Nothing
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")
})
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