tests/testthat/test_addAnimalsWithNoRelative.R

In nprcgenekeepr: Genetic Tools for Colony Management

#' Copyright(c) 2017-2024 R. Mark Sharp
#' This file is part of nprcgenekeepr
context("addAnimalsWithNoRelative")
library(testthat)
examplePedigree <- nprcgenekeepr::examplePedigree
ped <- qcStudbook(examplePedigree,
  minParentAge = 2L, reportChanges = FALSE,
  reportErrors = FALSE
)
kmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen, sparse = FALSE)
currentGroups <- list(1L)
currentGroups[[1L]] <- 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 = 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)

test_that("addAnimalsWithNoRelative adds correct animals", {
  expect_length(kin, 2416L)
  expect_length(kin[["1SPLS8"]], 14L)
})