R/getPossibleCols.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Get possible column names for a studbook.
#'
## Copyright(c) 2017-2020 R. Mark Sharp
## This file is part of nprcgenekeepr
#' Pedigree curation function
#'
#'  @return A character vector of the possible columns that can be in a
#'  studbook.
#' The possible columns are as follows:
#' \itemize{
#' \item{id} {-- character vector with unique identifier for an individual}
#' \item{sire} {-- character vector with unique identifier for an
#' individual's father (\code{NA} if unknown).}
#' \item{dam} {-- character vector with unique identifier for an
#' individual's mother (\code{NA} if unknown).}
#' \item{sex} {-- factor {levels: "M", "F", "U"} Sex specifier for an
#' individual}
#' \item{gen} {-- integer vector with the generation number of the individual}
#' \item{birth} {-- Date or \code{NA} (optional) with the individual's birth
#' date}
#' \item{exit} {-- Date or \code{NA} (optional) with the individual's exit date
#' (death, or departure if applicable)}
#' \item{ancestry} {-- character vector or \code{NA} (optional) that indicates
#' the geographic population to which the individual belongs.}
#' \item{age} {-- numeric or \code{NA} (optional) indicating the individual's
#' current age or age at exit.}
#' \item{population} {-- an optional logical argument indicating whether or not
#' the \code{id} is part of the extant population.}
#' \item{origin} {-- character vector or \code{NA} (optional) that indicates
#' the name of the facility that the individual was imported from.
#' \code{NA} indicates the individual was not imported.}
#' \item{status} {-- an optional factor indicating the status of an individual
#' with levels \code{ALIVE}, \code{DEAD}, and \code{SHIPPED}.}
#' \item{condition} {--  character vector or \code{NA} (optional) that indicates
#' the restricted status of an animal. "Nonrestricted" animals
#' are generally assumed to be naive.}
#' \item{spf} {-- character vector or \code{NA} (optional) indicating the
#' specific pathogen-free status of an individual.}
#' \item{vasxOvx} {-- character vector indicating the vasectomy/ovariectomy
#' status of an animal where \code{NA} indicates an intact animal and all other
#' values indicate surgical alteration.}
#' \item{pedNum} {-- integer vector indicating generation numbers for each id,
#' starting at 0 for individuals lacking IDs for both parents.}}
#' @examples
#' \donttest{
#' library(nprcgenekeepr)
#' getPossibleCols()
#' }
#'
#' @export
getPossibleCols <- function() {
  c("id", "sire", "dam", "sex", "gen", "birth", "exit", "death", "age",
    "ancestry", "population", "origin", "status", "condition", "departure",
    "spf", "vasxOvx", "pedNum", "first", "second", "first_name",
    "second_name", "recordStatus")
}