# 'DataSHIELD' Server Side Base Functions

## Documentation for package ‘dsBase’ version 6.3.4

- DESCRIPTION file
- Package README

## Help Pages

A B C D E G H I K L M N Q R S T U V

## -- A --

absDS | Computes the absolute values of the input variable
asCharacterDS | Coerces an R object into class character
asDataMatrixDS | asDataMatrixDS a serverside assign function called by ds.asDataMatrix
asFactorDS1 | Determines the levels of the input variable in each single study
asFactorDS2 | Converts a numeric vector into a factor
asFactorSimpleDS | Converts a numeric vector into a factor
asIntegerDS | Coerces an R object into class integer
asListDS | asListDS a serverside aggregate function called by ds.asList
asLogicalDS | Coerces an R object into class numeric
asMatrixDS | Coerces an R object into a matrix
asNumericDS | Coerces an R object into class numeric
aucDS | aucDS an aggregate function called by ds.auc

## -- B --

blackBoxDS | Secure ranking of "V2BR" (vector to be ranked) across all sources
blackBoxRanksDS | Secure ranking of "V2BR" (vector to be ranked) across all sources
BooleDS | BooleDS
boxPlotGGDS | Create the identity stats and necessary data to draw a plot on the client
boxPlotGG_data_TreatmentDS | Arrange data frame to pass it to the boxplot function
boxPlotGG_data_Treatment_numericDS | Arrange vector to pass it to the boxplot function
bp_standardsDS | Calculates Blood pressure z-scores

## -- C --

cbindDS | cbindDS called by ds.cbind
cDS | Concatenates objects into a vector or list
changeRefGroupDS | Changes a reference level of a factor
checkNegValueDS | Checks if a numeric variable has negative values
checkPermissivePrivacyControlLevel | checkPermissivePrivacyControlLevel
classDS | Returns the class of an object
colnamesDS | Returns the column names of a data frame or matrix
completeCasesDS | completeCasesDS: an assign function called by ds.completeCases
corDS | Computes the sum of each variable and the sum of products for each pair of variables
corTestDS | Tests for correlation between paired samples
covDS | Computes the sum of each variable and the sum of products for each pair of variables

## -- D --

dataFrameDS | dataFrameDS called by ds.dataFrame
dataFrameFillDS | dataFrameFillDS
dataFrameSortDS | Sorting and reordering data frames, vectors or matrices
dataFrameSubsetDS1 | dataFrameSubsetDS1 an aggregate function called by ds.dataFrameSubset
dataFrameSubsetDS2 | dataFrameSubsetDS2 an assign function called by ds.dataFrameSubset
densityGridDS | Generates a density grid with or without a priori defined limits
dimDS | Returns the dimension of a data frame or matrix
dmtC2SDS | Copy a clientside data.frame, matrix or tibble (DMT) to the serverside.

## -- E --

elsplineDS | Basis for a piecewise linear spline with meaningful coefficients
extractQuantilesDS1 | Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies
extractQuantilesDS2 | Secure ranking of "V2BR" (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies

## -- G --

gamlssDS | gamlssDS an aggregate function called by ds.gamlss
getWGSRDS | Computes the WHO Growth Reference z-scores of anthropometric data
glmDS1 | glmDS1 called by ds.glm
glmDS2 | glmDS2 called by ds.glm
glmerSLMADS.assign | Fitting generalized linear mixed effect models - serverside function
glmerSLMADS2 | Fitting generalized linear mixed effect models - serverside function
glmPredictDS.ag | predict regression responses from a glm object
glmPredictDS.as | predict regression responses from a glm object
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 | Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)
glmSummaryDS.ag | summarize a glm object on the serverside
glmSummaryDS.as | summarize a glm object on the serverside

## -- H --

heatmapPlotDS | Calculates the coordinates of the centroid of each n nearest neighbours
hetcorDS | Heterogeneous Correlation Matrix
histogramDS1 | returns the minimum and the maximum of the input numeric vector
histogramDS2 | Computes a histogram of the input variable without plotting.

