Nothing
context("phylomatic")
taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus")
test_that("phylomatic - GET (default) method works", {
skip_on_cran()
tree <- phylomatic(taxa = taxa)
expect_is(taxa, "character")
expect_is(tree, "phylo")
expect_is(tree, "phylomatic")
})
test_that("phylomatic - POST method works", {
skip_on_cran()
tree <- phylomatic(taxa = taxa, get = 'POST')
expect_is(tree, "phylo")
expect_is(tree, "phylomatic")
})
test_that("phylomatic - stored tree", {
skip_on_cran()
tree <- phylomatic(taxa, storedtree = 'smith2011')
expect_is(tree, "phylo")
expect_is(tree, "phylomatic")
})
test_that("phylomatic - nexml output format", {
skip_on_cran()
out <- phylomatic(taxa, outformat = "nexml")
expect_is(out, "phylomatic")
expect_is(out[1], "character")
expect_true(grepl("nexml", out))
})
# FIXME: dryad url is broken, can't find new url
# test_that("phylomatic - treeuri param", {
# skip_on_cran()
# spp <- c("Abies_nordmanniana", "Abies_bornmuelleriana", "Abies_cilicica", "Abies_cephalonica",
# "Abies_numidica", "Abies_pinsapo", "Abies_alba")
# url <- "http://datadryad.org/bitstream/handle/10255/dryad.8791/final_tree.tre?sequence=1"
# tree <- phylomatic(taxa = spp, treeuri = url)
# expect_is(tree, "phylo")
# expect_is(tree, "phylomatic")
# expect_equal(tree$tip.label, spp)
# })
test_that("phylomatic fails as expected", {
skip_on_cran()
# fails when no taxa given
expect_error(phylomatic(), "argument \"taxa\" is missing")
# fails when no taxnames FALSE and improper name strings passed
expect_error(phylomatic(taxa, taxnames = FALSE), "No taxa in common")
# fails when get isn't in allowed set
expect_error(phylomatic(taxa, get = "STUFF"), "get must be one of 'POST' or 'GET'")
# fails when too many taxa passed and get='GET'
library("taxize")
spp <- taxize::names_list("species", 200)
expect_error(phylomatic(spp, get = "GET"), "\\(414\\) Request-URI Too Long")
})
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