R/filterAge.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Removes kinship values where an animal is less than the minAge
#'
## Copyright(c) 2017-2020 R. Mark Sharp
## This file is part of nprcgenekeepr
#' Part of Group Formation
#'
#' @param kin a dataframe with columns \code{id1}, \code{id2}, and
#' \code{kinship}. This is the kinship data reformatted from a matrix,
#' to a long-format table.
#' @param ped dataframe of pedigree information including the IDs listed
#' in "candidates".
#' @param minAge numeric value representing minimum years of age of
#' animals to retain.
filterAge <- function(kin, ped, minAge = 1) {
  kin$sort.col <- seq_len(nrow(kin))

  a1 <- merge(kin, ped, by.x = "id1", by.y = "id", all.x = TRUE, all.y = FALSE)
  a2 <- merge(kin, ped, by.x = "id2", by.y = "id", all.x = TRUE, all.y = FALSE)

  a1 <- a1[with(a1, order(sort.col)), "age"]
  a2 <- a2[with(a2, order(sort.col)), "age"]

  keep <- (((a1 >= minAge) | is.na(a1)) & ((a2 >= minAge) | is.na(a2)))

  kin$sort.col <- NULL
  kin <- kin[keep, ]
  if (nrow(kin) > 0)
    rownames(kin) <- seq_len(nrow(kin))
  return(kin)
}