swh:1:snp:2c68a6c5a8af2f06ac2c0225927f25b54fd1f9d0
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Tip revision: 1b89ec86b6a914c4d45bee998d08eed1ef23f57f authored by Dominique Makowski on 20 July 2020, 08:30:03 UTC
version 0.7.2
Tip revision: 1b89ec8
test-emmGrid.R
if (require("rstanarm") && require("emmeans")) {
  context("emmGrid_*")

  library(rstanarm)
  library(emmeans)
  set.seed(300)
  model <- stan_glm(extra ~ group, data = sleep, refresh = 0)

  em_ <- emmeans(model, ~group)
  c_ <- pairs(em_)
  all_ <- rbind(em_, c_)
  all_summ <- summary(all_)


# .clean_emmeans_draws ----------------------------------------------------

  test_that("emmGrid .clean_emmeans_draws", {
    testthat::expect_equal(colnames(bayestestR:::.clean_emmeans_draws(em_)), c("1", "2"))
    testthat::expect_equal(colnames(bayestestR:::.clean_emmeans_draws(c_)), "1 - 2")
    testthat::expect_equal(colnames(bayestestR:::.clean_emmeans_draws(all_)), c("1, .", "2, .", "., 1 - 2"))
  })


# estimate + hdi ----------------------------------------------------------



  test_that("emmGrid hdi", {
    xhdi <- hdi(all_, ci = 0.95)
    testthat::expect_equal(xhdi$CI_low, all_summ$lower.HPD, tolerance = 0.1)
    testthat::expect_equal(xhdi$CI_high, all_summ$upper.HPD, tolerance = 0.1)
  })

  test_that("emmGrid point_estimate", {
    xpest <- point_estimate(all_, centrality = "median", dispersion = TRUE)
    testthat::expect_equal(xpest$Median, all_summ$emmean, tolerance = 0.1)
  })

  # test_that("emmGrid ci", {
  #   testthat::skip_on_travis()
  #   xci <- ci(all_, ci = 0.9)
  #   testthat::expect_equal(length(xci$CI_low), 3, tolerance = 0.2)
  #   testthat::expect_equal(length(xci$CI_high), 3, tolerance = 0.2)
  # })

  # test_that("emmGrid equivalence_test", {
  #   testthat::skip_on_travis()
  #   xeqtest <- equivalence_test(all_, ci = 0.9, range = c(-0.1, 0.1))
  #   testthat::expect_equal(length(xeqtest$ROPE_Percentage), 3)
  #   testthat::expect_equal(length(xeqtest$ROPE_Equivalence), 3)
  # })

  # test_that("emmGrid estimate_density", {
  #   testthat::skip_on_travis()
  #   xestden <- estimate_density(c_, method = "logspline", precision = 5)
  #   testthat::expect_equal(length(xestden$x), 5)
  #   testthat::expect_equal(length(log(xestden$y)), 5)
  # })

  # test_that("emmGrid p_direction", {
  #   testthat::skip_on_travis()
  #   xpd <- p_direction(all_, method = "direct")
  #   testthat::expect_equal(length(xpd$pd), 3)
  # })

  # test_that("emmGrid p_map", {
  #   testthat::skip_on_travis()
  #   xpmap <- p_map(all_, precision = 2^9)
  #   testthat::expect_equal(length(xpmap$p_MAP), 3)
  # })

  # test_that("emmGrid mhdior", {
  #   testthat::skip_on_travis()
  #   xprope <- mhdior(all_, range = c(-0.1, 0.1), precision = 0.5)
  #   testthat::expect_equal(length(xprope$mhdior), 3)
  # })

  # test_that("emmGrid rope", {
  #   testthat::skip_on_travis()
  #   xrope <- rope(all_, range = "default", ci = .9)
  #   testthat::expect_equal(length(xrope$ROPE_Percentage), 3)
  # })



# BFs ---------------------------------------------------------------------

  test_that("emmGrid bayesfactor_parameters", {
    testthat::skip_on_cran()
    set.seed(4)
    model_p <- update(model, prior_PD = TRUE)

    set.seed(4)
    testthat::expect_equal(
      bayesfactor_parameters(all_, prior = model),
      bayesfactor_parameters(all_, prior = model_p)
    )

    testthat::expect_warning(bayesfactor_parameters(all_))

