tests/testthat/test-PartitionDistance.R

In Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures

library("TreeTools", quietly = TRUE)

data("sq_trees")

test_that("SplitStatus works", {
  expect_equal(c(length(sq_trees), 8), dim(SplitStatus(sq_trees)))
  expect_equal(c(length(sq_trees), 8), dim(SplitStatus(sq_trees, sq_trees$opposite_tree)))
  expect_equal(SplitStatus(sq_trees, sq_trees$ref_tree), SplitStatus(sq_trees))
})

test_that("Splits are compared", {
  expect_equal(c(N=12L, P1=6L, P2=6L, s=5L, d1=1L, d2=1L, r1=0L, r2=0L),
               SharedSplitStatus(TreeTools::UnshiftTree(
                 ape::drop.tip(sq_trees$move_one_near, 10),
                 list(ape::drop.tip(sq_trees$ref_tree, 11))))[2, ])
  expect_equal(SharedSplitStatus(BalancedTree(9)),
               PairSharedSplitStatus(BalancedTree(9), BalancedTree(9)))
  expect_equal(SharedSplitStatus(BalancedTree(9), PectinateTree(9)),
               PairSharedSplitStatus(BalancedTree(9), PectinateTree(9)))
  expect_equal(SharedSplitStatus(list(BalancedTree(9)), PectinateTree(9)),
               SharedSplitStatus(c(BalancedTree(9)), PectinateTree(9)))
})

test_that("CompareSplits() works", {
  splits9 <- as.Splits(BalancedTree(9))
  splits9Fewer <- splits9[[-(4:6)]]
  
  expect_error(CompareSplits(matrix(FALSE, 2, 2), matrix(TRUE, 3, 3)))
  expect_equal(c(N = 6, P1 = 3, P2 = 3, s=3, d1=0, d2=0, r1=0, r2=0),
               CompareSplits(splits9Fewer, splits9Fewer))
  expect_equal(c(N = 9, P1 = 3, P2 = 6, s=3, d1=0, d2=0, r1=0, r2=3),
               CompareSplits(splits9Fewer, splits9))
  
  splitsA <- as.Splits(ape::read.tree(text="((((a, b, c, c2), g), h), (d, (e, f)));"))
  splitsB <- as.Splits(ape::read.tree(text="(((((a, b), (c, c2)), h), g), (d, e, f));"))
  
  expect_equal(c(N=9L, P1=4L, P2=5L, s=2L, d1=1L, d2=1L, r1=1L, r2=2L),
               CompareSplits(splitsA, splitsB))
  expect_equal(c(tree = 5L),
               RawSymmetricDifference(CompareSplits(splitsA, splitsB),
                                      similarity = FALSE))
  
  splitsC <- as.Splits(ape::read.tree(text="(((a, d), e), (b, (f, c)));"))
  splitsD <- as.Splits(ape::read.tree(text="((a, b, c), (d, (e, f)));"))
  splitsU <- as.Splits(ape::read.tree(text="(a, b, c, d, e, f);"))
  
  
  expect_equal(c(N=5L, P1=3L, P2=2L, s=0L, d1=3L, d2=2L, r1=0L, r2=0L),
               CompareSplits(splitsC, splitsD))
  expect_equal(c(tree = 5L), 
               RawSymmetricDifference(CompareSplits(splitsC, splitsD), 
                                      similarity = FALSE))

  expect_equal(c(N=3L, P1=3L, P2=0L, s=0L, d1=0L, d2=0L, r1=3L, r2=0L),
               CompareSplits(splitsC, splitsU))
  
  expect_equal(c(N=2L, P1=0L, P2=2L, s=0L, d1=0L, d2=0L, r1=0L, r2=2L),
               CompareSplits(splitsU, splitsD))
  
  funnyNodes5 <- structure(list(
    edge = matrix(c(6, 6, 6, 8, 8, 7, 7,
                    1, 2, 8, 3, 7, 4, 5), 7L, 2L),
    tip.label = paste0("t", 1:5),
    Nnode = 3L), class = "phylo")
  expect_equivalent(c(4, 2, 2, 2, 0, 0, 0, 0),
                    CompareSplits(funnyNodes5, unroot(PectinateTree(5))))
})