tests/testthat/test-int_to_tree.cpp.R

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

test_that("Failures are graceful", {
  expect_error(num_to_parent(10, 1), "`nTip` must be > 1")
  expect_error(num_to_parent(10, -1), "`nTip` must be > 1")
  expect_warning(num_to_parent(10, c(2, 3)),
                 "`nTip` should be a single integer")
  expect_error(num_to_parent(NA, 10), "`n` may not contain NA")
  expect_error(num_to_parent(-1, 10), "`n` may not be negative")
  
  expect_error(mixed_base_to_parent(10, 1), "`nTip` must be > 1")
  expect_error(mixed_base_to_parent(10, -1), "`nTip` must be > 1")
  expect_warning(mixed_base_to_parent(10, c(2, 3)),
                 "`nTip` should be a single integer")
  expect_error(mixed_base_to_parent(NA, 10), "`n` may not contain NA")
  expect_error(mixed_base_to_parent(-1, 10), "`n` may not be negative")
  
  expect_error(edge_to_num(1:10, 1:11, 6), "Parent and child .* same length")
  expect_error(edge_to_num(1:10, 1:10, 5), "nEdge must == nTip . nTip - 2")
  expect_error(edge_to_mixed_base(1:10, 1:11, 6),
               "Parent and child .* same length")
  expect_warning(expect_error(
    edge_to_mixed_base(1:10, 1:10, c(5, 6)),
    "nEdge must == nTip . nTip - 2"),
    "`nTip` should be a single integer"
    )
  expect_equal(as.phylo(0, 0), ZeroTaxonTree())
  
  expect_error(as.phylo(0, -1), "`nTip` may not be negative")
})

test_that("Edge cases handled", {
  expect_equal(SingleTaxonTree("singleton"), as.phylo(0, 1, "singleton"))
  expect_true(all.equal(BalancedTree(2), as.phylo(0, 2)))
  expect_equal(structure(as.integer64(0L), nTip = 2L, tip.label = c("t1", "t2"),
                         class = c("TreeNumber", "integer64")),
               as.TreeNumber(as.phylo(0, 2)))
  expect_equal(structure(integer64(1), nTip = 1L, tip.label = "t1",
                         class = c("TreeNumber", "integer64")),
               as.TreeNumber(SingleTaxonTree()))
})

test_that("Trees generated okay", {
  expect_true(all.equal(
    Preorder(ape::read.tree(text=("(0, (4, ((1, 5), (2, 3))));"))),
    as.phylo(10, 6, 0:5)))
  expect_equal(as.TreeNumber("10", 6, 0:5),
               as.TreeNumber(as.phylo.numeric(10, 6, 0:5)))
  Test <- function(i, nTip) {
    expect_equal(as.integer64(i),
                 as.integer64(as.TreeNumber(as.phylo(i, nTip, seq_len(nTip) - 1L))))
  }
  xx <- lapply(0:104, Test, 6)
  xx <- lapply(seq_len(NUnrooted(7)) - 1L, Test, 7)
  xx <- lapply(floor(runif(48) * NUnrooted(8)), Test, 8)
  xx <- lapply(floor(runif(48) * NUnrooted(10)), Test, 10)
  xx <- lapply(floor(runif(48) * NUnrooted(12)), Test, 12)

  nTip <- 14L
  treeNumber <- as.TreeNumber("123456789876", nTip, seq_len(nTip) - 1L)
  expect_equal(treeNumber, as.TreeNumber(as.phylo(treeNumber)))
  treeNumber <- as.TreeNumber("123456789876", nTip, seq_len(nTip) - 1L)
  expect_equal(treeNumber, as.TreeNumber(as.phylo(treeNumber)))
  
  expect_equal
})