tests/testthat/test-polyploids.R

In poppr: Genetic Analysis of Populations with Mixed Reproduction

context("Polyploid Tests")

test_that("recode_polyploids works as expected", {
  testdf <- data.frame(test = c("00/20/23/24", "20/24/26/43"))
  testgid <- df2genind(testdf, ploidy = 4, sep = "/")
  testrec <- recode_polyploids(testgid)
  expect_equal(testgid@ploidy, testrec@ploidy)
  expect_equivalent(testgid@tab[2, -1], testrec@tab[2, ])
  expect_equivalent(testrec@tab[1, ], c(1, 1, 1, 0, 0))
})

test_that("recode_polyploids won't take diploid data", {
  data(nancycats, package = "adegenet")
  expect_warning(
    recode_polyploids(nancycats),
    "Input is not a polyploid data set, returning original."
  )
})

test_that("recode_polyploids will go there and back again", {
  skip_on_cran()
  data(Pinf, package = "poppr")
  expect_warning(
    pr <- recode_polyploids(Pinf, addzero = TRUE),
    "addzero = TRUE"
  )
  pr <- recode_polyploids(Pinf, newploidy = TRUE)
  expect_output(
    show(pr),
    "86 diploid \\(55\\) and triploid \\(31\\) individuals"
  )
  # Printing is so weird...
  expect_output(print(pr), "diploid \\(55\\)")
  expect_that(length(unique(ploidy(pr))), equals(2))
  zpr <- recode_polyploids(pr, addzero = TRUE)
  expect_that(length(unique(ploidy(zpr))), equals(1))
  przpr <- recode_polyploids(zpr, newploidy = TRUE)
  rectab <- tab(przpr)
  expect_equivalent(rectab[, colnames(tab(pr))], tab(pr))
})


test_that("as.genambig will convert correctly", {
  skip_on_cran()
  testthat::skip_if_not_installed("polysat")
  data(Pinf, package = "poppr")
  expect_is(ps <- as.genambig(Pinf), "genambig")
})

test_that("haplodiploids will work", {
  skip_on_cran()
  df <- matrix(c("0/2", "2/1", "3/0", "0/1", "2/2", "1/1"), nrow = 3)
  x <- df2genind(df, sep = "/")
  expect_equal(ploidy(x), rep(2L, 3))
  y <- recode_polyploids(x, newploidy = TRUE)
  expect_equal(ploidy(y), c(1L, 2L, 2L))
  z <- recode_polyploids(y, addzero = TRUE)
  expect_equal(tab(x), tab(z))
})