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test.treedata.table.R
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test.treedata.table.R
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context("String length")
library(treedata.table)
library(ape)
data(anolis)
td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)
tdt_output <-
tdt(td,
geiger::fitContinuous(
phy,
extractVector(td, SVL),
model = "BM",
ncores = 1
))
test_that("The resulting td object is of class treedata.table", {
expect_is(td, "treedata.table")
})
test_that("Trees are the same", {
expect_true(all.equal.phylo(td$phy, anolis$phy))
})
test_that("Species in tree and trait dataframe are the same", {
expect_equal(td$phy$tip.label, td$dat$tip.label)
})
test_that("datasets are the same", {
expect_true(all(colnames(anolis$dat)[-1] == colnames(as.data.frame(td$dat))[-1]))
})
test_that("Check the match between tree and dataset", {
expect_true(attr(td, "tree_not_data") == "OK")
expect_true(attr(td, "data_not_tree") == "OK")
})
test_that("tdt function works fine", {
expect_is(tdt_output, "list")
})
test_that("Extracting a single column from the treedata.table object", {
expect_equal(ncol(td[, SVL]$dat), 1)
})
test_that(
"The number of rows is the same after filtering the original and tdt object
under the same criteria",
{
expect_equal(nrow(anolis$dat[anolis$dat$island == "Cuba" &
anolis$dat$ecomorph == "TG", ]),
nrow(td[island == "Cuba" & ecomorph == "TG", ]$dat))
}
)
test_that("[[ extracts a named character vector",{
expect_is(names(td[["SVL"]]), "character")
expect_is(td[["SVL"]], "numeric")
})
test_that("phy and dat objects can be extracted correctly using pull.treedata.table",{
expect_is(pull.treedata.table(td, type = "phy"), "phylo")
expect_is(pull.treedata.table(td, type = "dat"), "data.table")
})