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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:

Sources:

dsModellingClient

Installation command:

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

Functions:

  • checkClass Checks that an object has the same class in all studies
  • ds.gee Fits a Generalized Estimating Equation (GEE) model
  • ds.glm Runs a combined GLM analysis of non-pooled data
  • ds.lexis Generates an expanded version of a dataset that contains survival data
  • extract Splits character by ‘$’ and returns the single characters
  • findLoginObjects searches for opal login object in the environment
  • geeChecks Checks if the elements in a regression formula are defined and not empty
  • geeLoginData Information required to login to opal servers for the GEE test data
  • geeLogin_remoteServer Information required to login to opal servers for the GEE test data
  • geehelper1 Computes the pooled parameters alpha and phi
  • geehelper2 Produces the pooled beta values and standard errors
  • getOpals Gets the opal objects
  • glmChecks Checks if the elements in the glm model have the right characteristics
  • glmLoginData Information required to login to opal servers for the GLM test data
  • glmLogin_remoteServer Information required to login to opal servers for the GLM test data
  • isAssigned Checks an object has been generated on the server side
  • isDefined Checks if objects are defined in studies
  • lexisHelper1 Generates a default value to use as interval width
  • logical2int turns a logical operator into an integer
  • survivalLoginData Information required to login to opal servers for the GLM test data

Sources:

dsStatsClient

Installation command:

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

Functions:

  • checkClass Checks that an object has the same class in all studies
  • ds.cor Computes correlation between two or more vectors
  • ds.corTest Tests for correlation between paired samples
  • ds.cov Computes covariance between two or more vectors
  • ds.tTest Runs a student’s t-test
  • ds.var Computes the variance of a given vector
  • extract Splits character by ‘$’ and returns the single characters
  • findLoginObjects searches for opal login object in the environment
  • getOpals Gets the opal objects
  • getPooledMean Gets a pooled statistical mean
  • getPooledVar Gets a pooled variance
  • 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
  • login_remoteServer Information required to login to opal servers
  • logindata Information required to login to opal servers
  • tTestHelper1 runs a t-test for two continuous variables
  • tTestHelper2 Uses glm to compute means of numeric vector across factor vector

Sources:

dsGraphicsClient

Installation command:

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

Functions:

Sources:

opal

Installation command:

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

Functions:

Sources:

opaladmin

Installation command:

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

Functions:

Sources:

Server Packages

dsBase

Installation command:

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

Functions:

  • asFactorDS Turns a numeric vector into a factor vector
  • asListDS Converts a data.frame or matrix into a list
  • asMatrixDS Attempts to convert the input into a matrix
  • cDS Concatenates objects into a vector or list
  • changeRefGroupDS Changes a reference level of a factor
  • dataframeDS Creates a data frame
  • extract Splits character by ‘$’ and returns the single characters
  • isNaDS Checks if a vector is empty
  • isValidDS Checks if an input is valid
  • listDS Coerce objects into a list
  • meanDS Computes statistical mean of a vectores
  • namesDS Returns the names of a list
  • numNaDS Counts the number of missing values
  • quantileMeanDS Generates quantiles and mean information without maximum and minimum
  • recodeLevelsDS Recodes the levels of a categorical variables
  • replaceNaDS Replaces the missing values in a vector
  • rowColCalcDS Computes sums and means of rows or columns of numeric arrays
  • setFilterDS Sets the privacy level
  • 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 Creates 2-dimensional contingency tables
  • varDS Computes the variance of vector with more than 4 entries

Sources:

dsModelling

Installation command:

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

Functions:

  • alphaPhiDS Computes the parameters alpha and phi
  • checkNegValueDS Checks if a numeric variable has negative values
  • glmDS1 get matrix dimensions
  • glmDS2 Fits a generalized linear model
  • lexisDS Generates an expanded version of a dataset that contains survival data
  • lexishelper1 Computes time breaks given the exit time
  • lexishelper2 Computes time periods of each subject
  • scoreVectDS Generates the score vector and information matrix

Sources:

dsStats

Installation command:

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

Functions:

  • corDS Computes correlation between two or more vectors
  • covDS Computes covariance between two or more vectors
  • extract Splits character by ‘$’ and returns the single characters
  • isValidDS Checks if an input is valid
  • setFilterDS Sets the privacy level
  • varDS Computes the variance of vector with more than 4 entries

Sources:

dsGraphics

Installation command:

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

Functions:

  • densityGridDS Generates a density grid with or without a priori defined limits
  • extract Splits character by ‘$’ and returns the single characters
  • histogramDS Computes a histogram of the given data values without plotting.
  • rangeDS returns the minimum and maximum of a numeric vector
  • setFilterDS Sets the privacy level

Sources: