tests/testthat/test-var-mpd.R

In treestats: Phylogenetic Tree Statistics

context("var pair distance")

test_that("usage", {
  set.seed(42)
  focal_tree <- ape::rphylo(n = 100, birth = 1, death = 0)

  a1 <- treestats::var_pair_dist(focal_tree)

  n <- length(focal_tree$tip.label)

  a2 <- cophenetic(focal_tree)
  a2 <- a2[lower.tri(a2)]
  a3 <- var(a2, na.rm = TRUE, use = "everything")
  a3 <- a3 * (length(a2) - 1) / length(a2)  # var calculates / (n - 1), we use n

  testthat::expect_equal(a1, a3)

  ltab <- treestats::phylo_to_l(focal_tree)
  testthat::expect_equal(treestats::var_pair_dist(focal_tree),
                         treestats::var_pair_dist(ltab))
})

test_that("wrong_object", {
  testthat::expect_error(
    treestats::var_pair_dist(10),
    "input object has to be phylo or ltable"
  )

  testthat::expect_error(
    treestats::var_pair_dist(list()),
    "input object has to be phylo or ltable"
  )
})