R/makeRelationsClassesTable.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Make relation classes table from \code{kin} dataframe.
#'
## Copyright(c) 2017-2020 R. Mark Sharp
## This file is part of nprcgenekeepr
#' From Relations
#'
#' @return A data.frame with the number of instances of following relationship
#' classes: Parent-Offspring, Full-Siblings, Half-Siblings,
#' Grandparent-Grandchild, Full-Cousins, Cousin - Other, Full-Avuncular,
#' Avuncular - Other, Other, and No Relation.
#'
#' @examples
#' \donttest{
#' library(nprcgenekeepr)
#' suppressMessages(library(dplyr))
#'
#' qcPed <- nprcgenekeepr::qcPed
#' bkmat <- kinship(qcPed$id, qcPed$sire, qcPed$dam, qcPed$gen,
#'                  sparse = FALSE)
#' kin <- convertRelationships(bkmat, qcPed)
#' relClasses <- makeRelationClassesTable(kin)
#' relClasses$`Relationship Class` <-
#'    as.character(relClasses$`Relationship Class`)
#' relClassTbl <- kin[!kin$relation == "Self", ] %>%
#'   group_by(relation) %>%
#'   summarise(count = n())
#' relClassTbl
#' }
#'
#' @param kin a dataframe with columns \code{id1}, \code{id2}, \code{kinship},
#' and \code{relation}. It is a long-form table of pairwise kinships, with
#' relationship categories included for each pair.
#' @export
makeRelationClassesTable <- function(kin) {
  rel.class <- c("Self", "Parent-Offspring", "Full-Siblings", "Half-Siblings",
                 "Grandparent-Grandchild", "Full-Cousins", "Cousin - Other",
                 "Full-Avuncular", "Avuncular - Other", "Other", "No Relation")

  kin <- kin[kin$relation != "Self", ]
  r <- as.data.frame(table(kin$relation))
  colnames(r) <- c("Relationship Class", "Frequency")

  rel.class <- rel.class[rel.class %in% r[, "Relationship Class"]]
  return(r[match(rel.class, r[, "Relationship Class"]), ])
}