tests/_old_testthat/test_datelife_sdm.R

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

test_that("SDM correctly returns three birds tree", {
  skip_on_cran()
  skip_on_os("linux") # b/c no pathd8 on travis linux
  taxa <- c("Rhea americana", "Pterocnemia pennata", "Struthio camelus")
  results_list <- lapply(opentree_chronograms$trees, get_subset_array_dispatch, taxa = taxa, phy = NULL)
  datelife_result <- results_list_process(results_list, taxa, TRUE)
  result.tree <- datelife_result_sdm_phylo(datelife_result)
  expect_true(inherits(result.tree, "phylo"))
  ape::is.ultrametric(result.tree, options = 2)
})

test_that("subset2_taxa gives ultrametric summary trees", {
  # class(subset2_result)
  xx <- get_best_grove(subset2_result)
  # class(xx$best_grove)
  xx_median <- datelife_result_median(xx$best_grove)
  ape::is.ultrametric(xx_median, option = 2)
  # plot(xx_median, cex = 0.5, label.offset = 50)
  # abline(v= max(ape::branching.times(xx_median)))
  xx_sdm <- datelife_result_sdm_phylo(xx$best_grove)
  ape::is.ultrametric(xx_sdm, option = 2)
  # nrow(sdm.matrix)
})
test_that("datelife_result_sdm_phylo works with all clustering methods", {
  t0 <- datelife_result_sdm_phylo(cetacea_result)
  # t1 <- datelife_result_sdm_phylo(cetacea_result, clustering_method = "nj")
  # t2 <- datelife_result_sdm_phylo(cetacea_result, clustering_method = "upgma")
})