Defines functions checkDataDir setDataDir getDefaultDataDir

Documented in getDefaultDataDir setDataDir

#' Guess the default data directory
#' The R drive will be mounted in different paths for different systems.
#' This function guesses the path to be used as default in setDataDir
#' @export
#' @return NULL
#' @examples \dontrun{
getDefaultDataDir <- function()

	d <- switch(Sys.info()['sysname'],
		Darwin = "/Volumes/ALSPAC-data/",
		Linux = "~/.gvfs/data/",
		Windows = "R:/Data"

#' Set the data directory
#' This function is automatically called upon loading the package through `library(alspac)`
#' It creates a global option called `alspac_data_dir` which is used by the \code{extractVars}
#' function to locate the alspac data files.
#' This function guesses the path to be used as default in setDataDir. The defaults are:
#' \itemize{
#' \item{Windows: R:/Data/Useful_data/current_R/}
#' \item{Mac: /Volumes/data/Useful_data/current_R/}
#' \item{Linux: ~/.gvfs/data/Useful_data/current_R/}
#' }
#' @param datadir The directory where the ALSPAC data can be found
#' @export
#' @return Null. Assigns the option alspac_data_dir
#' @examples \dontrun{
#' setDataDir() # This sets the path based on the operating system's default
#' setDataDir("/some/other/path/") # This is how to supply a path manually
setDataDir <- function(datadir=getDefaultDataDir())

checkDataDir <- function(datadir) {
    test <- file.exists(datadir)
    if(test) {
        if(all(file.exists(paste0(datadir, c("/Syntax", "/Current", "/Useful_data")))))
        else {
            stop("The specified data directory exists but it is not the correct directory. ",
                 "It should have the directories 'Syntax', 'Current' and 'Useful_data' contained within. ",
                 "It is normally located on the remote R drive, R:/Data/")
    } else {
        stop("The data directory ", datadir, " has NOT been found. ",
             "It is normally located on the remote R drive, R:/Data/. ",
             "You will be able to search for variables from the dictionary but unable to extract them from the data. ",
             "Please check that the R: drive has been mounted onto your computer through the UoB VPN. ",
             "Run setDataDir(<directory name>) to try again.")
explodecomputer/alspac documentation built on Feb. 27, 2021, 2:51 a.m.