    # error - cannot deal with regrid / transform
    testthat::expect_error(bayesfactor_parameters(regrid(all_), prior = model))
  })

  # test_that("emmGrid bayesfactor_restricted", {
  #   testthat::skip_on_travis()
  #   testthat::skip_on_cran()
  #   testthat::skip_on_ci()
  #   set.seed(4)
  #   hyps <- c("`1` < `2`", "`1` < 0")
  #   xrbf <- bayesfactor_restricted(em_, prior = model, hypothesis = hyps)
  #   testthat::expect_equal(length(log(xrbf$BF)), 2)
  #   testthat::expect_equal(length(xrbf$Prior_prob), 2)
  #   testthat::expect_equal(length(xrbf$Posterior_prob), 2)
  #   testthat::expect_warning(bayesfactor_restricted(em_, hypothesis = hyps))
  # })

  # test_that("emmGrid si", {
  #   testthat::skip_on_travis()
  #   testthat::skip_on_cran()
  #   testthat::skip_on_ci()
  #   set.seed(4)
  #   xrsi <- si(em_, prior = model)
  #   testthat::expect_equal(length(xrsi$CI_low), 2)
  #   testthat::expect_equal(length(xrsi$CI_high), 2)
  # })


# For non linear models ---------------------------------------------------


  set.seed(333)
  df <- data.frame(
    G = rep(letters[1:3], each = 2),
    Y = rexp(6)
  )

  fit_bayes <- stan_glm(Y ~ G,
                        data = df,
                        family = Gamma(link = "identity"),
                        refresh = 0
  )
  fit_bayes_prior <- update(fit_bayes, prior_PD = TRUE)

  bayes_sum <- emmeans(fit_bayes, ~G)
  bayes_sum_prior <- emmeans(fit_bayes_prior, ~G)

  # test_that("emmGrid bayesfactor_restricted2", {
  #   testthat::skip_on_travis()
  #   testthat::skip_on_cran()
  #   testthat::skip_on_ci()
  #
  #   hyps <- c("a < b", "b < c")
  #   xrbf1 <- bayesfactor_restricted(bayes_sum, fit_bayes, hypothesis = hyps)
  #   xrbf2 <- bayesfactor_restricted(bayes_sum, bayes_sum_prior, hypothesis = hyps)
  #
  #   testthat::expect_equal(xrbf1, xrbf2, tolerance = 0.1)
  # })


  test_that("emmGrid bayesfactor_parameters", {
    set.seed(333)

    xsdbf1 <- bayesfactor_parameters(bayes_sum, prior = fit_bayes)
    xsdbf2 <- bayesfactor_parameters(bayes_sum, prior = bayes_sum_prior)

    testthat::expect_equal(log(xsdbf1$BF), log(xsdbf2$BF), tolerance = 0.1)
  })

  # link vs response
  test_that("emmGrid bayesfactor_parameters / describe w/ nonlinear models", {
    testthat::skip_on_cran()

    model <- stan_glm(vs ~ mpg,
                      data = mtcars,
                      family = "binomial",
                      refresh = 0)

    probs <- emmeans(model, "mpg", type = "resp")
    link <- emmeans(model, "mpg")

    probs_summ <- summary(probs)
    link_summ <- summary(link)

    xhdi <- hdi(probs, ci = 0.95)
    xpest <- point_estimate(probs, centrality = "median", dispersion = TRUE)
    testthat::expect_equal(xhdi$CI_low, probs_summ$lower.HPD, tolerance = 0.1)
    testthat::expect_equal(xhdi$CI_high, probs_summ$upper.HPD, tolerance = 0.1)
    testthat::expect_equal(xpest$Median, probs_summ$prob, tolerance = 0.1)


    xhdi <- hdi(link, ci = 0.95)
    xpest <- point_estimate(link, centrality = "median", dispersion = TRUE)
    testthat::expect_equal(xhdi$CI_low, link_summ$lower.HPD, tolerance = 0.1)
    testthat::expect_equal(xhdi$CI_high, link_summ$upper.HPD, tolerance = 0.1)
    testthat::expect_equal(xpest$Median, link_summ$emmean, tolerance = 0.1)
  })
}
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