tests/_old_testthat/test_opentree_taxonomy.R

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

test_that("clean_taxon_info_children works", {
  # Felis ott_id is 563165
  taxon_info <- rotl::taxonomy_taxon_info(563165, include_children = TRUE)
  # clean_taxon_info_children(taxon_info)
})
test_that("get_valid_children works", {
  xx <- get_valid_children("Felis")
  yy <- tnrs_match(rownames(xx$Felis$children))
  expect_false("EXTINCT" %in% yy$flags)
})
test_that("get_ott_lineage works", {
  xx <- get_ott_lineage(input = c("Homo"))
  xx <- get_ott_lineage(input = c("random", "Homo")) # fix: this does not work well yet
  xx <- get_ott_lineage(input = c("perro", "canis", "Homo"))
  xx <- get_ott_lineage(input = c("Lamiaceae", "Campanulaceae", "Fabaceae"))
  xx <- get_ott_lineage(input = c("Lamiaceae", "Campanulaceae", "Salvia"))
})
test_that("get_ott_clade works", {
  xx <- get_ott_clade(input = c("random", "Homo"))
  xx <- get_ott_clade(input = c("random", "Homo"), ott_rank = c("family", "order", "class"))
  xx <- get_ott_clade(input = c("perro", "canis", "Homo"), ott_rank = c("family", "order", "class", "genus"))
  xx <- get_ott_clade(input = c("Lamiaceae", "Campanulaceae", "Fabaceae"), ott_rank = "family")
  expect_false(all(is.na(xx$family))) # this should return the same lineages since they are all family level already
  xx <- get_ott_clade(input = c("Lamiaceae", "Campanulaceae", "Salvia"), ott_rank = "family")
  expect_false(all(is.na(xx$family))) # this should return the same lineages since they are all family level already
})