tests/testthat/test-random_effects_ci-glmmTMB.R

In easystats/parameters: Processing of Model Parameters

# Test Setup --------------------------------

skip_on_os(c("mac", "linux", "solaris"))
skip_if_not_installed("glmmTMB", minimum_version = "1.1.5")
skip_if_not_installed("lme4")
skip_on_cran()


# tests --------------------------------

## TODO also check messages for profiled CI

data(sleepstudy, package = "lme4")
data(cake, package = "lme4")
set.seed(123)
sleepstudy$Months <- sample.int(4, nrow(sleepstudy), TRUE)

set.seed(123)
m1 <- suppressWarnings(glmmTMB::glmmTMB(
  angle ~ temperature + (temperature | recipe) + (temperature | replicate),
  data = cake
))
m2 <- glmmTMB::glmmTMB(Reaction ~ Days + (Days | Subject), data = sleepstudy)
m3 <- suppressWarnings(glmmTMB::glmmTMB(angle ~ temperature + (temperature | recipe), data = cake))
m4 <- suppressWarnings(glmmTMB::glmmTMB(angle ~ temperature + (temperature | replicate), data = cake))
m5 <- suppressWarnings(glmmTMB::glmmTMB(Reaction ~ Days + (Days + Months | Subject), data = sleepstudy))

set.seed(123)
expect_message(
  {
    mp1 <- model_parameters(m1, ci_random = TRUE)
  },
  "singularity"
)
mp2 <- model_parameters(m2, ci_random = TRUE) # works
expect_message(
  {
    mp3 <- model_parameters(m3, ci_random = TRUE)
  },
  "singularity"
) # no SE/CI
mp4 <- model_parameters(m4, ci_random = TRUE)
expect_message(
  {
    mp5 <- model_parameters(m5, ci_random = TRUE)
  },
  "singularity"
) # no SE/CI

test_that("random effects CIs, two slopes, categorical", {
  ## FIXME: Results differ across R versions, no idea why...
  # expect_equal(
  #   mp1$CI_low,
  #   c(
  #     28.91277, 5.03129, -1.87302, -2.42033, -3.2702, -2.57721, 0.2157,
  #     4.20738, NaN, NaN, 0.26244, 0.34083, 0.02479, 0.66487, 0.40589,
  #     0.15295, 0.01405, 0.62939, -0.99996, -0.41209, NaN, NaN, NaN,
  #     -0.40223, NaN, NaN, NaN, NaN, NA, NA, NA, NA, NA, NA, NA, NA,
  #     NA, NaN, NA, NA, NA, NA, NA, NA, NA, NA, NA, NaN, 4.12596
  #   ),
  #   tolerance = 1e-2,
  #   ignore_attr = TRUE
  # )

  expect_identical(
    mp1$Parameter,
    c(
      "(Intercept)", "temperature.L", "temperature.Q", "temperature.C",
      "temperature^4", "temperature^5", "SD (Intercept)", "SD (Intercept)",
      "SD (temperature.L)", "SD (temperature.Q)", "SD (temperature.C)",
      "SD (temperature^4)", "SD (temperature^5)", "SD (temperature.L)",
      "SD (temperature.Q)", "SD (temperature.C)", "SD (temperature^4)",
      "SD (temperature^5)", "Cor (Intercept~temperature.L)", "Cor (Intercept~temperature.Q)",
      "Cor (Intercept~temperature.C)", "Cor (Intercept~temperature^4)",
      "Cor (Intercept~temperature^5)", "Cor (Intercept~temperature.L)",
      "Cor (Intercept~temperature.Q)", "Cor (Intercept~temperature.C)",
      "Cor (Intercept~temperature^4)", "Cor (Intercept~temperature^5)",
      "Cor (temperature.L~temperature.Q)", "Cor (temperature.L~temperature.C)",
      "Cor (temperature.L~temperature^4)", "Cor (temperature.L~temperature^5)",
      "Cor (temperature.Q~temperature.C)", "Cor (temperature.Q~temperature^4)",
      "Cor (temperature.Q~temperature^5)", "Cor (temperature.C~temperature^4)",
      "Cor (temperature.C~temperature^5)", "Cor (temperature^4~temperature^5)",
      "Cor (temperature.L~temperature.Q)", "Cor (temperature.L~temperature.C)",
      "Cor (temperature.L~temperature^4)", "Cor (temperature.L~temperature^5)",
      "Cor (temperature.Q~temperature.C)", "Cor (temperature.Q~temperature^4)",
      "Cor (temperature.Q~temperature^5)", "Cor (temperature.C~temperature^4)",
      "Cor (temperature.C~temperature^5)", "Cor (temperature^4~temperature^5)",
      "SD (Observations)"
    )
  )

