context("ph_rao")
sfile <- system.file("examples/sample_comstruct", package = "phylocomr")
pfile <- system.file("examples/phylo_comstruct", package = "phylocomr")
sampledf <- read.table(sfile, header = FALSE,
stringsAsFactors = FALSE)
phylo_str <- readLines(pfile)
test_that("ph_rao works with data.frame input", {
skip_on_appveyor()
skip_on_cran()
aa <- ph_rao(sample = sampledf, phylo = phylo_str)
expect_is(aa, "list")
expect_true("diversity_components" %in% names(aa))
expect_true("within_community_diveristy" %in% names(aa))
for (i in seq_along(aa)) expect_is(aa[[i]], "data.frame")
expect_type(aa$within_community_diveristy$plot, "character")
expect_type(aa$within_community_diveristy$nspp, "integer")
})
test_that("ph_rao works with file input", {
skip_on_appveyor()
skip_on_cran()
aa <- ph_rao(sample = sfile, phylo = pfile)
expect_is(aa, "list")
expect_true("diversity_components" %in% names(aa))
expect_true("within_community_diveristy" %in% names(aa))
for (i in seq_along(aa)) expect_is(aa[[i]], "data.frame")
expect_type(aa$within_community_diveristy$plot, "character")
expect_type(aa$within_community_diveristy$nspp, "integer")
})
test_that("ph_rao fails well", {
# required inputs
expect_error(ph_rao(),
"argument \"sample\" is missing, with no default")
expect_error(ph_rao("Adsf"),
"argument \"phylo\" is missing, with no default")
# types are correct
expect_error(ph_rao(5, "asdfad"),
"sample must be of class data.frame, character")
expect_error(ph_rao("adf", mtcars),
"phylo must be of class phylo, character")
})
test_that("ph_rao corrects mismatched cases in data.frame's/phylo objects", {
skip_on_appveyor()
skip_on_cran()
# mismatch in `sample` case is fixed internally
sampledf_err <- sampledf
sampledf_err$V3 <- toupper(sampledf_err$V3)
expect_is(ph_rao(sampledf_err, phylo_str), "list")
# mismatch in `phylo` case is fixed internally
phylo_str_err <- phylo_str
phylo_str_err <- toupper(phylo_str_err)
expect_is(ph_rao(sampledf, phylo_str_err), "list")
# mismatch in `sample` file is fixed internally
sampledf_err <- sampledf
sampledf_err$V3 <- toupper(sampledf_err$V3)
smp <- sample_check_nolower(sampledf_err)
expect_is(ph_rao(smp, phylo_str), "list")
# mismatch in `sample` file is fixed internally
phylo_str_err <- phylo_str
phylo_str_err <- toupper(phylo_str_err)
phylo_str_err_file <- tempfile("phylo_")
cat(phylo_str_err, file = phylo_str_err_file, sep = "\n")
expect_is(ph_rao(sampledf, phylo_str_err_file), "list")
})
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