Overview

Client Packages
Server Packages

Client Packages

dsBaseClient

Installation command:

# Install dsBaseClient package (client side)
install.packages('dsBaseClient', repos=c(getOption('repos'), 'http://cran.obiba.org'), dependencies=TRUE)

Functions:

checkClass Checks that an object has the same class in all studies
colPercent Produces column percentages
ds.Boole Converts a server-side R object into Boolean indicators
ds.abs Computes the absolute values of a variable
ds.asCharacter Converts a server-side R object into a character class
ds.asDataMatrix Converts a server-side R object into a matrix
ds.asFactor Converts a server-side numeric vector into a factor
ds.asFactorSimple Converts a numeric vector into a factor
ds.asInteger Converts a server-side R object into an integer class
ds.asList Converts a server-side R object into a list
ds.asLogical Converts a server-side R object into a logical class
ds.asMatrix Converts a server-side R object into a matrix
ds.asNumeric Converts a server-side R object into a numeric class
ds.assign Assigns an R object to a name in the server-side
ds.auc Calculates the Area under the curve (AUC)
ds.boxPlot Draw boxplot
ds.boxPlotGG Renders boxplot
ds.boxPlotGG_data_Treatment Take a data frame on the server side an arrange it to pass it to the boxplot function
ds.boxPlotGG_data_Treatment_numeric Take a vector on the server side an arrange it to pass it to the boxplot function
ds.boxPlotGG_numeric Draw boxplot with information from a numeric vector
ds.boxPlotGG_table Draw boxplot with information from a data frame
ds.bp_standards Calculates Blood pressure z-scores
ds.c Combines values into a vector or list in the server-side
ds.cbind Combines R objects by columns in the server-side
ds.changeRefGroup Changes the reference level of a factor in the server-side
ds.class Class of the R object in the server-side
ds.colnames Produces column names of the R object in the server-side
ds.completeCases Identifies complete cases in server-side R objects
ds.contourPlot Generates a contour plot
ds.cor Calculates the correlation of R objects in the server-side
ds.corTest Tests for correlation between paired samples in the server-side
ds.cov Calculates the covariance of R objects in the server-side
ds.dataFrame Generates a data frame object in the server-side
ds.dataFrameFill Creates missing values columns in the server-side
ds.dataFrameSort Sorts data frames in the server-side
ds.dataFrameSubset Sub-sets data frames in the server-side
ds.densityGrid Generates a density grid in the client-side
ds.dim Retrieves the dimension of a server-side R object
ds.dmtC2S Copy a clientside data.frame, matrix or tibble to the serverside
ds.elspline Basis for a piecewise linear spline with meaningful coefficients
ds.exists Checks if an object is defined on the server-side
ds.exp Computes the exponentials in the server-side
ds.extractQuantiles Secure ranking of a vector across all sources and use of these ranks to estimate global quantiles across all studies
ds.forestplot Forestplot for SLMA models
ds.gamlss Generalized Additive Models for Location Scale and Shape
ds.getWGSR Computes the WHO Growth Reference z-scores of anthropometric data
ds.glm Fits Generalized Linear Model
ds.glmPredict Applies predict.glm() to a serverside glm object
ds.glmSLMA Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)
ds.glmSummary Summarize a glm object on the serverside
ds.glmerSLMA Fits Generalized Linear Mixed-Effect Models via Study-Level Meta-Analysis
ds.heatmapPlot Generates a Heat Map plot
ds.hetcor Heterogeneous Correlation Matrix
ds.histogram Generates a histogram plot
ds.igb_standards Converts birth measurements to intergrowth z-scores/centiles
ds.isNA Checks if a server-side vector is empty
ds.isValid Checks if a server-side object is valid
ds.kurtosis Calculates the kurtosis of a numeric variable
ds.length Gets the length of an object in the server-side
ds.levels Produces levels attributes of a server-side factor
ds.lexis Represents follow-up in multiple states on multiple time scales
ds.list Constructs a list of objects in the server-side
ds.listClientsideFunctions Lists client-side functions
ds.listDisclosureSettings Lists disclosure settings
ds.listOpals Lists all Opal objects in the analytic environment
ds.listServersideFunctions Lists server-side functions
ds.lmerSLMA Fits Linear Mixed-Effect model via Study-Level Meta-Analysis
ds.log Computes logarithms in the server-side
