tests/testthat/test-p_adjust.R

In parameters: Processing of Model Parameters

skip_on_cran()


test_that("model_parameters, p-adjust", {
  model <- lm(mpg ~ wt * cyl + am + log(hp), data = mtcars)
  mp <- model_parameters(model)
  expect_equal(mp$p, c(0, 0.00304, 0.02765, 0.65851, 0.01068, 0.02312), tolerance = 1e-3)
  mp <- model_parameters(model, p_adjust = "BH")
  expect_equal(mp$p, c(0, 0.00912, 0.03318, 0.65851, 0.02137, 0.03318), tolerance = 1e-3)
  mp <- model_parameters(model, p_adjust = "bonferroni")
  expect_equal(mp$p, c(0, 0.01824, 0.16588, 1, 0.06411, 0.13869), tolerance = 1e-3)
})


test_that("model_parameters, p-adjust after keep/drop", {
  model <- lm(mpg ~ wt + cyl + gear + hp, data = mtcars)
  mp <- model_parameters(model, p_adjust = "bonferroni")
  expect_equal(
    mp[["p"]],
    p.adjust(coef(summary(model))[, 4], "bonferroni"),
    tolerance = 1e-4,
    ignore_attr = TRUE
  )

  expect_message(
    mp <- model_parameters(model, summary = TRUE, keep = c("wt", "hp"), p_adjust = "bonferroni"),
    "more than 1 element"
  )
  expect_equal(
    mp[["p"]],
    p.adjust(coef(summary(model))[c(2, 5), 4], "bonferroni"),
    tolerance = 1e-4,
    ignore_attr = TRUE
  )

  expect_message(
    mp <- model_parameters(model, summary = TRUE, keep = c("cyl", "gear"), p_adjust = "bonferroni"),
    "more than 1 element"
  )
  expect_equal(
    mp[["p"]],
    p.adjust(coef(summary(model))[3:4, 4], "bonferroni"),
    tolerance = 1e-4,
    ignore_attr = TRUE
  )
})

test_that("model_parameters, emmeans, p-adjust", {
  skip_if_not_installed("emmeans")
  m <- pairs(emmeans::emmeans(aov(Sepal.Width ~ Species, data = iris), ~Species))
  mp <- model_parameters(m)
  expect_equal(mp$p, as.data.frame(m)$p.value, tolerance = 1e-4)
})
test_that("model_parameters, emmeans, p-adjust", {
  skip_if_not_installed("emmeans")
  m <- pairs(emmeans::emmeans(aov(Sepal.Width ~ Species, data = iris), ~Species), adjust = "scheffe")
  mp <- model_parameters(m, p_adjust = "scheffe")
  expect_equal(mp$p, as.data.frame(m)$p.value, tolerance = 1e-4)
})