tests/testthat/test-tree_distance_spr.R

In ms609/TreeDist: Calculate and Map Distances Between Phylogenetic Trees

test_that("SPR.dist called safely", {
  library("TreeTools")
  PhangornSPR <- phangorn::SPR.dist
  expect_equal(PhangornSPR(structure(lapply(as.phylo(0:5, 6), Postorder),
                                     class = "multiPhylo"),
                           Postorder(BalancedTree(6))),
               SPRDist(as.phylo(0:5, 6), BalancedTree(6), symmetric = FALSE))
  expect_equal(SPRDist(BalancedTree(6), as.phylo(0:5, 6)),
               SPRDist(as.phylo(0:5, 6), BalancedTree(6)))
  expect_equal(SPRDist(BalancedTree(6), PectinateTree(6)),
               SPRDist(list(BalancedTree(6), PectinateTree(6)))[1],
               ignore_attr = TRUE)
  
  # https://github.com/KlausVigo/phangorn/issues/97
  tr1 <- structure(list(edge = structure(c(11L, 11L, 10L, 10L, 9L, 9L, 8L, 8L, 7L,
                                           7L, 2L, 6L, 5L, 11L, 4L, 10L, 3L, 9L, 
                                           1L, 8L), .Dim = c(10L, 2L)),
                        tip.label = c("t1", "t2", "t3", "t4", "t5", "t6"), 
                        Nnode = 5),
                   class = "phylo")
  
  tr2 <- structure(list(edge = structure(c(10L, 10L, 11L, 11L, 9L, 9L, 8L, 8L, 7L,
                                           7L, 2L, 6L, 3L, 4L, 5L, 10L, 11L, 9L, 
                                           1L, 8L), .Dim = c(10L, 2L)),
                        tip.label = c("t1", "t2", "t3", "t4", "t5", "t6"),
                        Nnode = 5),
                   class = "phylo")
  
  tr3 <- structure(list(edge = structure(c(9L, 9L, 11L, 11L, 10L, 10L, 8L, 8L, 7L, 
                                           7L, 1L, 2L, 4L, 5L, 6L, 11L, 3L, 9L, 
                                           8L, 10L), .Dim = c(10L, 2L)),
                        Nnode = 5L, 
                        tip.label = c("t1", "t2", "t3", "t4", "t5", "t6")),
                   class = "phylo")
  trs12 <- structure(list(tr1, tr2), class = "multiPhylo")
  trs123 <- structure(list("one" = tr1, "two" = tr2, "thr" = tr3),
                      class = "multiPhylo")
  SprpS <- function(...) SPRDist(..., symmetric = TRUE)
  expect_equal(SprpS(tr1, tr3), SprpS(tr3, tr1))
  expect_equal(2L, length(SprpS(trs12, tr3)))
  expect_equal(SprpS(trs12, tr3), SprpS(tr3, trs12))
  expect_equal(SprpS(trs12, trs123), t(SprpS(trs123, trs12)))
  expect_equal(SprpS(rev(trs123), trs123), t(SprpS(trs123, rev(trs123))))
  expect_equal(1 - diag(1, 3), as.matrix(SprpS(trs123)),
               ignore_attr = TRUE)
})