tests/testthat/test-calc-methods.R

In DomBennett/MoreTreeTools: Tools for manipulating phylogenetic trees

# Test calc-methods
# D.J. Bennett
# 13/06/2014

# LIBS
library (MoreTreeTools)
library (testthat)

# TEST DATA
data ('catarrhines')

# RUNNING TESTS
context ('Testing \'calc-methods\'')
test_that ('calcEdgeDiversity([basic]) works', {
  tree <- rtree (25)
  res <- calcEdgeDiversity (tree, n.intervals=2)
  # make sure all edges are accounted for
  expect_that (nrow (res) == nrow (tree$edge), is_true ())
  tip.edges <- which (tree$edge[ ,2] < getSize (tree))
  tip.edges <- which (res$edge %in% tip.edges)
  # make sure all tip edges are equal to 1
  expect_that (all (res$count[tip.edges] == 1), is_true ())
})

test_that ('reduceTree([basic]) works', {
  # There are 23 Catarrhine genera
  res <- reduceTree (catarrhines, 'genus')
  expect_that (length (res$tip.label), equals (23))
})

test_that ('calcED(type = \'FP\') works', {
  res <- calcED (catarrhines)
  # orangutan is the most distinct
  most.distinct <-
    as.character (rownames (res)[which (res[ ,1] == max (res[ ,1]))])
  expect_that ("Pongo pygmaeus", equals (most.distinct))
})

test_that ('calcED(type = \'PE\') works', {
  res <- calcED (catarrhines, type = 'PE')
  # orangutan is still the most distinct
  most.distinct <-
    as.character (rownames (res)[which (res[ ,1] == max (res[ ,1]))])
  expect_that ("Pongo pygmaeus", equals (most.distinct))
})

test_that ('calcED(type = \'ES\') works', {
  res <- calcED (catarrhines, type = 'ES')
  # orangutan is still the most distinct
  most.distinct <-
    as.character (rownames (res)[which (res[ ,1] == max (res[ ,1]))])
  expect_that ("Pongo pygmaeus", equals (most.distinct))
})
test_that ('calcDist([basic]) works', {
  tree1 <- compute.brlen (stree (10, 'left'))
  tree2 <- compute.brlen (stree (10, 'left'))
  distances <- calcDist (tree1, tree2)
  # trees are identical
  expect_that (0, equals (distances[['PH85']]))
  expect_that (0, equals (distances[['score']]))
  expect_that (0, equals (distances[['dmat']]))
  expect_that (0, equals (distances[['triplet']]))
  # rearrange to be maximally distant
  tree1$tip.label <- tree1$tip.label[c (10,2,8,4,6,5,7,3,9,1)]
  distances <- round (calcDist (tree1, tree2), 3)
  expect_that (1, equals (distances[['PH85']]))
  expect_that (1, equals (distances[['score']]))
  expect_that (0.652, equals (distances[['dmat']]))  # maxs for 10 tips
  expect_that (0.758, equals (distances[['triplet']]))
})
# test_that ('calcBalance([basic]) works', {
#   TODO
# })