nprcmanager: Genetic Tools for Colony Management

#' Genetic Management Functions
#'
## Copyright(c) 2017-2020 R. Mark Sharp
## This file is part of nprcgenekeepr
#'
###############################################################################
#' @description Primary Data Structure --- Pedigree
#'
#' Contains studbook information for a number of individuals.
#' ASSUME: All IDs listed in the sire or dam columns must have a row entry in
#'   the id column
#' @seealso \code{\link{getIncludeColumns}} to get set of columns that can
#' be used in a pedigree file
#'
#' A Pedigree is a data frame within the \code{R} environment with the following
#' possible columns:
#' \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} {-- logical (optional)
#' Is the id 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 if other than
#' local.\code{NA} indicates the individual was not imported.}
#'}
#'
#' Pedigree File Testing Functions
#'
#' \itemize{
#' \item{\link{qcStudbook}} {--- Main pedigree curation function that performs
#' basic quality control on pedigree information}
#' \item{\link{fixColumnNames}} {--- Changes original column names and into
#' standardized names.}
#' \item{\link{checkRequiredCols}} {--- Examines column names, cols, to see if
#' all required column names are present.}
#' \item{\link{correctParentSex}} {--- Sets sex for animals listed as either a
#' sire or dam.}
#' \item{\link{getDateErrorsAndConvertDatesInPed}} {--- Converts columns of
#' dates in text form to \code{Date} object columns}
#' \item{\link{checkParentAge}} {--- Check parent ages to be at least
#'  \code{minParentAge}}
#' \item{\link{removeDuplicates}} {--- Remove duplicate records from pedigree}
#' }
#' Gene Dropping Function
#'
#' \itemize{
#' \item{\link{geneDrop}} {--- Performs a gene drop simulation based on the
#' provided pedigree information}
#' }
#' Genetic Value Analysis Functions
#'
#' Contains functions to calculate the kinship coefficient and genome
#' uniqueness for animals listed in a Pedigree table.
#' \itemize{
#' \item{\link{meanKinship}} {--- Calculates the mean kinship for each animal
#' in a kinship matrix}
#' \item {\link{calcA}} {--- Calculates \code{a}, the number of an individual's
#' alleles that are rare in each simulation.}
#' \item{\link{alleleFreq}} {--- Calculates the count of each allele in the
#' provided vector.}
#' \item{\link{calcFE}} {--- Calculates founder equivalents.}
#' \item{\link{calcFG}} {--- Calculates founder genome equivalents.}
#' \item{\link{calcFEFG}}{--- Returns founder equivalents \code{FE} and
#' \code{FG} as elements in a list.}
#' \item{\link{calcGU}} {--- Calculates genome uniqueness for each ID that is
#' part of the population.}
#' \item{\link{geneDrop}} {--- Performs a gene drop simulation based on the
#' pedigree information.}
#' \item{\link{chooseAlleles}} {--- Combines two vectors of alleles by randomly
#' selecting one allele or the other at each position.}
#' \item{\link{calcRetention}} {--- Calculates allelic retention.}
#' \item{\link{filterKinMatrix}} {--- Filters a kinship matrix to include only
#' the egos
#' listed in 'ids'}
#' \item{\link{kinship}} {--- Generates a kinship matrix}
#' \item{\link{reportGV}} {--- Generates a genetic value report for a provided
#' pedigree.}
#' }
#' Plotting Functions
#'
#' \itemize{
#' \item{\link{meanKinship}} {--- Calculates the mean kinship for each animal
#' in a kinship matrix}
#' }
#' Breeding Group Formation Functions
#'
#' \itemize{
#' \item{\link{meanKinship}} {--- Calculates the mean kinship for each animal
#' in a kinship matrix}
#' }
#' @docType package
#' @name nprcgenekeepr
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