tests/testthat/test-rstanarm.R

In DominiqueMakowski/bayestestR: Understand and Describe Bayesian Models and Posterior Distributions

test_that("rstanarm", {
  skip_on_cran()
  skip_if_offline()
  skip_if_not_or_load_if_installed("rstanarm")
  skip_if_not_or_load_if_installed("httr")

  set.seed(333)
  model <- insight::download_model("stanreg_lm_1")
  expect_equal(rope_range(model, verbose = FALSE)[1], -0.602, tolerance = 0.1)

  model <- insight::download_model("stanreg_meanfield_lm_1")
  expect_equal(rope_range(model, verbose = FALSE)[1], -0.602, tolerance = 0.1)

  model <- insight::download_model("stanreg_fullrank_lm_1")
  expect_equal(rope_range(model, verbose = FALSE)[1], -0.602, tolerance = 0.1)

  model <- insight::download_model("stanreg_lmerMod_1")
  expect_equal(rope_range(model, verbose = FALSE)[1], -0.097, tolerance = 0.1)

  model <- insight::download_model("stanreg_glm_1")
  expect_equal(rope_range(model, verbose = FALSE)[1], -0.18, tolerance = 0.1)

  model <- insight::download_model("stanreg_merMod_1")
  expect_equal(rope_range(model, verbose = FALSE)[1], -0.18, tolerance = 0.1)

  model <- insight::download_model("stanreg_gamm4_1")
  expect_equal(rope_range(model, verbose = FALSE)[1], -0.043, tolerance = 0.1)

  model <- insight::download_model("stanreg_gam_1")
  invisible(capture.output(
    expect_warning(params <- describe_posterior(model,
      centrality = "all",
      test = "all", dispersion = TRUE
    ))
  ))
  expect_equal(c(nrow(params), ncol(params)), c(4, 22))

  expect_s3_class(hdi(model), "data.frame")
  expect_s3_class(ci(model), "data.frame")
  expect_s3_class(rope(model, verbose = FALSE), "data.frame")
  expect_true("equivalence_test" %in% class(equivalence_test(model)))
  expect_s3_class(map_estimate(model), "data.frame")
  expect_s3_class(p_map(model), "data.frame")
  expect_s3_class(p_direction(model), "data.frame")

  expect_error(equivalence_test(model, range = c(0.1, 0.3, 0.5)))
})

test_that("rstanarm", {
  skip_on_cran()
  skip_if_offline()
  skip_if_not_or_load_if_installed("rstanarm")
  skip_if_not_or_load_if_installed("httr")

  set.seed(333)
  model <- insight::download_model("stanreg_glm_3")

  out <- describe_posterior(model, effects = "all", component = "all", centrality = "mean")
  s <- summary(model)
  expect_identical(colnames(out), c(
    "Parameter", "Mean", "CI", "CI_low", "CI_high", "pd", "ROPE_CI",
    "ROPE_low", "ROPE_high", "ROPE_Percentage", "Rhat", "ESS"
  ))
  expect_equal(as.vector(s[1:4, 1, drop = TRUE]), out$Mean, tolerance = 1e-3)
  expect_equal(as.vector(s[1:4, 8, drop = TRUE]), out$Rhat, tolerance = 1e-1)
})

test_that("rstanarm", {
  skip_on_cran()
  skip_if_offline()
  skip_if_not_or_load_if_installed("rstanarm")
  skip_if_not_or_load_if_installed("httr")

  set.seed(333)
  model <- insight::download_model("stanreg_merMod_3")

  out <- describe_posterior(model, effects = "all", component = "all", centrality = "mean")
  s <- summary(model)
  expect_identical(colnames(out), c(
    "Parameter", "Effects", "Mean", "CI", "CI_low", "CI_high",
    "pd", "ROPE_CI", "ROPE_low", "ROPE_high", "ROPE_Percentage",
    "Rhat", "ESS"
  ))
  expect_equal(as.vector(s[1:8, 1, drop = TRUE]), out$Mean, tolerance = 1e-3)
  expect_equal(as.vector(s[1:8, 8, drop = TRUE]), out$Rhat, tolerance = 1e-1)
})

test_that("rstanarm", {
  skip_on_cran()
  skip_if_offline()
  skip_if_not_or_load_if_installed("rstanarm")
  skip_if_not_or_load_if_installed("httr")

  set.seed(333)
  model <- insight::download_model("stanmvreg_1")

  out <- describe_posterior(model, effects = "fixed", component = "all", centrality = "mean", test = NULL)
  s <- summary(model)
  expect_identical(colnames(out), c(
    "Parameter", "Response", "Mean", "CI", "CI_low", "CI_high",
    "Rhat", "ESS"
  ))
  expect_equal(as.vector(s[c(1:2, 5:7), 1, drop = TRUE]), out$Mean, tolerance = 1e-3)
  expect_equal(as.vector(s[c(1:2, 5:7), 10, drop = TRUE]), out$Rhat, tolerance = 1e-1)
})


test_that("rstanarm", {
  skip_on_cran()
  skip_if_offline()
  skip_if_not_or_load_if_installed("rstanarm")
  skip_if_not_or_load_if_installed("httr")

  set.seed(333)
  model <- insight::download_model("stanmvreg_1")

  out <- describe_posterior(
    model,
    effects = "fixed",
    component = "all",
    centrality = "mean",
    test = NULL,
    priors = TRUE
  )
  expect_identical(colnames(out), c(
    "Parameter", "Response", "Mean", "CI", "CI_low", "CI_high",
    "Rhat", "ESS", "Prior_Distribution", "Prior_Location",
    "Prior_Scale"
  ))
  expect_equal(nrow(out), 5)
})