tests/testthat/test-combinatorics.R

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

test_that("Factorials are calculated correctly", {
  expect_equal(c(1L, 1L, 1L, 2L, 3L, 2L * 4L, 3L * 5L,
                 2L * 4L * 6L, 3L * 5L * 7L,
                 2L * 4L * 6L * 8L,
                 3L * 5L * 7L * 9L,
                 2L * 4L * 6L * 8L * 10L,
                 3L * 5L * 7L * 9L * 11L),
               as.integer(DoubleFactorial((-1):11)))
  expect_equal(floor(doubleFactorials[1:19]),
               ceiling(doubleFactorials[1:19]))
  expect_equal(doubleFactorials[1:20], DoubleFactorial(1:20))
  expect_equal(LnDoubleFactorial(-1:10), log(DoubleFactorial(-1:10)))
  expect_equal(logDoubleFactorials[1:20], log(DoubleFactorial(1:20)))
  expect_equal(log2DoubleFactorials[1:20], log2(DoubleFactorial(1:20)))
  expect_equal(LnDoubleFactorial(50001) - log(50001), LnDoubleFactorial.int(49999L))
  expect_equal(Log2DoubleFactorial(50000 - 2 + -1:1) + log2(50000 + -1:1),
               Log2DoubleFactorial(50000 + -1:1))
  expect_equal(LnDoubleFactorial.int(-1L), 0L)
  expect_equal(LnRooted.int(-1L), 0L)

  expect_error(DoubleFactorial(301))
})

test_that("N consistent with splits calculated correctly", {
  Test <- function(nExpectation, ...) {
    expect_equal(nExpectation, NUnrootedSplits(...))
    expect_equal(log(nExpectation), LnUnrootedSplits(...))
    expect_equal(log2(nExpectation), Log2UnrootedSplits(...))
  }
  Test(NUnrooted(8), 8)
  Test(NRooted(3) * NRooted(5), 3, 5)
  Test(doubleFactorials[12 + 12 - 5] / doubleFactorials[17] *
         doubleFactorials[4 + 4 - 3] ^ 3, c(4, 4, 4))


  Test <- function(...) {
    splits <- c(...)
    if (length(splits) < 3L) {
      stop("Designed to test through to NUnrootedMult")
    }
    splits <- splits[splits > 0]
    totalTips <- sum(splits)
    expect_equal(
      round(DoubleFactorial(totalTips + totalTips - 5L) /
              DoubleFactorial(2L * (totalTips - length(splits)) - 1L)
              * prod(DoubleFactorial(splits + splits - 3L))),
      NUnrootedSplits(...))
    expect_equal(log(NUnrootedSplits(...)), LnUnrootedSplits(...))
  }
  Test(49:51)
  Test(29:32)
  Test(1:10)
  expect_error(NUnrootedSplits(c(10, 152)))

})

test_that("N[Un]RootedMult() works", {
  Test <- function(...) {
    splits <- c(...)
    splits <- splits[splits > 0]
    totalTips <- sum(splits)
    # Carter et al. 1990, Theorem 2 in full
    expect_equal(1, NUnrootedMult(...) /
                   round(DoubleFactorial(totalTips + totalTips - 5L) /
                         DoubleFactorial(2L * (totalTips - length(splits)) - 1L)
                       * prod(DoubleFactorial(splits + splits - 3L))),
                 tolerance = 1e-7)
  }
  expect_equal(NUnrootedMult(c(5, 10)), NUnrootedMult(5, 10))
  Test(5, 10)
  Test(5, 0, 10)
  Test(5, 5, 10)
  expect_equal(0L, NUnrootedMult(0, 0))
  Test(0:5)
  Test(c(0, 10))
  Test(10)
})

test_that("Log rooted calculated correctly", {
  expect_equal(Log2Rooted(10:30), LnRooted(10:30) / log(2))
  expect_equal(Log2Rooted(10:30), Log2Rooted.int(10:30))
})

test_that("SPR distances calculated correctly", {
  expect_equal(0L, N1Spr(0))
  expect_equal(c(rep(0L, 3), 2L * (3:10 - 3L) * (2L * 3:10 - 7L)),
               vapply(0:10, N1Spr, integer(1)))
  expect_equal(-log2((1L + N1Spr(0:10)) / NUnrooted(0:10)), IC1Spr(0:10))
})