#' Copyright(c) 2017-2024 R. Mark Sharp
#' This file is part of nprcgenekeepr
context("calcRetention")
library(testthat)
library(stringi)
data("lacy1989Ped")
data("lacy1989PedAlleles")
ped <- lacy1989Ped
alleles <- lacy1989PedAlleles
retention <- calcRetention(ped, alleles)

## Prior to forcing the pedigree to have id, sire, and dam as character vectors
## inside calcFG, the two calculations above with ped (characters) and
## feFactors (factors) resulted 2.189855 and 1.857998 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 2.18 as the answer, which was truncated and not precise enough
## for this specific comparison.
test_that(stri_c(
  "calcRetention correctly calculates mean number of alleles retained from ",
  "each founder"), {
    expect_equal(retention[["A"]], 0.7500)
    expect_equal(retention[["B"]], 0.7507)
    expect_equal(retention[["E"]], 0.7452)
  })