library(DivNet)
context("Test simplification of beta diversities")
data(Lee)
Lee_phylum <- phyloseq::tax_glom(Lee, taxrank="Phylum")
divnet_phylum_char <- divnet(Lee_phylum, X = "char", tuning = "test")
test_that("simplifyBeta returns a dataframe",
{
expect_is(simplifyBeta(dv = divnet_phylum_char,
physeq = Lee_phylum,
measure = "bray-curtis",
x = "char"),
"data.frame")
})
test_that("error when sample names have non-standard characters", {
upd_divnet_phylum_char <- divnet_phylum_char
colnames(upd_divnet_phylum_char$`bray-curtis`)[1] <- "error!"
expect_error(simplifyBeta(dv = upd_divnet_phylum_char,
physeq = Lee_phylum,
measure = "bray-curtis",
x = "char"),
"Your sample names contain non-standard characters, please change that :)")
})
test_that("Aitchison distance works", {
expect_is(simplifyBeta(dv = divnet_phylum_char,
physeq = Lee_phylum,
measure = "Aitchison",
x = "char"),
"data.frame")
})
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