tests/testthat/test_betapart.R

In daijiang/dli55: Functions collected/wrote by Daijiang Li

context("test partitioning of phylogenetic beta diversity")

x = comm_a
x[x > 1] = 1
tol = 0.0001

test_that("testing phylo_betapart and betapart::phylo.beta.pair", {
  expect_equal(phylo_betapart(x, tree)$out_pair_jaccard, betapart::phylo.beta.pair(x, tree, "jaccard"), tolerance = tol)
  expect_equal(phylo_betapart(x, tree)$out_pair_sorensen, betapart::phylo.beta.pair(x, tree, "sorensen"), tolerance = tol)
  expect_equal(phylo_betapart(x, tree)$out_pair_jaccard$phylo.beta.jac, unifrac2(x, tree), tolerance = tol, check.attributes = F)
  expect_equal(phylo_betapart(x, tree)$out_multi_jaccard, betapart::phylo.beta.multi(x, tree, "jaccard"), tolerance = tol)
  expect_equal(phylo_betapart(x, tree)$out_multi_sorensen, betapart::phylo.beta.multi(x, tree), tolerance = tol)
})

# test_that("testing whether get_pd_beta works or not", {
#   expect_success(get_pd_alpha(x, tree, null.model = T, n.item = 10))
#   expect_success(get_pd_beta(x, tree, null.model = T, n.item = 10))
# })