help ds.sample native R help sample().","code":""},{"path":"/reference/sampleDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"random sampling and permuting of vectors, dataframes and matrices — sampleDS","text":"Paul Burton, DataSHIELD Development Team, 15/4/2020 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/scatterPlotDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the coordinates of the data to be plot — scatterPlotDS","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"function uses two disclosure control methods generate non-disclosive coordinates returned client generates non-disclosive scatter plots.","code":""},{"path":"/reference/scatterPlotDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"","code":"scatterPlotDS(x.name, y.name, method.indicator, k, noise)"},{"path":"/reference/scatterPlotDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"x.name character string providing name server-side numeric vector, x-variable. y.name character string providing name server-side numeric vector, y-variable. method.indicator integer either 1 2. user selects deterministic method client side function method.indicator set 1 user selects probabilistic method argument set 2. k number nearest neighbours centroid calculated deterministic method selected. noise percentage initial variance used variance embedded noise probabilistic method selected.","code":""},{"path":"/reference/scatterPlotDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"list x y coordinates data plot, along classes x y inputs (class.x class.y)","code":""},{"path":"/reference/scatterPlotDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"user chooses deterministic approach, function finds k-1 nearest neighbours data point 2-dimensional space. nearest neighbours data points minimum Euclidean distances point interest. point interest k-1 nearest neighbours used calculation coordinates centroid k points. Centroid referred centre mass, .e. x-coordinate centroid average value x-coordinates k nearest neighbours y-coordinate centroid average y-coordinates k nearest neighbours. user chooses probabilistic approach, function adds random noise $x$ $y$ separately. random noise follows normal distribution zero mean variance equal 10 disclosure fix random number generator value specified input variables. Thus function returns always noisy data given pair variables.","code":""},{"path":"/reference/scatterPlotDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the coordinates of the data to be plot — scatterPlotDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/seqDS.html","id":null,"dir":"Reference","previous_headings":"","what":"seqDS a serverside assign function called by ds.seq — seqDS","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"assign function seqDS called ds.seq","code":""},{"path":"/reference/seqDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"","code":"seqDS( FROM.value.char, TO.value.char, BY.value.char, LENGTH.OUT.value.char, ALONG.WITH.name )"},{"path":"/reference/seqDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":".value.char starting value sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. .value.char terminal value sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. .value.char value increment step sequence expressed integer real number decimal point character form. Fully specified <.value.char> argument ds.seq. LENGTH..value.char length sequence point extension stopped, expressed integer real number decimal point character form. Fully specified argument ds.seq. ALONG..name convenience, rather specifying value LENGTH.can often better specify variable name argument. Fully specified argument ds.seq.","code":""},{"path":"/reference/seqDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"object specified argument ds.seq (default name newObj) written serverside. well writing output object serverside, two validity messages returned indicating whether created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.seq() also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating studysideMessage saved. error created without problems studysideMessage saved ds.message(\"\") return message: \"OK: studysideMessage(s) datasource\".","code":""},{"path":"/reference/seqDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"assign function uses native R function seq() create one flexible range sequence vectors can used help manage analyse data. assign function resultant vector written new object specified data source servers. Please see \"details\" ds.seq information allowable combinations arguments etc.","code":""},{"path":"/reference/seqDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"seqDS a serverside assign function called by ds.seq — seqDS","text":"Paul Burton DataSHIELD Development Team, 17/9/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/setSeedDS.html","id":null,"dir":"Reference","previous_headings":"","what":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"aggregate serverside function primes pseudorandom number generator data source","code":""},{"path":"/reference/setSeedDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"","code":"setSeedDS(seedtext = NULL, kind = NULL, normal.kind = NULL)"},{"path":"/reference/setSeedDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"seedtext simply value argument ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois ds.rBinom coerced character format. done clientside functions require DataSHIELD user anything. Please see help clientside functions, particular, information argument details. kind see help set.seed() function native R normal.kind see help set.seed() function native R","code":""},{"path":"/reference/setSeedDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"Sets values vector integers length 626 known .Random.seed data source true current state random seed source.","code":""},{"path":"/reference/setSeedDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"setSeedDS effectively equivalent native R function set.seed() help function can provide many additional details. minor difference first argument setSeedDS, takes integer priming seed character format. However, user integer still specified directly integer argument one clientside functions ds.setSeed, ds.rNorm ..... clientside functions coerces integer character format calls setSeedDS first active line code setSeedDS converts character string back integer treats first argument native R function set.seed(). two arguments set.seed() native R, defaulted specifying NULL. defaulting hard wired setSeedDS function changed analyst means setSeedDS much less flexible native R's set.seed() function. DataSHIELD user requires aspect flexibility returned development team can approached, unless actually theoretical work random number generators likely ","code":""},{"path":"/reference/setSeedDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom — setSeedDS","text":"Paul Burton DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/skewness1DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the skewness of a numeric variable — skewness1DS","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"function calculates skewness numeric variable study separately.","code":""},{"path":"/reference/skewness1DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"","code":"skewness1DS(x, method)"},{"path":"/reference/skewness1DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"x string character, name numeric variable. method integer 1 3 selecting one algorithms computing skewness detailed headers client-side ds.skewness function.","code":""},{"path":"/reference/skewness1DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"list including skewness input numeric variable, number valid observations class, class input object client-side consistency checking.","code":""},{"path":"/reference/skewness1DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"function calculates skewness input variable x three different methods. method specified argument method client-side ds.skewness function.","code":""},{"path":"/reference/skewness1DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the skewness of a numeric variable — skewness1DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/skewness2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the skewness of a numeric variable — skewness2DS","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"function calculates summary statistics returned client-side used estimation combined skewness numeric variable across studies.","code":""},{"path":"/reference/skewness2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"","code":"skewness2DS(x, global.mean)"},{"path":"/reference/skewness2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"x string character, name numeric variable. global.mean numeric, combined mean input variable across studies.","code":""},{"path":"/reference/skewness2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"list including sum cubed differences values x global mean x across studies, sum squared differences values x global mean x across studies, number valid observations (.e. length x excluding missing values), class, class input object client-side consistency checking.","code":""},{"path":"/reference/skewness2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"function calculates sum squared differences values x global mean x across studies, sum cubed differences values x global mean x across studies number valid observations input variable x.","code":""},{"path":"/reference/skewness2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the skewness of a numeric variable — skewness2DS","text":"Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/sqrtDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the square root values of the input variable — sqrtDS","title":"Computes the square root values of the input variable — sqrtDS","text":"function similar R function sqrt.","code":""},{"path":"/reference/sqrtDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the square root values of the input variable — sqrtDS","text":"","code":"sqrtDS(x)"},{"path":"/reference/sqrtDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the square root values of the input variable — sqrtDS","text":"x string character, name numeric integer vector","code":""},{"path":"/reference/sqrtDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the square root values of the input variable — sqrtDS","text":"object specified newobj argument ds.sqrt (default name sqrt.newobj) written server-side. output object class numeric integer.","code":""},{"path":"/reference/sqrtDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the square root values of the input variable — sqrtDS","text":"function computes square root values input numeric integer vector.","code":""},{"path":"/reference/sqrtDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the square root values of the input variable — sqrtDS","text":"Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/table1DDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates 1-dimensional contingency tables — table1DDS","title":"Creates 1-dimensional contingency tables — table1DDS","text":"function generates 1-dimensional table potentially disclosive cells. (based set threshold) replaced missing value ('NA').","code":""},{"path":"/reference/table1DDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates 1-dimensional contingency tables — table1DDS","text":"","code":"table1DDS(xvect)"},{"path":"/reference/table1DDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates 1-dimensional contingency tables — table1DDS","text":"xvect numerical vector discrete values - usually factor.","code":""},{"path":"/reference/table1DDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates 1-dimensional contingency tables — table1DDS","text":"list contains two elements: 'table', 1-dimensional table 'message' message informs validity table.","code":""},{"path":"/reference/table1DDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates 1-dimensional contingency tables — table1DDS","text":"generates 1-dimensional tables valid (non-disclosive) 1-dimensional tables defined data sources table cells counts 1 set threshold. output table invalid cells total count replaced missing values. total count visible table returned client side. message also returned 1-dimensional; message says \"invalid table - invalid counts present\" table invalid 'valid table' otherwise.","code":""},{"path":"/reference/table1DDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Creates 1-dimensional contingency tables — table1DDS","text":"Gaye .","code":""},{"path":"/reference/table2DS.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"Helps creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/table2DS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"","code":"table2DS(newobj, rvar.transmit, cvar.transmit, stvar.transmit)"},{"path":"/reference/table2DS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"newobj character string providing name output table object written serverside TRUE. explicit name table object specified, nevertheless TRUE, name serverside table object defaults 'newObj'. Fully specified argument ds.table. information see help ds.table rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table","code":""},{"path":"/reference/table2DS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"information see help ds.table","code":""},{"path":"/reference/table2DS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":" argument ds.table set TRUE, aggregate function returns non-disclosive information table object written serverside tableDS.assign. information see help ds.table, tableDS.assign tableDS DataSHIELD table function native R.","code":""},{"path":"/reference/table2DS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS is the second of two serverside aggregate functions called by ds.table — table2DS","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tableDS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"helps creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/tableDS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"","code":"tableDS.assign( rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, cvar.all.unique.levels.transmit, stvar.all.unique.levels.transmit, exclude.transmit, useNA.transmit )"},{"path":"/reference/tableDS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table rvar..unique.levels.transmit character string containing unique level rvar, across studies, separated ','. cvar..unique.levels.transmit character string containing unique level cvar, across studies, separated ','. stvar..unique.levels.transmit character string containing unique level stvar, across studies, separated ','. exclude.transmit information see help argument ds.table. Fully specified argument ds.table useNA.transmit information see help argument ds.table. Fully specified argument ds.table","code":""},{"path":"/reference/tableDS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"information see help ds.table","code":""},{"path":"/reference/tableDS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":" argument ds.table set TRUE, assign function writes table requested format specified ds.table function object named argument ds.table. information see help ds.table DataSHIELD table function native R.","code":""},{"path":"/reference/tableDS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS.assign is the serverside assign function called by ds.table — tableDS.assign","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tableDS.html","id":null,"dir":"Reference","previous_headings":"","what":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"creates 1-dimensional, 2-dimensional 3-dimensional tables using table function native R.","code":""},{"path":"/reference/tableDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"","code":"tableDS( rvar.transmit, cvar.transmit, stvar.transmit, rvar.all.unique.levels.transmit, cvar.all.unique.levels.transmit, stvar.all.unique.levels.transmit, exclude.transmit, useNA.transmit, force.nfilter.transmit )"},{"path":"/reference/tableDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"rvar.transmit character string (inverted commas) specifying name variable defining rows 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table cvar.transmit character string specifying name variable defining columns 2 dimensional tables form output. Fully specified argument ds.table. information see help ds.table stvar.transmit character string specifying name variable indexes separate two dimensional tables output call specifies 3 dimensional table. Fully specified argument ds.table. information see help ds.table rvar..unique.levels.transmit character string containing unique level rvar, across studies, separated ','. cvar..unique.levels.transmit character string containing unique level cvar, across studies, separated ','. stvar..unique.levels.transmit character string containing unique level stvar, across studies, separated ','. exclude.transmit information see help argument ds.table. Fully specified argument ds.table useNA.transmit information see help argument ds.table. Fully specified argument ds.table force.nfilter.transmit information see help argument ds.table. Fully specified argument ds.table","code":""},{"path":"/reference/tableDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"information see help ds.table","code":""},{"path":"/reference/tableDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"serverside function workhorse ds.table - creating table requested format specified ds.table. information see help ds.table DataSHIELD table function native R.","code":""},{"path":"/reference/tableDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tableDS is the first of two serverside aggregate functions called by ds.table — tableDS","text":"Paul Burton DataSHIELD Development Team, 13/11/2019 Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tapplyDS.assign.html","id":null,"dir":"Reference","previous_headings":"","what":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"Apply one selected range functions summarize outcome variable one indexing factors write resultant summary newobj serverside","code":""},{"path":"/reference/tapplyDS.assign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"","code":"tapplyDS.assign(X.name, INDEX.names.transmit, FUN.name)"},{"path":"/reference/tapplyDS.assign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"X.name, name variable summarized. Specified via argument ds.tapply.assign function INDEX.names.transmit, name single factor vector names factors index variable summarized. Specified via argument ds.tapply.assign function FUN.name, name one allowable summarizing functions applied. Specified via argument ds.tapply.assign function.","code":""},{"path":"/reference/tapplyDS.assign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"array summarized values created tapplyDS.assign function. array written newobj serverside. number dimensions INDEX.","code":""},{"path":"/reference/tapplyDS.assign.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"see details ds.tapply.assign function","code":""},{"path":"/reference/tapplyDS.assign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tapplyDS.assign called by ds.tapply.assign — tapplyDS.assign","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/tapplyDS.html","id":null,"dir":"Reference","previous_headings":"","what":"tapplyDS called by ds.tapply — tapplyDS","title":"tapplyDS called by ds.tapply — tapplyDS","text":"Apply one selected range functions summarize outcome variable one indexing factors write resultant summary clientside","code":""},{"path":"/reference/tapplyDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tapplyDS called by ds.tapply — tapplyDS","text":"","code":"tapplyDS(X.name, INDEX.names.transmit, FUN.name)"},{"path":"/reference/tapplyDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tapplyDS called by ds.tapply — tapplyDS","text":"X.name, name variable summarized. Specified via argument ds.tapply function INDEX.names.transmit, name single factor vector names factors index variable summarized. Specified via argument ds.tapply function FUN.name, name one allowable summarizing functions applied. Specified via argument ds.tapply function.","code":""},{"path":"/reference/tapplyDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tapplyDS called by ds.tapply — tapplyDS","text":"array summarized values created tapplyDS function. array returned clientside. number dimensions INDEX.","code":""},{"path":"/reference/tapplyDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"tapplyDS called by ds.tapply — tapplyDS","text":"see details ds.tapply function","code":""},{"path":"/reference/tapplyDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tapplyDS called by ds.tapply — tapplyDS","text":"Paul Burton, Demetris Avraam DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/unListDS.html","id":null,"dir":"Reference","previous_headings":"","what":"unListDS a serverside assign function called by ds.unList — unListDS","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"function based native R function unlist coerces object list class back class coerced list","code":""},{"path":"/reference/unListDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"","code":"unListDS(x.name)"},{"path":"/reference/unListDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"x.name name input object unlisted. must specified inverted commas e.g. x.name=\"input.object.name\". Fully specified x.name argument ds.unList","code":""},{"path":"/reference/unListDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"object specified newobj argument ds.unList function (default \"unlist.newobj\" newobj argument NULL). written serverside. well writing output object newobj serverside, two validity messages returned indicating whether newobj created data source whether valid form. form valid least one study - e.g. disclosure trap tripped creation full output object blocked - ds.seq