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Overview

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.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.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.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.exists Checks if an object is defined on the server-side
  • ds.exp Computes the exponentials in the server-side
  • 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.histogram Generates a histogram plot
  • 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.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.names Return the names of a list object
  • ds.numNA Gets the number of missing values in a server-side vector
  • 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.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.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 objecs are defined in 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:

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
  • 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
  • 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
  • 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
  • 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
  • extract Splits character by ‘$’ and returns the single characters
  • 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.assing 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
  • histogramDS1 returns the minimum and the maximum of the input numeric vector
  • histogramDS2 Computes a histogram of the input variable without plotting.
  • 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
  • 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
  • namesDS Return the names of a list object
  • numNaDS Counts the number of missing values
  • 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
  • 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
  • varDS Computes the variance of vector

Sources: