tests/testthat/test_filtering.R

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

data(data_fungi)
data(enterotype)

test_that("filt_taxa_pq works", {
  result <- filt_taxa_pq(data_fungi, min_nb_seq = 20)
  expect_s4_class(result, "phyloseq")
  expect_identical(ntaxa(result), 1388L)

  result <- filt_taxa_pq(data_fungi, min_occurence = 2)
  expect_s4_class(result, "phyloseq")
  expect_identical(ntaxa(result), 1214L)

  result <- filt_taxa_pq(
    data_fungi,
    min_occurence = 2,
    min_nb_seq = 10,
    clean_pq = FALSE
  )
  expect_s4_class(result, "phyloseq")
  expect_identical(ntaxa(result), 1208L)

  result <- filt_taxa_pq(
    data_fungi,
    min_occurence = 4,
    min_nb_seq = 100,
    combination = "OR"
  )
  expect_s4_class(result, "phyloseq")
  expect_identical(ntaxa(result), 1261L)
})

test_that("filt_taxa_wo_NA works", {
  result <- filt_taxa_wo_NA(data_fungi, "Class")
  expect_s4_class(result, "phyloseq")
  expect_identical(ntaxa(result), 1327L)
})

test_that("distri_1_taxa works", {
  result <- distri_1_taxa(data_fungi, "Height", "ASV2")
  expect_s3_class(result, "data.frame")
})