R/getGVPopulation.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Get the population of interest for the Genetic Value analysis.
#'
## Copyright(c) 2017-2020 R. Mark Sharp
## This file is part of nprcgenekeepr
#' If user has limited the population of interest by defining \code{pop},
#' that information is incorporated via the \code{ped$population} column.
#'
#' @return A logical vector corresponding to the IDs in the vector of
#' animal IDs provided to the function in \code{pop}.
#'
#' @examples
#' \donttest{
#' ## Example from Analysis of Founder Representation in Pedigrees: Founder
#' ## Equivalents and Founder Genome Equivalents.
#' ## Zoo Biology 8:111-123, (1989) by Robert C. Lacy
#' library(nprcgenekeepr)
#' ped <- data.frame(
#' id = c("A", "B", "C", "D", "E", "F", "G"),
#' sire = c(NA, NA, "A", "A", NA, "D", "D"),
#' dam = c(NA, NA, "B", "B", NA, "E", "E"),
#' stringsAsFactors = FALSE
#' )
#' ped["gen"] <- findGeneration(ped$id, ped$sire, ped$dam)
#' ped$population <- getGVPopulation(ped, NULL)
#' }
#' @param ped the pedigree information in datatable format
#' @param pop character vector with animal IDs to consider as the population of
#' interest. The default is NULL.
#' @export
getGVPopulation <- function(ped, pop) {
  if (!is.null(pop)) {
    ped$population <- FALSE
    ped$population[ped$id %in% pop] <- TRUE
  } else if (is.null(ped$population)) {
    ped$population <- TRUE
  }
  ped$population
}