tests/testthat/test-private.R

In poppr: Genetic Analysis of Populations with Mixed Reproduction

context("Private Allele Tests")

data("Pinf", package = "poppr")

test_that("Private alleles can be calculated for hierarchies", {
  by_continent <- private_alleles(Pinf, all ~ Continent)
  by_country   <- private_alleles(Pinf, all ~ Country)
  expect_true(nrow(by_continent) <= nPop(setPop(Pinf, ~Continent)))
  expect_true(nrow(by_country) <= nPop(setPop(Pinf, ~Country)))
})

test_that("Private alleles can be tabluated over loci", {
  locus_dose <- private_alleles(Pinf, locus ~ .)
  locus_nodose <- private_alleles(Pinf, locus ~ ., count.alleles = FALSE)
  expect_that(ncol(locus_dose), equals(ncol(locus_nodose)))
  expect_true(all(locus_nodose <= locus_dose))
})

test_that("Private alleles can be tabulated over individuals", {
	skip_on_cran()
	res <- private_alleles(Pinf, level = "indiv")
	expect_is(res, "matrix")
})

test_that("Private alleles can handle genpop objects", {
	skip_on_cran()
	pinfpop <- genind2genpop(Pinf, quiet = TRUE)
	expect_is(private_alleles(pinfpop), "matrix")
})

test_that("Private alleles throws appropriate errors", {
	skip_on_cran()
	expect_error(private_alleles(Pinf, LOCUS ~ .), "Left hand side of LOCUS \\~ \\.")
	expect_error(private_alleles(Pinf, locus ~ people), "strata:.+?people")
})