tests/testthat/test-real-data.R

In TreeDist: Calculate and Map Distances Between Phylogenetic Trees

#if (requireNamespace("rwty", quietly = TRUE)) {
#  test_that("Fungi MSID/PID differ", {
#    data("fungus", package = "rwty")
#    trees <- fungus[[1]]$trees
#    
#    expect_equal(PhylogeneticInfoDistance(trees[[1]], trees[[2]]),
#                 PhylogeneticInfoDistance(trees[1:2])[1])
#    expect_equal(MatchingSplitInfoDistance(trees[[1]], trees[[2]]),
#                 MatchingSplitInfoDistance(trees[1:2])[1])
#    expect_false(identical(PhylogeneticInfoDistance(trees[1:4]),
#                           MatchingSplitInfoDistance(trees[1:4])))
#  })
#  
#  if (requireNamespace("whalehead", quietly = TRUE)) {
#    test_that("Whalehead MSID/PID differ", {
#      whaleRoot <- system.file("Data", package = "whalehead", mustWork = TRUE)
#      whaleRoot <- "../ProjectWhalehead/Data"
#      treeFiles <- list.files(path = paste0(whaleRoot, "/CombinedTrees"),
#                              pattern = "*.nex",
#                              full.names = TRUE, recursive = FALSE)
#      trees <- unname(rwty::load.trees(treeFiles[2], trim = 100, skip = 0)$trees)
#      
#      expect_equal(PhylogeneticInfoDistance(trees[[1]], trees[[2]]),
#                   PhylogeneticInfoDistance(trees[1:2])[1])
#      expect_equal(MatchingSplitInfoDistance(trees[[1]], trees[[2]]),
#                   MatchingSplitInfoDistance(trees[1:2])[1])
#      expect_false(identical(PhylogeneticInfoDistance(trees[1:4]),
#                             MatchingSplitInfoDistance(trees[1:4])))
#    })
#  }
#}
#