tests/testthat/test_calcFE.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Copyright(c) 2017-2020 R. Mark Sharp
#' This file is part of nprcgenekeepr
context("calcFE")
library(testthat)
ped <- data.frame(
  id = c("A", "B", "C", "D", "E", "F", "G"),
  sire = c(NA, NA, "A", "A", NA, "D", "D"),
  dam = c(NA, NA, "B", "B", NA, "E", "E"),
  stringsAsFactors = FALSE
)
ped["gen"] <- findGeneration(ped$id, ped$sire, ped$dam)
ped$population <- getGVPopulation(ped, NULL)
pedFactors <- data.frame(
  id = c("A", "B", "C", "D", "E", "F", "G"),
  sire = c(NA, NA, "A", "A", NA, "D", "D"),
  dam = c(NA, NA, "B", "B", NA, "E", "E"),
  stringsAsFactors = TRUE
)
pedFactors["gen"] <- findGeneration(pedFactors$id, pedFactors$sire,
                                    pedFactors$dam)
pedFactors$population <- getGVPopulation(pedFactors, NULL)
fe <- calcFE(ped)
feFactors <- calcFE(pedFactors)
## Prior to forcing the pedigree to have id, sire, and dam as character vectors
## inside calcFE, the two calculations above with ped (characters) and
## feFactors (factors) resulted 2.9090 and 2.000 respectively.
##
## Used example from Analysis of Founder Representation in Pedigrees: Founder
## Equivalents and Founder Genome Equivalents.
## Zoo Biology 8:111-123, (1989) by Robert C. Lacy
## He presented 2.91 as the answer, which was not precise enough for this
## specific comparison.
test_that("calcFE correctly calculates the number of founder equivalents in
          the pedigree", {
            expect_equal(fe, feFactors)
            expect_equal(fe, 2.9090909091)
})