tests/testthat/test-spic.R

In Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees

test_that("Roguehalla() handles odd input", {
  trees <- list(ape::read.tree(text = '(a, (b, (c, (d, (e, X)))));'),
                ape::read.tree(text = '((a, X), (b, (c, (d, e))));'))
  ic <- ConsensusInfo(lapply(trees, DropTip, 'X'), 'p', p = 0.5)
  expect_equal(data.frame(num = 0:1,
                          taxNum = c(NA_character_, '6'),
                          taxon = c(NA_character_, 'X'),
                          rawImprovement = c(NA, ic),
                          IC = c(0, ic),
                          stringsAsFactors = FALSE),
                Roguehalla(trees))

  expect_error(RogueTaxa(trees, info = 'Error'))
  expect_error(RogueTaxa(trees, return = 'Error'))
  expect_equal(data.frame(num = 0,
                          taxNum = NA_character_,
                          taxon = NA_character_,
                          rawImprovement = NA_real_,
                          IC = SplitwiseInfo(trees[[1]]),
                          stringsAsFactors = FALSE),
               Roguehalla(trees[[1]]))
  expect_error(Roguehalla(trees = 'Error'))
})

test_that("QuickRogue()", {
  expect_error(QuickRogue("Error"))

  trees <- TreeTools::AddTipEverywhere(TreeTools::BalancedTree(8), 'Rogue')
  expect_equal(2L, nrow(QuickRogue(trees)))
  expect_equal(1L, nrow(QuickRogue(trees, neverDrop = c('t2', 'Rogue'))))
  expect_equal(2L, nrow(QuickRogue(trees, neverDrop = 't1')))
  expect_equal(QuickRogue(trees, 'phy'), QuickRogue(trees, 'spic'))
  expect_equal(QuickRogue(trees, 'phy', p = 1.0),
               QuickRogue(trees, 'spic', p = 1.0))
  expect_equal(data.frame(num = 0,
                          taxNum = NA_character_,
                          taxon = NA_character_,
                          rawImprovement = NA_real_,
                          IC = SplitwiseInfo(trees[[1]]),
                          stringsAsFactors = FALSE),
               QuickRogue(trees[[1]]))

  expect_equal(ClusteringInfo(trees[[1]]),
               QuickRogue(trees[[1]], info = 'scic')[, 'IC'])
  expect_equal(SplitwiseInfo(trees[[1]]),
               QuickRogue(trees[[1]], info = 'spic')[, 'IC'])
  expect_equal(0, QuickRogue(trees, fullSeq = TRUE)[10, 'IC'])
})

test_that("Rogues found", {

  library("TreeTools", quietly = TRUE)
  trees <- AddTipEverywhere(BalancedTree(8), 'Rogue')
  instab <- TipInstability(trees)
  expect_equal('Rogue', names(which.max(instab)))

  ci <- TipVolatility(trees)
  expect_equal('Rogue', names(which.max(ci)))

  dists <- TreeDist::PhylogeneticInfoDistance(trees, normalize = TRUE)
  expect_equal(mean(dists) - 0, max(ci))

  expect_equal(8L, NTip(RogueTaxa(trees, return = 'TREE')))
  expect_equal(9L, NTip(RogueTaxa(trees, neverDrop = 'Rogue', return = 'Tree')))
  expect_equal(8L, NTip(RogueTaxa(trees, neverDrop = 't1', return = 'Tree')))
  expect_equal(8L, NTip(RogueTaxa(trees, info = 'fsp', return = 'tr')))
  expect_equal(2L, nrow(Roguehalla(trees, 1)))
  expect_equal(8L, NTip(RogueTaxa(trees, info = 'sp', return = 'tr')))


  trees[] <- lapply(trees, AddTip, 'Rogue', 'Rogue2')
  ci <- TipVolatility(trees)
  expect_equal(c('Rogue', 'Rogue2'), names(ci[ci == max(ci)]))

  # Interesting aside: Majority rule consensus favours balanced splits!
  bc <- RogueTaxa(trees, info = 'fsp', return = 'TR')
  expect_equal(10L, NTip(bc))
  expect_equal(9L, bc$Nnode)

  bc <- RogueTaxa(trees, info = 'fsc', return = 'TR')
  expect_equal(10L, NTip(bc))
  expect_equal(9L, bc$Nnode)

  bc <- RogueTaxa(trees[-11], info = 'fsp', return = 'TR')
  expect_equal(8L, NTip(bc))
  expect_equal(7L, bc$Nnode)

  expect_equal(1L, nrow(RogueTaxa(trees[-11], drop = 1, 'r')))
  expect_equal(1L, nrow(RogueTaxa(trees[-11], drop = 1, 'phy')))
  expect_equal(1L, nrow(RogueTaxa(trees[-11], drop = 1, 'clu')))
  expect_equal(2L, nrow(RogueTaxa(trees[-11], drop = 2, 'r')))
  expect_equal(2L, nrow(RogueTaxa(trees[-11], drop = 2, 'sp')))
  expect_equal(2L, nrow(RogueTaxa(trees[-11], drop = 2, 'sci')))
  # Check trees are created
  expect_equal(8L, NTip(RogueTaxa(trees[-11], dr = 2, ret = 'Tr', 'r')))
  expect_equal(8L, NTip(RogueTaxa(trees[-11], dr = 2, ret = 'Tr', 'sp')))
  expect_equal(8L, NTip(RogueTaxa(trees[-11], dr = 2, ret = 'Tr', 'sci')))

})

test_that("QuickRogue() restores leaves", {
  trees150 <- ape::read.tree(system.file('example/150.bs', package = 'Rogue'))
  expect_equal(nrow(QuickRogue(trees150[80:89])), 5)
})

#
# test_that("Benchmarking", {
#         skip_if(TRUE)
#
#         trees <- read.tree(paste0('c:/research/r/rogue-ms/data-raw/simulations/1/all.bs'))
#         profvis::profvis(Roguehalla(trees[1:5], dropset = 1))
# })