tests/testthat/test-ancombc.R

In ANCOMBC: Analysis of compositions of microbiomes with bias correction

context("Testing ancombc function")
library(ANCOMBC)
library(testthat)
library(tidyverse)
library(microbiome)

data(atlas1006)
# Subset to baseline
pseq = subset_samples(atlas1006, time == 0)
# Re-code the bmi group
sample_data(pseq)$bmi_group = recode(sample_data(pseq)$bmi_group,
                                     underweight = "lean",
                                     lean = "lean",
                                     overweight = "overweight",
                                     obese = "obese",
                                     severeobese = "obese",
                                     morbidobese = "obese")
# Re-code the nationality group
sample_data(pseq)$nation = recode(sample_data(pseq)$nationality,
                                  Scandinavia = "NE",
                                  UKIE = "NE",
                                  SouthEurope = "SE",
                                  CentralEurope = "CE",
                                  EasternEurope = "EE")

# Aggregate to phylum level
phylum_data = aggregate_taxa(pseq, "Phylum")

# Test
test_that("`ancombc` function provides expected results", {
   phyloseq = phylum_data; formula = "age + nation + bmi_group"
   p_adj_method = "holm"; zero_cut = 0.90; lib_cut = 1000; group = "nation"
   struc_zero = TRUE; neg_lb = TRUE; tol = 1e-5; max_iter = 100
   conserve = TRUE; alpha = 0.05; global = TRUE

   out = ancombc(phyloseq, formula, p_adj_method,
                 zero_cut, lib_cut, group, struc_zero, neg_lb,
                 tol, max_iter, conserve, alpha, global)

   res = out$res
   res_global = out$res_global


   # Testing
   test_output = signif(c(res$W[1, 1], res_global$W[2]), 2)

   expect_equal(test_output, c(-9.8, 75))
})