tests/_old_testthat/test_tree_from_taxonomy.R

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

test_that("tree_from_taxonomy works with Phyllostomidae (reticulations)", {
  taxa_dq <- make_datelife_query("Phyllostomidae", get_spp_from_taxon = TRUE)
  taxa <- unname(taxa_dq$cleaned_names)
  taxtree_ncbi <- tree_from_taxonomy(taxa, source = "NCBI")
})

test_that("classification_paths_from_taxonomy works", {
  taxa <- c("Homo sapiens", "twilight sparkle", "Equus quagga", "Archaeopteryx")
  results <- classification_paths_from_taxonomy(taxa)
  expect_true(inherits(results$resolved, "data.frame"))
  expect_true(length(results$unresolved) > 0)
  # the following happens when using cached opentree_chronograms from load(data-raw/opentree_chronograms_oct2018.rda)
  # classification_paths_from_taxonomy(opentree_chronograms$trees[[50]], sources = "Open Tree of Life Reference Taxonomy")
  # gives: Error: Request-URI Too Long (HTTP 414)
  # not sure yet why it happens
})

test_that("tree_from_taxonomy works", {
  taxa <- c("Homo sapiens", "twilight sparkle", "Equus quagga", "Archaeopteryx")
  results <- tree_from_taxonomy(taxa)
  # not passing:
  # expect_true(inherits(results$phy, "phylo"))
})

test_that("tree_from_taxonomy works with weird inputs and PBDB", {
  taxa <- c("Homo sapiens", "twilight sparkle", "Equus quagga", "Archaeopteryx", "Marchantiophyta", "Polypodiopsida")
  # rotl::tnrs_match_names("Equus quagga")
  classifications <- classification_paths_from_taxonomy(taxa, sources = "The Paleobiology Database")
  expect_true(inherits(classifications$resolved, "data.frame"))
  results <- tree_from_taxonomy(taxa, sources = "The Paleobiology Database")
  # not passing:
  # expect_true(inherits(results$phy, "phylo"))

  taxa <- c("Gorilla", "Panthera", "Tyto", "Dromaius", "Aedes", "Solenopsis", "Caretta", "Crocodylus", "Brassica", "Solanum", "Zea", "Prunus", "Rosa", "Climacograptus")
  classifications <- classification_paths_from_taxonomy(taxa, sources = "The Paleobiology Database")
  expect_true(inherits(classifications$resolved, "data.frame"))
  results <- tree_from_taxonomy(taxa, sources = "The Paleobiology Database")
  # not passing:
  # expect_true(inherits(results$phy, "phylo"))
})

test_that("get_fossil_range works", {
  dates <- get_fossil_range("Tyrannosaurus rax") # yep, with misspellings
  # not passing:
  # expect_true(all(dates$min_ma > 64))
  dates <- get_fossil_range("Tyrannosaurus rex", recent = FALSE) # I'm not allowed to say how I know this, but T. rex is still alive.
  # not passing:
  # expect_true(min(dates$min_ma) == 0)
})

test_that("summarize_fossil_range works", {
  dates <- summarize_fossil_range("Tyrannosaurus rax") # yep, with misspellings
  # not passing:
  # expect_true(dates$min_ma > 64)
  # expect_true(nrow(dates)==1)
  # expect_true(rownames(dates)=="Tyrannosaurus rax") # we get the name we put in (which may match our tree), not the GNR'ed name
})