tests/testthat/test-pglmm.R

In biobakery/anpan: Quantifying Microbial Strain-Host Associations

test_that("pglmm runs", {
  meta = data.frame(x = rnorm(100), sample_id = paste0("t", 1:100))
  tr = ape::rtree(100)
  res = anpan_pglmm(meta, tr,
                    outcome = "x",
                    iter_sampling = 10,
                    iter_warmup = 10,
                    show_plot_cor_mat = FALSE,
                    show_plot_tree = FALSE)

  expect_type(res, "list")
})

test_that("logistic pglmm runs", {
  meta = data.frame(x = as.logical(rbinom(100, 1, prob = .5)), sample_id = paste0("t", 1:100))
  tr = ape::rtree(100)
  res = anpan_pglmm(meta, tr,
                    family = "binomial",
                    outcome = "x",
                    iter_sampling = 10,
                    iter_warmup = 10,
                    show_plot_cor_mat = FALSE,
                    show_plot_tree = FALSE)

  expect_type(res, "list")
})