ds.cor: Calculates the correlation of R objects in the server-side

In datashield/dsBaseClient: DataSHIELD Client Functions

Calculates the correlation of R objects in the server-side

Description

This function calculates the correlation of two variables or the correlation matrix for the variables of an input data frame.

Usage

ds.cor(x = NULL, y = NULL, type = "split", datasources = NULL)

Arguments

x	a character string providing the name of the input vector, data frame or matrix.
y	a character string providing the name of the input vector, data frame or matrix. Default NULL.
type	a character string that represents the type of analysis to carry out. This must be set to 'split' or 'combine'. Default 'split'. For more information see details.
datasources	a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Details

In addition to computing correlations; this function produces a table outlining the number of complete cases and a table outlining the number of missing values to allow the user to decide the 'relevance' of the correlation based on the number of complete cases included in the correlation calculations.

If the argument y is not NULL, the dimensions of the object have to be compatible with the argument x.

The function calculates the pairwise correlations based on casewise complete cases which means that it omits all the rows in the input data frame that include at least one cell with a missing value, before the calculation of correlations.

If type is set to 'split' (default), the correlation of two variables or the variance-correlation matrix of an input data frame and the number of complete cases and missing values are returned for every single study. If type is set to 'combine', the pooled correlation, the total number of complete cases and the total number of missing values aggregated from all the involved studies, are returned.

Server function called: corDS

Value

ds.cor returns a list containing the number of missing values in each variable, the number of missing variables casewise, the correlation matrix, the number of used complete cases. The function applies two disclosure controls. The first disclosure control checks that the number of variables is not bigger than a percentage of the individual-level records (the allowed percentage is pre-specified by the 'nfilter.glm'). The second disclosure control checks that none of them is dichotomous with a level having fewer counts than the pre-specified 'nfilter.tab' threshold.

Author(s)

DataSHIELD Development Team

Examples

## Not run: 

## Version 6, for version 5 see the Wiki
  # Connecting to the Opal servers

  require('DSI')
  require('DSOpal')
  require('dsBaseClient')

  builder <- DSI::newDSLoginBuilder()
  builder$append(server = "study1", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "CNSIM.CNSIM1", driver = "OpalDriver")
  builder$append(server = "study2", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "CNSIM.CNSIM2", driver = "OpalDriver")
  builder$append(server = "study3",
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "CNSIM.CNSIM3", driver = "OpalDriver")
  logindata <- builder$build()
  
  # Log onto the remote Opal training servers
  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
  
  # Example 1: Get the correlation matrix of two continuous variables
  ds.cor(x="D$LAB_TSC", y="D$LAB_TRIG", type="combine", datasources = connections)
  
  # Example 2: Get the correlation matrix of the variables in a dataframe
  ds.dataFrame(x=c("D$LAB_TSC", "D$LAB_TRIG", "D$LAB_HDL", "D$PM_BMI_CONTINUOUS"), 
               newobj="D.new", check.names=FALSE, datasources=connections)
  ds.cor("D.new", type="combine", datasources = connections)

  # clear the Datashield R sessions and logout
  datashield.logout(connections)


## End(Not run)

datashield/dsBaseClient documentation built on Nov. 16, 2024, 2:07 p.m.