Package: dsBase 6.3.6.9000

dsBase: 'DataSHIELD' Server Side Base Functions

Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for the automated output checks. For more details, see 'citation("dsBase")'.

Authors:Paul Burton [aut], Rebecca Wilson [aut], Olly Butters [aut], Patricia Ryser-Welch [aut], Alex Westerberg [aut], Leire Abarrategui [aut], Roberto Villegas-Diaz [aut], Demetris Avraam [aut], Yannick Marcon [aut], Tom Bishop [aut], Amadou Gaye [aut], Xavier Escribà-Montagut [aut], Stuart Wheater [aut, cre]

dsBase_6.3.6.9000.tar.gz
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manual.pdf |manual.html
card.svg |card.png
dsBase/json (API)

# Install 'dsBase' in R:
install.packages('dsBase', repos = c('https://stuartwheater.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stuartwheater/dsbase/issues

On CRAN:

Conda:

6.20 score 1 packages 35 scripts 327 downloads 139 exports 110 dependencies

Last updated from:69a7c1263e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK192
source / vignettesOK237
linux-release-x86_64OK187
macos-release-arm64OK133
macos-oldrel-arm64OK162
windows-develOK139
windows-releaseOK146
windows-oldrelOK147
wasm-releaseOK130

Exports:absDSasCharacterDSasDataMatrixDSasFactorDS1asFactorDS2asFactorSimpleDSasIntegerDSasListDSasLogicalDSasMatrixDSasNumericDSaucDSblackBoxDSblackBoxRanksDSBooleDSboxPlotGG_data_Treatment_numericDSboxPlotGG_data_TreatmentDSboxPlotGGDSbp_standardsDScbindDScDSchangeRefGroupDScheckNegValueDScheckPermissivePrivacyControlLevelclassDScolnamesDScompleteCasesDScorDScorTestDScovDSdataFrameDSdataFrameFillDSdataFrameSortDSdataFrameSubsetDS1dataFrameSubsetDS2densityGridDSdimDSdmtC2SDSelsplineDSextractQuantilesDS1extractQuantilesDS2fixClassDSfixColsDSfixLevelsDSgamlssDSgetAllLevelsDSgetClassAllColsDSgetWGSRDSglmDS1glmDS2glmerSLMADS.assignglmerSLMADS2glmPredictDS.agglmPredictDS.asglmSLMADS.assignglmSLMADS1glmSLMADS2glmSummaryDS.agglmSummaryDS.asheatmapPlotDShetcorDShistogramDS1histogramDS2igb_standardsDSisNaDSisValidDSkurtosisDS1kurtosisDS2lengthDSlevelsDSlexisDS1lexisDS2lexisDS3listDisclosureSettingsDSlistDSlmerSLMADS.assignlmerSLMADS2lsDSlsplineDSmatrixDetDS1matrixDetDS2matrixDiagDSmatrixDimnamesDSmatrixDSmatrixInvertDSmatrixMultDSmatrixTransposeDSmdPatternDSmeanDSmeanSdGpDSmergeDSmessageDSmetadataDSmiceDSminMaxRandDSnamesDSnsDSnumNaDSqlsplineDSquantileMeanDSrangeDSranksSecureDS1ranksSecureDS2ranksSecureDS3ranksSecureDS4ranksSecureDS5rbindDSrBinomDSrecodeLevelsDSrecodeValuesDSrepDSreplaceNaDSreShapeDSrmDSrNormDSrowColCalcDSrPoisDSrUnifDSsampleDSscatterPlotDSseqDSsetSeedDSskewnessDS1skewnessDS2sqrtDSsubsetByClassDSsubsetDStable1DDStable2DDStableDStableDS.assigntableDS2tapplyDStapplyDS.assigntestObjExistsDSuniqueDSunListDSvarDSvectorDS

Dependencies:admiscaskpassbackportsbitbit64bootbroomcellrangerchildsdsclassclicliprcodetoolscolorspacecpp11crayoncurldata.tabledeldirDescToolsdplyre1071Exactexpmfarverforcatsforeachfsgamlssgamlss.datagamlss.distgenericsggplot2gldglmnetgluegtablehavenhmshttrinterpisobanditeratorsjomojsonlitelabelinglatticelifecyclelme4lmomlubridatemagrittrMASSMatrixmicemimeminqamitmlmvtnormnlmenloptrnnetnumDerivopensslordinalpanpillarpkgconfigplyrpolycorprettyunitsprogressproxypurrrpurrrlyrR6RANNrbibutilsRColorBrewerRcppRcppEigenRdpackreadrreadxlreformulasrematchreshape2rlangrootSolverpartrstudioapiS7scalesshapestringistringrsurvivalsystibbletidyrtidyselecttimechangetzdbucminfutf8vctrsVGAMviridisLitevroomwithr

Readme and manuals

Help Manual

Help pageTopics
Computes the absolute values of the input variableabsDS
Coerces an R object into class characterasCharacterDS
asDataMatrixDS a serverside assign function called by ds.asDataMatrixasDataMatrixDS
Determines the levels of the input variable in each single studyasFactorDS1
Converts a numeric vector into a factorasFactorDS2
Converts a numeric vector into a factorasFactorSimpleDS
Coerces an R object into class integerasIntegerDS
asListDS a serverside aggregate function called by ds.asListasListDS
Coerces an R object into class numericasLogicalDS
Coerces an R object into a matrixasMatrixDS
Coerces an R object into class numericasNumericDS
aucDS an aggregate function called by ds.aucaucDS
Secure ranking of "V2BR" (vector to be ranked) across all sourcesblackBoxDS
Secure ranking of "V2BR" (vector to be ranked) across all sourcesblackBoxRanksDS
BooleDSBooleDS
Arrange vector to pass it to the boxplot functionboxPlotGG_data_Treatment_numericDS
Arrange data frame to pass it to the boxplot functionboxPlotGG_data_TreatmentDS
Create the identity stats and necessary data to draw a plot on the clientboxPlotGGDS
Calculates Blood pressure z-scoresbp_standardsDS
cbindDS called by ds.cbindcbindDS
Concatenates objects into a vector or listcDS
Changes a reference level of a factorchangeRefGroupDS
Checks if a numeric variable has negative valuescheckNegValueDS
checkPermissivePrivacyControlLevelcheckPermissivePrivacyControlLevel
Returns the class of an objectclassDS
Returns the column names of a data frame or matrixcolnamesDS
completeCasesDS: an assign function called by ds.completeCasescompleteCasesDS
Computes the sum of each variable and the sum of products for each pair of variablescorDS
Tests for correlation between paired samplescorTestDS
Computes the sum of each variable and the sum of products for each pair of variablescovDS
dataFrameDS called by ds.dataFramedataFrameDS
dataFrameFillDSdataFrameFillDS
Sorting and reordering data frames, vectors or matricesdataFrameSortDS
dataFrameSubsetDS1 an aggregate function called by ds.dataFrameSubsetdataFrameSubsetDS1
dataFrameSubsetDS2 an assign function called by ds.dataFrameSubsetdataFrameSubsetDS2
Generates a density grid with or without a priori defined limitsdensityGridDS
Returns the dimension of a data frame or matrixdimDS
Copy a clientside data.frame, matrix or tibble (DMT) to the serverside.dmtC2SDS
Basis for a piecewise linear spline with meaningful coefficientselsplineDS
Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studiesextractQuantilesDS1
Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studiesextractQuantilesDS2
Change Class of Target Variables in a Data FramefixClassDS
Add Missing Columns with NA ValuesfixColsDS
Set Factor Levels for Specific Columns in a Data FramefixLevelsDS
gamlssDS an aggregate function called by ds.gamlssgamlssDS
Retrieve Factor Levels for Specific ColumnsgetAllLevelsDS
Get the Class of All Columns in a Data FramegetClassAllColsDS
Computes the WHO Growth Reference z-scores of anthropometric datagetWGSRDS
glmDS1 called by ds.glmglmDS1
glmDS2 called by ds.glmglmDS2
Fitting generalized linear mixed effect models - serverside functionglmerSLMADS.assign
Fitting generalized linear mixed effect models - serverside functionglmerSLMADS2
predict regression responses from a glm objectglmPredictDS.ag
predict regression responses from a glm objectglmPredictDS.as
Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)glmSLMADS.assign
Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)glmSLMADS1
Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)glmSLMADS2
summarize a glm object on the serversideglmSummaryDS.ag
summarize a glm object on the serversideglmSummaryDS.as
Calculates the coordinates of the centroid of each n nearest neighboursheatmapPlotDS
Heterogeneous Correlation MatrixhetcorDS
returns the minimum and the maximum of the input numeric vectorhistogramDS1
Computes a histogram of the input variable without plotting.histogramDS2
Converts birth measurements to intergrowth z-scores/centilesigb_standardsDS
Checks if a vector is emptyisNaDS
Checks if an input is validisValidDS
Calculates the kurtosis of a numeric variablekurtosisDS1
Calculates the kurtosis of a numeric variablekurtosisDS2
Returns the length of a vector or listlengthDS
Returns the levels of a factor vectorlevelsDS
lexisDS1lexisDS1
lexisDS2lexisDS2
@title lexisDS3lexisDS3
listDisclosureSettingsDSlistDisclosureSettingsDS
Coerce objects into a listlistDS
Fitting linear mixed effect models - serverside functionlmerSLMADS.assign
Fitting linear mixed effect models - serverside functionlmerSLMADS2
lists all objects on a serverside environmentlsDS
Basis for a piecewise linear spline with meaningful coefficientslsplineDS
matrixDetDS aggregate function called by ds.matrixDet.reportmatrixDetDS1
matrixDetDS assign function called by ds.matrixDetmatrixDetDS2
matrixDiagDS assign function called by ds.matrixDiagmatrixDiagDS
matrixDimnamesDS assign function called by ds.matrixDimnamesmatrixDimnamesDS
matrixDS assign function called by ds.matrixmatrixDS
matrixInvertDS serverside assign function called by ds.matrixInvertmatrixInvertDS
matrixMultDS serverside assign function called by ds.matrixMultmatrixMultDS
matrixTransposeDS serverside assign function called by ds.matrixTransposematrixTransposeDS
Missing data pattern with disclosure controlmdPatternDS
Computes statistical mean of a vectormeanDS
MeanSdGpDSmeanSdGpDS
mergeDS (assign function) called by ds.mergemergeDS
messageDSmessageDS
Returns the metadata, if any, about the specified variablemetadataDS
Aggregate function called by ds.micemiceDS
Secure ranking of "V2BR" (vector to be ranked) across all sourcesminMaxRandDS
Return the names of a list objectnamesDS
Generate a Basis Matrix for Natural Cubic SplinesnsDS
Counts the number of missing valuesnumNaDS
Basis for a piecewise linear spline with meaningful coefficientsqlsplineDS
Generates quantiles and mean information without maximum and minimumquantileMeanDS
returns the minimum and maximum of a numeric vectorrangeDS
Secure ranking of "V2BR" (vector to be ranked) across all sourcesranksSecureDS1
Secure ranking of "V2BR" (vector to be ranked) across all sourcesranksSecureDS2
Secure ranking of "V2BR" (vector to be ranked) across all sourcesranksSecureDS3
Secure ranking of "V2BR" (vector to be ranked) across all sourcesranksSecureDS4
Secure ranking of "V2BR" (vector to be ranked) across all sourcesranksSecureDS5
rbindDS called by ds.rbindrbindDS
rBinomDS serverside assign functionrBinomDS
Recodes the levels of a categorical variablesrecodeLevelsDS
recodeValuesDS an assign function called by ds.recodeValuesrecodeValuesDS
repDS called by ds.reprepDS
Replaces the missing values in a vectorreplaceNaDS
reShapeDS (assign function) called by ds.reShapereShapeDS
rmDS an aggregate function called by ds.rmrmDS
rNormDS serverside assign functionrNormDS
Computes sums and means of rows or columns of numeric arraysrowColCalcDS
rPoisDS serverside assign functionrPoisDS
rUnifDS serverside assign functionrUnifDS
random sampling and permuting of vectors, dataframes and matricessampleDS
Calculates the coordinates of the data to be plotscatterPlotDS
seqDS a serverside assign function called by ds.seqseqDS
setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinomsetSeedDS
Calculates the skewness of a numeric variableskewnessDS1
Calculates the skewness of a numeric variableskewnessDS2
Computes the square root values of the input variablesqrtDS
Breaks down a dataframe or a factor into its sub-classessubsetByClassDS
Generates a valid subset of a table or a vectorsubsetDS
Creates 1-dimensional contingency tablestable1DDS
table2DDS (aggregate function) called by ds.table2Dtable2DDS
tableDS is the first of two serverside aggregate functions called by ds.tabletableDS
tableDS.assign is the serverside assign function called by ds.tabletableDS.assign
tableDS is the second of two serverside aggregate functions called by ds.tabletableDS2
tapplyDS called by ds.tapplytapplyDS
tapplyDS.assign called by ds.tapply.assigntapplyDS.assign
testObjExistsDStestObjExistsDS
Applies the 'unique' method to a server-side variable.uniqueDS
'unListDS' a serverside assign function called by 'ds.unList'unListDS
Computes the variance of vectorvarDS
Creates a vector on the server-side.vectorDS