Form breeding groups to match a target sex ratio

The sex ratio is the number of non-males (females and animals of other or unknown sex) per male. A male is placed only if he is at least minAge years old; a male younger than that, or with no birth date, is left out of the groups.

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 a single integer group number, 1 through numGp, as made by makeGroupNum.

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 ids.

minAge

integer value indicating the minimum age to consider in group formation. Pairwise kinships involving an animal younger than this age are ignored; an animal exactly this old is not ignored. There is no default.

numGp

integer value indicating the number of groups that should be formed from the list of IDs. There is no default.

sexRatio

numeric value indicating the number of non-males per male. Values from 0.5 to 20 in steps of 0.5 are typical, but the range is not enforced.

Value

The groupMembers list, with one character vector of animal IDs per group (numGp groups), each filled so that its sex ratio is as close as possible to the ratio specified by sexRatio.

Examples

library(nprcgenekeepr)
examplePedigree <- nprcgenekeepr::examplePedigree
examplePedigree <- examplePedigree[1:300, ] # Comment out for full example
ped <- qcStudbook(examplePedigree,
  minParentAge = 2L, reportChanges = FALSE,
  reportErrors = FALSE
)
#> Warning: The `minParentAge` argument of `qcStudbook()` is deprecated as of nprcgenekeepr
#> 2.0.0.
#> ℹ Use minSireAge and minDamAge instead.

kmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen, sparse = FALSE)
currentGroups <- list(1)
currentGroups[[1]] <- examplePedigree$id[1L:3L]
candidates <- examplePedigree$id[examplePedigree$status == "ALIVE"]
threshold <- 0.015625
kin <- getAnimalsWithHighKinship(kmat, ped, threshold, currentGroups,
  ignore = list(c("F", "F")), minAge = 1L
)
# 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 <- 1.0
numGp <- 1L
harem <- FALSE
sexRatio <- 0.0
withKin <- FALSE
groupMembers <- nprcgenekeepr::makeGroupMembers(numGp,
  currentGroups,
  candidates,
  ped,
  harem = harem,
  minAge = minAge
)
groupMembersStart <- groupMembers
grpNum <- nprcgenekeepr::makeGroupNum(numGp)

groupMembers <- fillGroupMembersWithSexRatio(
  candidates, groupMembers, grpNum, kin, ped, minAge, numGp,
  sexRatio = 1.0
)