tests/testthat/test-NNI.R

In TreeSearch: Phylogenetic Analysis with Discrete Character Data

test_that("Errors fail gracefully", {
  expect_error(nni(TreeTools::BalancedTree(2)$edge, 0, 0))
})

test_that("cNNI()", {
  tr <- Preorder(root(TreeTools::BalancedTree(letters[1:7]), "a", resolve.root = TRUE))
  expect_equal(ape::read.tree(text="(a,(b,((c,d),((e,g),f))));"),
               cNNI(tr, 0, 1)) # Edge "9"
  expect_equal(ape::read.tree(text="(a,(b,((c,d),((f,g),e))));"),
               cNNI(tr, 0, 0)) # Edge "9"
  expect_equal(cNNI(tr, 0, 1), cNNI(tr, 4, 1))
  expect_equal(ape::read.tree(text="(a, (b, (g, ((c, d), (e, f)))));"), # Edge 8
               cNNI(tr, 1, 1))
  expect_equal(cNNI(tr, 1, 1), cNNI(tr, 1, 3))
  expect_equal(ape::read.tree(text="(a, (b, ((e, f), ((c, d), g))));"), # Edge 8
               cNNI(tr, 1, 2))
  expect_equal(cNNI(tr, 1, 2), cNNI(tr, 1, 0))
  expect_equal(ape::read.tree(text="(a, (b, (d, (c, (g, (e, f))))));"), # Edge 5
               cNNI(tr, 2, 1))
  expect_equal(ape::read.tree(text="(a, ((b, (c, d)), ((e, f), g)));"), # Edge 4
               cNNI(tr, 3, 1))
  suppressWarnings(RNGversion("3.5.0"))
  set.seed(0) # sample.int gives 4, 1
  expect_equal(cNNI(tr, 0, 1), cNNI(tr))
})