add the new ds.abs/absDS function

Author: davraam

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(ds.Boole)
+export(ds.abs)
 export(ds.asCharacter)
 export(ds.asDataMatrix)
 export(ds.asFactor)

R/ds.abs.R

@@ -0,0 +1,118 @@
+#'
+#' @title Computes the absolute values of a variable
+#' @description Computes the absolute values for a specified numeric or integer vector. 
+#' This function is similar to R function \code{abs}.
+#' @details The function calls the server-side function \code{absDS} that computes the 
+#' absolute values of the elements of a numeric or integer vector and assigns a new vector 
+#' with those absolute values on the server-side. The name of the new generated vector is 
+#' specified by the user through the argument \code{newobj}, otherwise is named by default to
+#' \code{abs.newobj}.
+#' @param x a character string providing the name of a numeric or an integer vector.
+#' @param newobj a character string that provides the name for the output variable
+#' that is stored on the data servers. Default name is set to \code{abs.newobj}. 
+#' @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.abs} assigns a vector for each study that includes the absolute values of
+#' the input numeric or integer vector specified in the argument \code{x}. The created vectors
+#' are stored in the servers.
+#' @author Demetris Avraam for DataSHIELD Development Team
+#' @export
+#' @examples
+#' \dontrun{
+#'
+#'   # 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: Generate a normally distributed variable with zero mean and variance equal
+#'   #  to one and then get their absolute values
+#'   ds.rNorm(samp.size=100, mean=0, sd=1, newobj='var.norm', datasources=connections)
+#'   # check the quantiles
+#'   ds.summary(x='var.norm', datasources=connections)
+#'   ds.abs(x='var.norm', newobj='var.norm.abs', datasources=connections)
+#'   # check now the changes in the quantiles
+#'   ds.summary(x='var.norm.abs', datasources=connections)  
+#'
+#'   # Example 2: Generate a sequence of negative integer numbers from -200 to -100
+#'   # and then get their absolute values
+#'   ds.seq(FROM.value.char = '-200', TO.value.char = '-100', BY.value.char = '1', 
+#'          newobj='negative.integers', datasources=connections)
+#'   # check the quantiles
+#'   ds.summary(x='negative.integers', datasources=connections)
+#'   ds.abs(x='negative.integers', newobj='positive.integers', datasources=connections)
+#'   # check now the changes in the quantiles
+#'   ds.summary(x='positive.integers', datasources=connections)
+#'
+#'   # clear the Datashield R sessions and logout
+#'   datashield.logout(connections) 
+#'
+#' }
+#'
+ds.abs <- function(x=NULL, newobj=NULL, datasources=NULL){
+
+  # look for DS connections
+  if(is.null(datasources)){
+    datasources <- datashield.connections_find()
+  }
+
+  if(is.null(x)){
+    stop("Please provide the name of the input object!", call.=FALSE)
+  }
+
+  # the input variable might be given as column table (i.e. D$x)
+  # or just as a vector not attached to a table (i.e. x)
+  # we have to make sure the function deals with each case
+  xnames <- extract(x)
+  varname <- xnames$elements
+  obj2lookfor <- xnames$holders
+
+  # check if the input object(s) is(are) defined in all the studies
+  if(is.na(obj2lookfor)){
+    defined <- isDefined(datasources, varname)
+  }else{
+    defined <- isDefined(datasources, obj2lookfor)
+  }
+
+  # call the internal function that checks the input object is of the same class in all studies.
+  typ <- checkClass(datasources, x)
+
+  # call the internal function that checks the input object(s) is(are) of the same class in all studies.
+  if(!('numeric' %in% typ) && !('integer' %in% typ)){
+      stop("Only objects of type 'numeric' or 'integer' are allowed.", call.=FALSE)
+  }
+
+  # create a name by default if the user did not provide a name for the new variable
+  if(is.null(newobj)){
+    newobj <- "abs.newobj"
+  }
+
+  # call the server side function that does the operation
+  cally <- call("absDS", x)
+  DSI::datashield.assign(datasources, newobj, cally)
+
+  # check that the new object has been created and display a message accordingly
+  finalcheck <- isAssigned(datasources, newobj)
+
+}