R/setPopulation.R

In nprcgenekeepr: Genetic Tools for Colony Management

#' Population designation function
#'
## Copyright(c) 2017-2024 R. Mark Sharp
## This file is part of nprcgenekeepr
#' Part of the pedigree filtering toolset.
#'
#' @return An updated pedigree with the \code{population} column added or
#' updated by being set to \code{TRUE} for the animal IDs in \code{ped$id} and
#' \code{FALSE} otherwise.
#'
#' @param ped datatable that is the `Pedigree`. It contains pedigree
#' information. The \code{id} column is required.
#' @param ids character vector of IDs to be flagged as part of the population
#' under consideration.
#' @export
#' @examples
#' examplePedigree <- nprcgenekeepr::examplePedigree
#' breederPed <- qcStudbook(examplePedigree,
#'   minParentAge = 2,
#'   reportChanges = FALSE,
#'   reportErrors = FALSE
#' )
#' focalAnimals <- breederPed$id[!(is.na(breederPed$sire) &
#'   is.na(breederPed$dam)) &
#'   is.na(breederPed$exit)]
#' breederPed <- setPopulation(ped = breederPed, ids = focalAnimals)
#' nrow(breederPed[breederPed$population, ])
setPopulation <- function(ped, ids) {
  ped$population <- FALSE

  if (length(ids) == 0L) {
    ped$population <- TRUE
  } else {
    ped$population[ped$id %in% ids] <- TRUE
  }
  ped
}