# context("phylomatic")
# test_that("phylomatic executable works", {
# expect_output(phylomatic(), "Cam Webb")
# expect_is(phylomatic(intern = TRUE), "character")
# expect_match(phylomatic(intern = TRUE), "Cam Webb")
# })
#
#
# context("ph_phylomatic")
#
# taxa_file <- system.file("examples/taxa", package = "phylocomr")
# phylo_file <- system.file("examples/phylo", package = "phylocomr")
#
# taxa_str <- readLines(taxa_file)
# phylo_str <- readLines(phylo_file)
#
# test_that("ph_phylomatic works with chr string input", {
# skip_on_appveyor()
# skip_on_cran()
#
# aa <- ph_phylomatic(taxa = taxa_str, phylo = phylo_str)
#
# expect_is(aa, "character")
# expect_is(attr(aa, "taxa_file"), "character")
# expect_match(attr(aa, "taxa_file"), "taxa")
# expect_is(attr(aa, "phylo_file"), "character")
# expect_match(attr(aa, "phylo_file"), "phylo")
#
# expect_match(aa, "lobelia_conferta")
# expect_match(aa, "narcissus_cuatrecasasii")
# expect_match(aa, "poales_to_asterales")
#
# if (requireNamespace('ape')) {
# library(ape)
# tree <- read.tree(text = aa)
# expect_is(tree, "phylo")
# }
# })
#
# test_that("ph_phylomatic works with file input", {
# skip_on_appveyor()
# skip_on_cran()
#
# taxa_file2 <- tempfile()
# cat(taxa_str, file = taxa_file2, sep = '\n')
# phylo_file2 <- tempfile()
# cat(phylo_str, file = phylo_file2, sep = '\n')
#
# aa <- ph_phylomatic(taxa = taxa_file2, phylo = phylo_file2)
#
# expect_is(aa, "character")
# expect_is(attr(aa, "taxa_file"), "character")
# expect_is(attr(aa, "phylo_file"), "character")
#
# expect_match(aa, "lobelia_conferta")
# expect_match(aa, "narcissus_cuatrecasasii")
# expect_match(aa, "poales_to_asterales")
#
# if (requireNamespace('ape')) {
# library(ape)
# tree <- read.tree(text = aa)
# expect_is(tree, "phylo")
# }
# })
#
# test_that("ph_phylomatic fails well", {
# # required inputs
# expect_error(ph_phylomatic(),
# "argument \"taxa\" is missing, with no default")
# expect_error(ph_phylomatic("Adsf"),
# "argument \"phylo\" is missing, with no default")
#
# # types are correct
# expect_error(ph_phylomatic(5, "asdfad"),
# "taxa must be of class character")
# expect_error(ph_phylomatic("adf", 5),
# "phylo must be of class phylo, character")
#
# expect_error(ph_phylomatic(taxa_str, phylo_str, tabular = 5),
# "tabular must be of class logical")
# expect_error(ph_phylomatic(taxa_str, phylo_str, lowercase = 5),
# "lowercase must be of class logical")
# expect_error(ph_phylomatic(taxa_str, phylo_str, nodes = 5),
# "nodes must be of class logical")
# })
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