ds.look Performs direct call to a server-side aggregate function
ds.ls lists all objects on a server-side environment
ds.lspline Basis for a piecewise linear spline with meaningful coefficients
ds.make Calculates a new object in the server-side
ds.matrix Creates a matrix on the server-side
ds.matrixDet Calculates de determinant of a matrix in the server-side
ds.matrixDet.report Returns matrix determinant to the client-side
ds.matrixDiag Calculates matrix diagonals in the server-side
ds.matrixDimnames Specifies the dimnames of the server-side matrix
ds.matrixInvert Inverts a server-side square matrix
ds.matrixMult Calculates tow matrix multiplication in the server-side
ds.matrixTranspose Transposes a server-side matrix
ds.mean Computes server-side vector statistical mean
ds.meanByClass Computes the mean and standard deviation across categories
ds.meanSdGp Computes the mean and standard deviation across groups defined by one factor
ds.merge Merges two data frames in the server-side
ds.message Returns server-side messages to the client-side
ds.metadata Gets the metadata associated with a variable held on the server
ds.mice Multivariate Imputation by Chained Equations
ds.names Return the names of a list object
ds.ns Generate a Basis Matrix for Natural Cubic Splines
ds.numNA Gets the number of missing values in a server-side vector
ds.qlspline Basis for a piecewise linear spline with meaningful coefficients
ds.quantileMean Computes the quantiles of a server-side variable
ds.rBinom Generates Binomial distribution in the server-side
ds.rNorm Generates Normal distribution in the server-side
ds.rPois Generates Poisson distribution in the server-side
ds.rUnif Generates Uniform distribution in the server-side
ds.ranksSecure Secure ranking of a vector across all sources
ds.rbind Combines R objects by rows in the server-side
ds.reShape Reshapes server-side grouped data
ds.recodeLevels Recodes the levels of a server-side factor vector
ds.recodeValues Recodes server-side variable values
ds.rep Creates a repetitive sequence in the server-side
ds.replaceNA Replaces the missing values in a server-side vector
ds.rm Deletes server-side R objects
ds.rowColCalc Computes rows and columns sums and means in the server-side
ds.sample Performs random sampling and permuting of vectors, dataframes and matrices
ds.scatterPlot Generates non-disclosive scatter plots
ds.seq Generates a sequence in the server-side
ds.setDefaultOpals Creates a default set of Opal objects called ‘default.opals’
ds.setSeed Server-side random number generation
ds.skewness Calculates the skewness of a server-side numeric variable
ds.sqrt Computes the square root values of a variable
ds.subset Generates a valid subset of a table or a vector
ds.subsetByClass Generates valid subset(s) of a data frame or a factor
ds.summary Generates the summary of a server-side object
ds.table Generates 1-, 2-, and 3-dimensional contingency tables with option of assigning to serverside only and producing chi-squared statistics
ds.table1D Generates 1-dimensional contingency tables
ds.table2D Generates 2-dimensional contingency tables
ds.tapply Applies a Function Over a Server-Side Ragged Array
ds.tapply.assign Applies a Function Over a Ragged Array on the server-side
ds.testObjExists Checks if an R object exists on the server-side
ds.unList Flattens Server-Side Lists
ds.unique Perform ‘unique’ on a variable on the server-side
ds.var Computes server-side vector variance
ds.vectorCalc Performs a mathematical operation on two or more vectors
extract Splits character by ‘$’ and returns the single characters
getPooledMean Gets a pooled statistical mean
getPooledVar Gets a pooled variance
glmChecks Checks if the elements in the glm model have the right characteristics
isAssigned Checks an object has been generated on the server side
isDefined Checks if the objects are defined in all studies
logical2int Turns a logical operator into an integer
meanByClassHelper0a Computes the mean values of a numeric vector across a factor vector
meanByClassHelper0b Runs the computation if variables are within a table structure
meanByClassHelper1 Generates subset tables
meanByClassHelper2 Generates a table for pooled results
meanByClassHelper3 Generates results tables for each study separately
meanByClassHelper4 Gets the subset tables out of the list (i.e. unlist)
rowPercent Produces row percentages
subsetHelper Ensures that the requested subset is not larger than the original object

