tests/testthat/test-stability.R

In Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees

library('TreeTools', quietly = TRUE, warn.conflicts = FALSE)

test_that("TipInstability() error handling", {
  expect_error(TipInstability(as.phylo(0:3, 6), dev = 'error'))
  expect_error(TipInstability(as.phylo(0:3, 6), ave = 'error'))
})

test_that("TipInstability() null output", {
  expect_equal(TipInstability(BalancedTree(4)),
               setNames(rep(0, 4), paste0('t', 1:4)))
})

test_that("GraphGeodesic() works", {
  Test <- function (tr) {
    tr <- Preorder(tr)
    tr$edge.length <- rep(1, nrow(tr$edge))
    tips <- seq_along(tr$tip.label)
    expect_equal(unname(ape::dist.nodes(tr)[tips, tips]), GraphGeodesic(tr))
    expect_equal(log(GraphGeodesic(tr)), GraphGeodesic(tr, log = TRUE))
  }
  Test(BalancedTree(4))
  Test(BalancedTree(6))
  Test(PectinateTree(7))
  Test(CollapseNode(BalancedTree(101), 104:111))
  Test(as.phylo(201, 1201))
})

test_that("ColByStability()", {
  expect_error(ColByStability(list(BalancedTree(7), BalancedTree(8))))
  trees <- AddTipEverywhere(BalancedTree(8), 'Rogue')
  tipCol <- col2rgb(ColByStability(trees[3:6]))
  # plot(consensus(trees[3:6], p = 0.5), tip.col = ColByStability(trees[3:6]))
  expect_gt(tipCol[1, 'Rogue'], tipCol['red', 't1'])
  expect_equal(tipCol['t2'], tipCol['t1'])
})