tests/testthat/test_adonis.R

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

skip_on_cran()

data(data_fungi)
data(enterotype, package = "phyloseq")

test_that("adonis function works fine", {
  expect_s3_class(adonis_pq(data_fungi, "Tree_name"), "anova")
  expect_s3_class(adonis_pq(data_fungi, "Height", na_remove = TRUE), "anova")
  expect_s3_class(
    adonis_pq(data_fungi, "Tree_name", correction_for_sample_size = TRUE),
    "anova"
  )
  expect_s3_class(
    adonis_pq(data_fungi, "Tree_name", rarefy_nb_seqs = TRUE),
    "anova"
  )
  expect_s3_class(
    adonis_pq(
      subset_samples(
        data_fungi,
        !is.na(data_fungi@sam_data$Time) & !is.na(data_fungi@sam_data$Height)
      ),
      "Time*Height"
    ),
    "anova"
  )
  expect_error(adonis_pq(data_fungi, "Time*Tree_name"))
  expect_error(adonis_pq(enterotype, "SeqTech*Enterotype"))
  expect_s3_class(
    adonis_pq(enterotype, "SeqTech*Enterotype", na_remove = TRUE),
    "anova"
  )
  expect_error(adonis_pq(enterotype, "SecTech"))
  expect_error(adonis_pq(enterotype, "SeqTech", dist_method = "aitchison"))
})