context("ph_pd")
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_pd works with data.frame input", {
skip_on_appveyor()
skip_on_cran()
aa <- ph_pd(sample = sampledf, phylo = phylo_str)
expect_is(aa, "tbl_df")
expect_is(aa, "data.frame")
expect_named(aa, c("sample", "ntaxa", "pd", "treebl", "proptreebl"))
expect_is(aa$sample, "character")
expect_type(aa$ntaxa, "integer")
expect_type(aa$pd, "double")
expect_type(aa$treebl, "double")
expect_type(aa$proptreebl, "double")
})
test_that("ph_pd works with file input", {
skip_on_appveyor()
skip_on_cran()
sample_str <- paste0(readLines(sfile), collapse = "\n")
sfile2 <- tempfile()
cat(sample_str, file = sfile2, sep = '\n')
pfile2 <- tempfile()
phylo_str <- readLines(pfile)
cat(phylo_str, file = pfile2, sep = '\n')
aa <- ph_pd(sample = sfile2, phylo = pfile2)
expect_is(aa, "tbl_df")
expect_is(aa, "data.frame")
expect_named(aa, c("sample", "ntaxa", "pd", "treebl", "proptreebl"))
expect_is(aa$sample, "character")
expect_type(aa$ntaxa, "integer")
expect_type(aa$pd, "double")
expect_type(aa$treebl, "double")
expect_type(aa$proptreebl, "double")
})
test_that("ph_pd fails well", {
# required inputs
expect_error(ph_pd(), "argument \"sample\" is missing, with no default")
expect_error(ph_pd("Adsf"), "argument \"phylo\" is missing, with no default")
# types are correct
expect_error(ph_pd(5, "asdfad"),
"sample must be of class data.frame, character")
expect_error(ph_pd("adf", mtcars),
"phylo must be of class phylo, character")
})
test_that("ph_pd 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_pd(sampledf_err, phylo_str), "data.frame")
# mismatch in `phylo` case is fixed internally
phylo_str_err <- phylo_str
phylo_str_err <- toupper(phylo_str_err)
expect_is(ph_pd(sampledf, phylo_str_err), "data.frame")
# 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_pd(smp, phylo_str), "data.frame")
# 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_pd(sampledf, phylo_str_err_file), "data.frame")
})
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