R/createExampleFiles.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Creates a folder with CSV files containing example pedigrees and ID lists
#' used to demonstrate the package.
#'
## Copyright(c) 2017-2020 R. Mark Sharp
## This file is part of nprcgenekeepr
#' Creates a folder named \code{~/tmp/ExamplePedigrees} if it does not already
#' exist. It then proceeds to write each example pedigree into a CSV file named
#' based on the name of the example pedigree.
#'
#' @return A vector of the names of the files written.
#'
#' @examples
#' \donttest{
#' library(nprcgenekeepr)
#' files <- createExampleFiles()
#' }
#' @export
createExampleFiles <- function() {
  examplePedigrees <-
    list(examplePedigree = nprcgenekeepr::examplePedigree,
         focalAnimals = nprcgenekeepr::focalAnimals,
         lacy1989Ped = nprcgenekeepr::lacy1989Ped,
         pedDuplicateIds = nprcgenekeepr::pedDuplicateIds,
         pedFemaleSireMaleDam = nprcgenekeepr::pedFemaleSireMaleDam,
         pedGood = nprcgenekeepr::pedGood,
         pedInvalidDates = nprcgenekeepr::pedInvalidDates,
         pedMissingBirth = nprcgenekeepr::pedMissingBirth,
         pedOne = nprcgenekeepr::pedOne,
         pedSameMaleIsSireAndDam = nprcgenekeepr::pedSameMaleIsSireAndDam,
         pedSix = nprcgenekeepr::pedSix,
         pedWithGenotype = nprcgenekeepr::pedWithGenotype,
         qcBreeders = as.data.frame(nprcgenekeepr::qcBreeders, drop = FALSE),
         qcPed = nprcgenekeepr::qcPed,
         smallPed = nprcgenekeepr::smallPed)
  pedigreeDir <-  tempdir()
  suppressWarnings(dir.create(pedigreeDir))
  pedigreeDir <- paste0(pedigreeDir, "/ExamplePedigrees")
  suppressWarnings(dir.create(pedigreeDir))
  message(paste0("Example pedigree files ",
                 get_and_or_list(names(examplePedigrees)),
                 " will be created in ", pedigreeDir, ".\n"))
  saveDataframesAsFiles(examplePedigrees, baseDir = pedigreeDir, "csv")
}