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ds.log.R
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ds.log.R
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#'
#' @title Computes logarithms in the server-side
#' @description Computes the logarithms for a specified numeric vector.
#' This function is similar to the R \code{log} function. by default natural logarithms.
#' @details Server function called: \code{log}
#' @param x a character string providing the name of a numerical vector.
#' @param base a positive number, the base for which logarithms are computed.
#' Default \code{exp(1)}.
#' @param newobj a character string that provides the name for the output variable
#' that is stored on the server-side. Default \code{log.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.log} returns a vector for each study of the transformed values for the numeric vector
#' specified in the argument \code{x}. The created vectors are stored in the server-side.
#' @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()
#'
#' # Log onto the remote Opal training servers
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' # Calculating the log value of the 'PM_BMI_CONTINUOUS' variable
#'
#' ds.log(x = "D$PM_BMI_CONTINUOUS",
#' base = exp(2),
#' newobj = "log.PM_BMI_CONTINUOUS",
#' datasources = connections[1]) #only the first Opal server is used (study1)
#'
#' # clear the Datashield R sessions and logout
#' datashield.logout(connections)
#'}
#'
ds.log <- function(x=NULL, base=exp(1), newobj=NULL, datasources=NULL){
# look for DS connections
if(is.null(datasources)){
datasources <- datashield.connections_find()
}
# ensure datasources is a list of DSConnection-class
if(!(is.list(datasources) && all(unlist(lapply(datasources, function(d) {methods::is(d,"DSConnection")}))))){
stop("The 'datasources' were expected to be a list of DSConnection-class objects", call.=FALSE)
}
if(is.null(x)){
stop("Please provide the name of the input vector!", call.=FALSE)
}
# check if the input object is defined in all the studies
isDefined(datasources, x)
# call the internal function that checks the input object is of the same class in all studies.
typ <- checkClass(datasources, x)
# the input object must be a vector
if(!('integer' %in% typ) & !('numeric' %in% typ)){
message(paste0(x, " is of type ", typ, "!"))
stop("The input object must be an integer or numeric vector.", call.=FALSE)
}
# create a name by default if user did not provide a name for the new variable
if(is.null(newobj)){
newobj <- "log.newobj"
}
# call the server side function that does the job
cally <- paste0("log(", x, ",", base, ")")
DSI::datashield.assign(datasources, newobj, as.symbol(cally))
# check that the new object has been created and display a message accordingly
finalcheck <- isAssigned(datasources, newobj)
}