Sources:

dsDangerClient

Installation command:

# Install dsDangerClient package (client side)
install.packages('dsDangerClient', repos=c(getOption('repos'), 'http://cran.obiba.org'), dependencies=TRUE)

Functions:

ds.DANGERc2sMATDF DANGER FUNCTION copying clientside matrix to serverside
ds.DANGERdfEXTRACT DANGER function returning data.frame (df) from processing servers to clientside - ** DEPRECATED BY ds.DANGERdmtEXTRACT **
ds.DANGERdmtEXTRACT DANGER function returning data.frame, Matrix or tibble (DMT) from processing servers to clientside
ds.DANGERlistcode list the code for a function
ds.DANGERpassPARSER determines how a given R object or character string is managed by the DataSHIELD parser
ds.DANGERplot DANGER function
ds.DANGERprint DANGER function
ds.DANGERsearch lists all R environments on serverside
ds.DANGERseedEXTRACT ds.DANGERseedEXTRACT
ds.DANGERvarsEXTRACT ds.DANGERvarsEXTRACT

Sources:

Server Packages

dsBase

Installation command:

# Install dsBase package (server side)
library(opaladmin)
o<-opal.login(...)
dsadmin.install_package(o, 'dsBase')

Functions:

BooleDS BooleDS
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
blackBoxDS Secure ranking of “V2BR” (vector to be ranked) across all sources
blackBoxRanksDS Secure ranking of “V2BR” (vector to be ranked) across all sources
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
cDS Concatenates objects into a vector or list
cbindDS cbindDS called by ds.cbind
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
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.
elsplineDS Basis for a piecewise linear spline with meaningful coefficients
extract Splits character by ‘$’ and returns the single characters
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
gamlssDS gamlssDS an aggregate function called by ds.galmss
getWGSRDS Computes the WHO Growth Reference z-scores of anthropometric data
glmDS1 glmDS1 called by ds.glm
glmDS2 glmDS2 called by ds.glm
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
glmerSLMADS.assign Fitting generalized linear mixed effect models - serverside function
glmerSLMADS2 Fitting generalized linear mixed effect models - serverside function
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.
igb_standardsDS Converts birth measurements to intergrowth z-scores/centiles
isNaDS Checks if a vector is empty
isValidDS Checks if an input is valid
kurtosisDS1 Calculates the kurtosis of a numeric variable
kurtosisDS2 Calculates the kurtosis of a numeric variable
lengthDS Returns the length of a vector or list
levelsDS Returns the levels of a factor vector
lexisDS1 lexisDS1
lexisDS2 lexisDS2
lexisDS3 @title lexisDS3
listDS Coerce objects into a list
listDisclosureSettingsDS listDisclosureSettingsDS
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
matrixDS matrixDS assign function called by ds.matrix
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
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 vectores
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
namesDS Return the names of a list object
nsDS Generate a Basis Matrix for Natural Cubic Splines
numNaDS Counts the number of missing values
qlsplineDS Basis for a piecewise linear spline with meaningful coefficients
quantileMeanDS Generates quantiles and mean information without maximum and minimum
rBinomDS rBinomDS serverside assign function
rNormDS rNormDS serverside assign function
rPoisDS rPoisDS serverside assign function
rUnifDS rUnifDS serverside assign function
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
reShapeDS reShapeDS (assign function) called by ds.reShape
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
rmDS rmDS an aggregate function called by ds.rm
rowColCalcDS Computes sums and means of rows or columns of numeric arrays
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
setFilterDS Sets the privacy level
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
subsetByClassHelper1 generates subsets vectors from a factor vector
subsetByClassHelper2 generates subset tables from a data frame
subsetByClassHelper3 generates subset tables from a data frame
subsetDS Generates a valid subset of a table or a vector
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
unListDS unListDS a serverside assign function called by ds.unList
uniqueDS Applies the ‘unique’ method to a server-side variable.
varDS Computes the variance of vector
vectorDS Creates a vector on the server-side.

Sources:

dsDanger

Installation command:

# Install dsDanger package (server side)
library(opaladmin)
o<-opal.login(...)
dsadmin.install_package(o, 'dsDanger')

Functions:

DANGERc2sMATDFDS DANGER FUNCTION copying clientside matrix to serverside
DANGERdfEXTRACTDS DANGER function returning data.frame (df) from processing servers to clientside - ** DEPRECATED DANGERdmtEXTRACTDS **
DANGERdmtEXTRACTDS DANGER function returning data.frame, Matrix or tibble (DMT) from processing servers to clientside
DANGERlistcodeDS lists the code for a function
DANGERpassPARSERDS determines how a given R object or character string is managed by the DataSHIELD parser
DANGERplotDS DANGERplotDS
DANGERprintDS DANGERprintDS
DANGERsearchDS lists all environments on serverside
DANGERseedEXTRACTDS DANGERseedEXTRACT
DANGERvarsEXTRACTDS DANGERvarsEXTRACT

Sources: