Forms breeding group(s) with an effort to match a specified sex ratio — fillGroupMembersWithSexRatio • nprcgenekeepr

The sex ratio is the ratio of females to males.

Usage

fillGroupMembersWithSexRatio(
  candidates,
  groupMembers,
  grpNum,
  kin,
  ped,
  minAge,
  numGp,
  sexRatio
)

Arguments

candidates: character vector of IDs of the animals available for use in the group.
groupMembers: list initialized and ready to receive groups with the desired sex ratios that are created within this function
grpNum: is a list numGp long with each member an integer vector of 1:numGp.
kin: list of animals and those animals who are related above a threshold value.
ped: dataframe that is the Pedigree. It contains pedigree information including the IDs listed in candidates.
minAge: integer value indicating the minimum age to consider in group formation. Pairwise kinships involving an animal of this age or younger will be ignored. Default is 1 year.
numGp: integer value indicating the number of groups that should be formed from the list of IDs. Default is 1.
sexRatio: numeric value indicating the ratio of females to males x from 0.5 to 20 by increments of 0.5.

Value

A list containing one character vector of animal IDs such that the sex ratio of the group is as close as possible to the ratio specified by sexRatio.

Examples

examplePedigree <- nprcgenekeepr::examplePedigree
ped <- qcStudbook(examplePedigree, minParentAge = 2, reportChanges = FALSE,
                  reportErrors = FALSE)

kmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen, sparse = FALSE)
currentGroups <- list(1)
currentGroups[[1]] <- examplePedigree$id[1:3]
candidates <- examplePedigree$id[examplePedigree$status == "ALIVE"]
threshold <- 0.015625
kin <- getAnimalsWithHighKinship(kmat, ped, threshold, currentGroups,
                                 ignore = list(c("F", "F")), minAge = 1)
# Filtering out candidates related to current group members
conflicts <- unique(c(unlist(kin[unlist(currentGroups)]),
                      unlist(currentGroups)))
candidates <- setdiff(candidates, conflicts)

kin <- addAnimalsWithNoRelative(kin, candidates)

ignore <- NULL
minAge <- 1
numGp <- 1
harem <- FALSE
sexRatio <- 0
withKin <- FALSE
groupMembers <- nprcgenekeepr:::makeGroupMembers(numGp,
                                                 currentGroups,
                                                 candidates,
                                                 ped,
                                                 harem = harem,
                                                 minAge = minAge)
groupMembersStart <- groupMembers
grpNum <- nprcgenekeepr:::makeGrpNum(numGp)

groupMembers <- fillGroupMembersWithSexRatio(
  candidates, groupMembers, grpNum, kin, ped, minAge, numGp, sexRatio = 1)