addAnimalsWithNoRelative: Adds an NA value for all animals without a relative

In nprcgenekeepr: Genetic Tools for Colony Management

Adds an NA value for all animals without a relative

Description

This allows kin to be used with setdiff when there are no relatives otherwise an error would occur because kin[['animal_with_no_relative']] would not be found. See the following: in groupAddAssign

Usage

addAnimalsWithNoRelative(kin, candidates)

Arguments

kin	dataframe with kinship values
candidates	character vector of IDs of the animals available for use in the group.

Details

\code{available[[i]] <- setdiff(available[[i]], kin[[id]])}

Value

A dataframe with kinships in long form after adding a row for each animal without a relative.

Examples

library(nprcgenekeepr)
qcPed <- nprcgenekeepr::qcPed
ped <- qcStudbook(qcPed,
  minParentAge = 2.0, reportChanges = FALSE,
  reportErrors = FALSE
)
kmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen, sparse = FALSE)
currentGroups <- list(1L)
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 = 1.0
)
# 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)
length(kin) # should be 259
kin[["0DAV0I"]] # should have 34 IDs

nprcgenekeepr documentation built on June 8, 2025, 10:55 a.m.