also returns studysideMessages can explain error creating full output object. well appearing screen run time,wish see relevant studysideMessages later date can use ds.message function. type ds.message(\"\") print relevant studysideMessage datasource error creating newobj studysideMessage saved. outcome object ds.unList typically list object names, errors creating message returned ds.message(\"\") study read \"Outcome object list without names. studysideMessage may hidden. Please check output OK\". suggests - case specific function - one check far one can nature output call ds.unList - e.g. ds.class, ds.length etc","code":""},{"path":"/reference/unListDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"See details native R function unlist. function represents substantive restructuring earlier version created Amadou Gaye. details working please see 'details' help ds.unList.","code":""},{"path":"/reference/unListDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"unListDS a serverside assign function called by ds.unList — unListDS","text":"Amadou Gaye (2016), Paul Burton (19/09/2019) DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/uniqueDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Applies the unique method to a server-side variable. — uniqueDS","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"function similar R function unique.","code":""},{"path":"/reference/uniqueDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"","code":"uniqueDS(x.name.transmit = NULL)"},{"path":"/reference/uniqueDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"x.name.transmit name variable upon unique method applied","code":""},{"path":"/reference/uniqueDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"object specified newobj argument written server-side.","code":""},{"path":"/reference/uniqueDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"function computes uniques values variable.","code":""},{"path":"/reference/uniqueDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Applies the unique method to a server-side variable. — uniqueDS","text":"Stuart Wheater DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/varDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the variance of vector — varDS","title":"Computes the variance of vector — varDS","text":"Calculates variance.","code":""},{"path":"/reference/varDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the variance of vector — varDS","text":"","code":"varDS(x)"},{"path":"/reference/varDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the variance of vector — varDS","text":"x character string, name numeric integer vector","code":""},{"path":"/reference/varDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the variance of vector — varDS","text":"list, sum input variable, sum squares input variable, number missing values, number valid values, number total length variable, class, class input object client-side consistency checking","code":""},{"path":"/reference/varDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the variance of vector — varDS","text":"length input vector less set filter missing value returned.","code":""},{"path":"/reference/varDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the variance of vector — varDS","text":"Amadou Gaye, Demetris Avraam, DataSHIELD Development Team Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands","code":""},{"path":"/reference/vectorDS.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates a vector on the server-side. — vectorDS","title":"Creates a vector on the server-side. — vectorDS","text":"function similar R function c.","code":""},{"path":"/reference/vectorDS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates a vector on the server-side. — vectorDS","text":"","code":"vectorDS(...)"},{"path":"/reference/vectorDS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates a vector on the server-side. — vectorDS","text":"... parameter used form vector.","code":""},{"path":"/reference/vectorDS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates a vector on the server-side. — vectorDS","text":"object specified newobj argument written server-side.","code":""},{"path":"/reference/vectorDS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates a vector on the server-side. — vectorDS","text":"function computes vectors values.","code":""},{"path":"/reference/vectorDS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Creates a vector on the server-side. — vectorDS","text":"Stuart Wheater DataSHIELD Development Team","code":""}] diff --git a/docs/sitemap.xml b/docs/sitemap.xml index f9770fa1..8b4c8583 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -54,6 +54,7 @@ /reference/glmPredictDS.ag.html /reference/glmPredictDS.as.html /reference/glmSLMA11DS.html +/reference/glmSLMA1DS.html /reference/glmSLMA2DS.html /reference/glmSLMADS.assign.html /reference/glmSummaryDS.ag.html diff --git a/man/glmSLMA11DS.Rd b/man/glmSLMA1DS.Rd similarity index 94% rename from man/glmSLMA11DS.Rd rename to man/glmSLMA1DS.Rd index a3a79bc7..5fde80bf 100644 --- a/man/glmSLMA11DS.Rd +++ b/man/glmSLMA1DS.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/glmSLMA1DS.R -\name{glmSLMA11DS} -\alias{glmSLMA11DS} +\name{glmSLMA1DS} +\alias{glmSLMA1DS} \title{Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)} \usage{ -glmSLMA11DS(formula, family, weights, offset, data) +glmSLMA1DS(formula, family, weights, offset, data) } \arguments{ \item{formula}{a glm formula, specified in call to ds.glmSLMA}