context("Geiger tests (may take 15+ minutes)")
has_geiger <- require(geiger)
test_that("We can write caudata data to nexml", {
skip_if_not(has_geiger)
skip_on_cran()
data(caudata)
nexml_write(trees = caudata$phy, characters = caudata$dat, file="tmp.xml")
expect_true_or_null(nexml_validate("tmp.xml"))
unlink("tmp.xml") # cleanup
})
test_that("We can write geospiza data to nexml", {
skip_on_cran()
skip_if_not(has_geiger)
data(geospiza)
nexml_write(trees = geospiza$phy, characters = geospiza$dat, file="tmp.xml")
expect_true_or_null(nexml_validate("tmp.xml"))
unlink("tmp.xml") # cleanup
})
test_that("We can write chelonia data to nexml", {
skip_on_cran()
skip_if_not(has_geiger)
data(chelonia)
nexml_write(trees = chelonia$phy, characters = chelonia$dat, file="tmp.xml")
expect_true_or_null(nexml_validate("tmp.xml"))
unlink("tmp.xml") # cleanup
})
test_that("We can write primates data to nexml", {
skip_on_cran()
skip_if_not(has_geiger)
data(primates)
nexml_write(trees = primates$phy, characters = primates$dat, file="tmp.xml")
expect_true_or_null(nexml_validate("tmp.xml"))
unlink("tmp.xml") # cleanup
})
test_that("We can write whales data to nexml", {
skip_on_cran()
skip_if_not(has_geiger)
data(whales)
# taxa need to be rownames not separate column
skip_on_cran()
whales$dat <- whales$richness[[2]]
names(whales$dat) <- whales$richness[[1]]
nexml_write(trees = whales$phy, characters = whales$dat, file="tmp.xml")
expect_true_or_null(nexml_validate("tmp.xml"))
unlink("tmp.xml") # cleanup
})
test_that("We can write amphibia multiphylo to nexml. Two of these phylogenies each have nearly 3K taxa, so this may take around 12 minutes", {
# multiphylo, where two phylogenies have each nearly 3K taxa
skip_on_cran()
skip_if_not(has_geiger)
data(amphibia)
class(amphibia) <- "multiPhylo"
runtime <- system.time(nexml_write(amphibia, file="tmp.xml")) # Slow! about 12 minutes
expect_true_or_null(nexml_validate("tmp.xml"))
unlink("tmp.xml") # cleanup
})
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