## -- I --

igb_standardsDS | Converts birth measurements to intergrowth z-scores/centiles
isNaDS | Checks if a vector is empty
isValidDS | Checks if an input is valid

## -- K --

kurtosisDS1 | Calculates the kurtosis of a numeric variable
kurtosisDS2 | Calculates the kurtosis of a numeric variable

## -- L --

lengthDS | Returns the length of a vector or list
levelsDS | Returns the levels of a factor vector
lexisDS1 | lexisDS1
lexisDS2 | lexisDS2
lexisDS3 | @title lexisDS3
listDisclosureSettingsDS | listDisclosureSettingsDS
listDS | Coerce objects into a list
lmerSLMADS.assign | Fitting linear mixed effect models - serverside function
lmerSLMADS2 | Fitting linear mixed effect models - serverside function
lsDS | lists all objects on a serverside environment
lsplineDS | Basis for a piecewise linear spline with meaningful coefficients

## -- M --

matrixDetDS1 | matrixDetDS aggregate function called by ds.matrixDet.report
matrixDetDS2 | matrixDetDS assign function called by ds.matrixDet
matrixDiagDS | matrixDiagDS assign function called by ds.matrixDiag
matrixDimnamesDS | matrixDimnamesDS assign function called by ds.matrixDimnames
matrixDS | matrixDS assign function called by ds.matrix
matrixInvertDS | matrixInvertDS serverside assign function called by ds.matrixInvert
matrixMultDS | matrixMultDS serverside assign function called by ds.matrixMult
matrixTransposeDS | matrixTransposeDS serverside assign function called by ds.matrixTranspose
meanDS | Computes statistical mean of a vector
meanSdGpDS | MeanSdGpDS
mergeDS | mergeDS (assign function) called by ds.merge
messageDS | messageDS
metadataDS | Returns the metadata, if any, about the specified variable
miceDS | Aggregate function called by ds.mice
minMaxRandDS | Secure ranking of "V2BR" (vector to be ranked) across all sources

## -- N --

namesDS | Return the names of a list object
nsDS | Generate a Basis Matrix for Natural Cubic Splines
numNaDS | Counts the number of missing values

## -- Q --

qlsplineDS | Basis for a piecewise linear spline with meaningful coefficients
quantileMeanDS | Generates quantiles and mean information without maximum and minimum

## -- R --

rangeDS | returns the minimum and maximum of a numeric vector
ranksSecureDS1 | Secure ranking of "V2BR" (vector to be ranked) across all sources
ranksSecureDS2 | Secure ranking of "V2BR" (vector to be ranked) across all sources
ranksSecureDS3 | Secure ranking of "V2BR" (vector to be ranked) across all sources
ranksSecureDS4 | Secure ranking of "V2BR" (vector to be ranked) across all sources
ranksSecureDS5 | Secure ranking of "V2BR" (vector to be ranked) across all sources
rbindDS | rbindDS called by ds.rbind
rBinomDS | rBinomDS serverside assign function
recodeLevelsDS | Recodes the levels of a categorical variables
recodeValuesDS | recodeValuesDS an assign function called by ds.recodeValues
repDS | repDS called by ds.rep
replaceNaDS | Replaces the missing values in a vector
reShapeDS | reShapeDS (assign function) called by ds.reShape
rmDS | rmDS an aggregate function called by ds.rm
rNormDS | rNormDS serverside assign function
rowColCalcDS | Computes sums and means of rows or columns of numeric arrays
rPoisDS | rPoisDS serverside assign function
rUnifDS | rUnifDS serverside assign function

## -- S --

sampleDS | random sampling and permuting of vectors, dataframes and matrices
scatterPlotDS | Calculates the coordinates of the data to be plot
seqDS | seqDS a serverside assign function called by ds.seq
setSeedDS | setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom
skewnessDS1 | Calculates the skewness of a numeric variable
skewnessDS2 | Calculates the skewness of a numeric variable
sqrtDS | Computes the square root values of the input variable
subsetByClassDS | Breaks down a dataframe or a factor into its sub-classes
subsetDS | Generates a valid subset of a table or a vector

## -- T --

table1DDS | Creates 1-dimensional contingency tables
table2DDS | table2DDS (aggregate function) called by ds.table2D
tableDS | tableDS is the first of two serverside aggregate functions called by ds.table
tableDS.assign | tableDS.assign is the serverside assign function called by ds.table
tableDS2 | tableDS is the second of two serverside aggregate functions called by ds.table
tapplyDS | tapplyDS called by ds.tapply
tapplyDS.assign | tapplyDS.assign called by ds.tapply.assign
testObjExistsDS | testObjExistsDS

## -- U --

uniqueDS | Applies the 'unique' method to a server-side variable.
unListDS | 'unListDS' a serverside assign function called by 'ds.unList'

## -- V --

varDS | Computes the variance of vector
vectorDS | Creates a vector on the server-side.