tests/testthat/test_comparetrees.R

In phylotastic/rphylotastic: An R Interface to 'Phylotastic' Web Services

test_that("Comparing two trees works", {
  phy1 <- ape::read.tree(text="(((((((EU368025_Uncult_marine_euk_FS14JA72_30Mar05_5m:0.00329,EU368020_Uncult_marine_euk_FS04GA95_01Aug05_5m:-0.00002):0.00002,EU368013_Uncult_marine_euk_FS01D014_01Aug05_65m:-0.00002):0.00010,(EU368034_Uncult_marine_euk_OC413NSS_Q007_15m:-0.00000,(EU368007_Uncult_marine_euk_FS01B026_30Mar05_5m:-0.00001,EU368004_Uncult_marine_euk_FS01AA94_01Aug05_5m:0.00328):0.00000):0.00317):0.00725,(EU368005_Uncult_marine_euk_FS01B033_30Mar05_5m:-0.00002,(EF172850_Uncult_euk_SSRPB47:-0.00003,EU368022_Uncult_marine_euk_FS04H169_01Aug05_89m:0.00166):0.00002):0.00597):0.00202,((DQ060523_Uncult_marine_euk_NOR46.29:0.01559,(HQ868826_Uncult_euk_SHAX1073:0.00155,EU368038_Uncult_marine_euk_EN351CTD040_4mN11:0.00172):0.00429):0.00017,(EU368023_Uncult_marine_euk_FS04H153_01Aug05_89m:0.00504,(DQ222879_Uncult_photo_euk_RA000907.18:0.00166,HM858468_Uncult_marine_euk_MO.011.5m.00036:-0.00003):0.00152):0.00566):0.00662):0.00941,(HQ868882_Uncult_euk_SHAX1135:0.00170,HQ868810_Uncult_euk_SHAX1056:-0.00007):0.02449):0.00648,(EU368021_Uncult_marine_euk_FS04GA46_01Aug05_5m:0.02285,(HQ869075_Uncult_euk_SHAX587:0.00000,HQ869035_Uncult_euk_SHAX540:0.00000):0.04720):0.01029,HQ156863_Uncult_marine_ciliate_170609_08:0.17059);")
  phy2 <- ape::read.tree(text="((HQ869075_Uncult_euk_SHAX587:0.00000,HQ869035_Uncult_euk_SHAX540:0.00000):0.04484,(EU368021_Uncult_marine_euk_FS04GA46_01Aug05_5m:0.02285,(((((EU368005_Uncult_marine_euk_FS01B033_30Mar05_5m:-0.00002,(EF172850_Uncult_euk_SSRPB47:-0.00003,EU368022_Uncult_marine_euk_FS04H169_01Aug05_89m:0.00166):0.00002):0.00597,(((EU368025_Uncult_marine_euk_FS14JA72_30Mar05_5m:0.00329,EU368020_Uncult_marine_euk_FS04GA95_01Aug05_5m:-0.00002):0.00002,EU368013_Uncult_marine_euk_FS01D014_01Aug05_65m:-0.00002):0.00010,(EU368034_Uncult_marine_euk_OC413NSS_Q007_15m:-0.00000,(EU368007_Uncult_marine_euk_FS01B026_30Mar05_5m:-0.00001,EU368004_Uncult_marine_euk_FS01AA94_01Aug05_5m:0.00328):0.00000):0.00317):0.00725):0.00202,((DQ060523_Uncult_marine_euk_NOR46.29:0.01559,(HQ868826_Uncult_euk_SHAX1073:0.00155,EU368038_Uncult_marine_euk_EN351CTD040_4mN11:0.00172):0.00429):0.00017,(EU368023_Uncult_marine_euk_FS04H153_01Aug05_89m:0.00504,(DQ222879_Uncult_photo_euk_RA000907.18:0.00166,HM858468_Uncult_marine_euk_MO.011.5m.00036:-0.00003):0.00152):0.00566):0.00662):0.00941,(HQ868882_Uncult_euk_SHAX1135:0.00170,HQ868810_Uncult_euk_SHAX1056:-0.00007):0.02449):0.00648,HQ156863_Uncult_marine_ciliate_170609_08:0.17059):0.01029):0.00236);")
  trees <- c(phy1, phy2)
  result <- phylo_compare(trees)
  expect_true(result)
  result <- phylo_compare(phylo1 = phy1, phylo2 = phy2)
  expect_true(result)
  # just one tree as input should give error
  expect_error(phylo_compare(phylo1 = phy1, phylo2 = NULL))  
})