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ds.corTest.R
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ds.corTest.R
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#'
#' @title Tests for correlation between paired samples in the server-side
#' @description This is similar to the R base function \code{cor.test}.
#' @details Runs a two-sided Pearson test with a 0.95 confidence level.
#'
#' Server function called: \code{cor.test}
#' @param x a character string providing the name of a numerical vector.
#' @param y a character string providing the name of a numerical vector.
#' @param datasources a list of \code{\link{DSConnection-class}}
#' objects obtained after login. If the \code{datasources} argument is not specified
#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
#' @return \code{ds.corTest} returns to the client-side the results of the Pearson test.
#' @author DataSHIELD Development Team
#' @export
#' @examples
#' \dontrun{
#'
#' ## 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()
#'
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' # test for correlation
#' ds.corTest(x = "D$LAB_TSC",
#' y = "D$LAB_HDL",
#' datasources = connections[1]) #Only first server is used ("study1")
#'
#' # Clear the Datashield R sessions and logout
#' datashield.logout(connections)
#'
#' }
#'
#'
ds.corTest = function(x=NULL, y=NULL, datasources=NULL){
# look for DS connections
if(is.null(datasources)){
datasources <- datashield.connections_find()
}
if(is.null(x)){
stop("x=NULL. Please provide the names of the 1st numeric vector!", call.=FALSE)
}
if(is.null(y)){
stop("y=NULL. Please provide the names of the 2nd numeric vector!", call.=FALSE)
}
# the input variable might be given as column table (i.e. D$object)
# or just as a vector not attached to a table (i.e. object)
# we have to make sure the function deals with each case
objects <- c(x,y)
xnames <- extract(objects)
varnames <- xnames$elements
obj2lookfor <- xnames$holders
# check if the input object(s) is(are) defined in all the studies
for(i in 1:length(varnames)){
if(is.na(obj2lookfor[i])){
defined <- isDefined(datasources, varnames[i])
}else{
defined <- isDefined(datasources, obj2lookfor[i])
}
}
# call the internal function that checks the input object(s) is(are) of the same class in all studies.
for(i in 1:length(objects)){
typ <- checkClass(datasources, objects[i])
}
# call the server side function
cally <- call("corTestDS", x, y)
res.local <- DSI::datashield.aggregate(datasources, cally)
return(res.local)
}