fillGroupMembersWithSexRatio: Forms breeding group(s) with an effort to match a specified...

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Forms breeding group(s) with an effort to match a specified sex ratio

Description

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)

rmsharp/nprcmanager documentation built on Feb. 2, 2025, 12:45 a.m.