tests/testthat/test-ArtificialExtinction.R

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

nTax <- 6L
dataset <- matrix(seq_len(nTax), nrow = nTax, ncol = 6,
                  dimnames = list(LETTERS[1:nTax], 1:6))
dataset[4, 3:5] <- "-"
dataset[5:6, 4:6] <- "?"
dataset[6, 3] <- "?"

test_that("Errors are handled", {
  expect_error(ArtificialExtinction(dataset, "A", "E", replaceAmbiguous = "INVALID"))
  expect_error(ArtificialExtinction(dataset, "A", "E", replaceCoded = "INVALID"))
})

test_that("Replacements ok", {
  expectation <- matrix(rep("?", 6), 2, 3, dimnames = list(c("A", "B"), 4:6))
  expect_equal(expectation,
               ArtificialExtinction(dataset, subject = c("A", "B"),
                                    template = "E",
                                    replaceAmbiguous = "ambig")[1:2, 4:6])

  expectation[] <- 1
  colnames(expectation) <- NULL
  expect_equal(PhyDatToMatrix(ArtificialExtinction(
                 MatrixToPhyDat(dataset),
                 c("A", "B"), "F", "unif", sampleFrom = "A"
                ))[1:2, 4:6],
               expectation
               )

  expect_true(all(!"?" == ArtificialExtinction(
    dataset[-6, ], 1:2, 5, "freq"
    )[1:2, 4:6]))


  expect_true(all(ArtificialExtinction(dataset, subject = "E", template = "F",
                                       replaceAmbiguous = "binary")["E", 3:6] %in% 0:1))

  expect_equal(setNames(rep("?", 3), 4:6),
               ArtificialExtinction(dataset, subject = "E", template = "F",
                                    replaceAmbiguous = "binary",
                                    replaceAll = FALSE)["E", 4:6])

  nChar <- 100
  dataset <- rbind(subj = c(rep(2, nChar)),
                   templ = c(rep(3, nChar / 2), rep("?", nChar / 2)))
  suppressWarnings(expect_gt(chisq.test(as.integer(
    ArtEx(dataset, 1, 2, "binary", "binary")[1, ]))$p.value, 0.05))
})