  expect_identical(
    mp1$Group,
    c(
      "", "", "", "", "", "", "recipe", "replicate", "recipe", "recipe",
      "recipe", "recipe", "recipe", "replicate", "replicate", "replicate",
      "replicate", "replicate", "recipe", "recipe", "recipe", "recipe",
      "recipe", "replicate", "replicate", "replicate", "replicate",
      "replicate", "recipe", "recipe", "recipe", "recipe", "recipe",
      "recipe", "recipe", "recipe", "recipe", "recipe", "replicate",
      "replicate", "replicate", "replicate", "replicate", "replicate",
      "replicate", "replicate", "replicate", "replicate", "Residual"
    )
  )
})


test_that("random effects CIs, simple slope", {
  expect_equal(
    mp2$CI_low,
    c(238.40611, 7.52295, 15.01709, 3.80546, -0.48781, 22.80047),
    tolerance = 1e-2,
    ignore_attr = TRUE
  )

  expect_identical(
    mp2$Parameter,
    c(
      "(Intercept)", "Days", "SD (Intercept)", "SD (Days)", "Cor (Intercept~Days)",
      "SD (Observations)"
    )
  )
})


test_that("random effects CIs, categorical slope-1", {
  ## FIXME: Results differ across R versions, no idea why...
  # expect_equal(
  #   mp3$CI_low,
  #   c(
  #     31.20278, 4.35879, -2.63767, -2.80041, -3.54983, -3.16627,
  #     0, 0, NaN, NaN, 0, 0, -1, NaN, NaN, NaN, NaN, NA, NA, NA, NA,
  #     NA, NA, NA, NA, NA, NaN, 7.08478
  #   ),
  #   tolerance = 1e-2,
  #   ignore_attr = TRUE
  # )

  expect_identical(
    mp3$Parameter,
    c(
      "(Intercept)", "temperature.L", "temperature.Q", "temperature.C",
      "temperature^4", "temperature^5", "SD (Intercept)", "SD (temperature.L)",
      "SD (temperature.Q)", "SD (temperature.C)", "SD (temperature^4)",
      "SD (temperature^5)", "Cor (Intercept~temperature.L)", "Cor (Intercept~temperature.Q)",
      "Cor (Intercept~temperature.C)", "Cor (Intercept~temperature^4)",
      "Cor (Intercept~temperature^5)", "Cor (temperature.L~temperature.Q)",
      "Cor (temperature.L~temperature.C)", "Cor (temperature.L~temperature^4)",
      "Cor (temperature.L~temperature^5)", "Cor (temperature.Q~temperature.C)",
      "Cor (temperature.Q~temperature^4)", "Cor (temperature.Q~temperature^5)",
      "Cor (temperature.C~temperature^4)", "Cor (temperature.C~temperature^5)",
      "Cor (temperature^4~temperature^5)", "SD (Observations)"
    )
  )

  expect_identical(
    mp3$Group,
    c(
      "", "", "", "", "", "", "recipe", "recipe", "recipe", "recipe",
      "recipe", "recipe", "recipe", "recipe", "recipe", "recipe", "recipe",
      "recipe", "recipe", "recipe", "recipe", "recipe", "recipe", "recipe",
      "recipe", "recipe", "recipe", "Residual"
    )
  )
})


test_that("random effects CIs, categorical slope-2", {
  ## FIXME: Results differ across R versions, no idea why...
  # expect_equal(
  #   mp4$CI_low,
  #   c(
  #     29.01106, 5.01248, -1.89447, -1.96271, -2.66795, -2.50896,
  #     4.23401, 0.62943, 0.36949, 0.13979, 0.01129, 0.6074, 0.50155,
  #     -0.30497, -0.94063, -0.13156, -0.32484, NA, NA, NA, NA, NA, NA,
  #     NA, NA, NA, 0.42465, 4.2358
  #   )
  #   ,
  #   tolerance = 1e-2,
  #   ignore_attr = TRUE
  # )

  expect_identical(
    mp4$Parameter,
    c(
      "(Intercept)", "temperature.L", "temperature.Q", "temperature.C",
      "temperature^4", "temperature^5", "SD (Intercept)", "SD (temperature.L)",
      "SD (temperature.Q)", "SD (temperature.C)", "SD (temperature^4)",
      "SD (temperature^5)", "Cor (Intercept~temperature.L)", "Cor (Intercept~temperature.Q)",
      "Cor (Intercept~temperature.C)", "Cor (Intercept~temperature^4)",
      "Cor (Intercept~temperature^5)", "Cor (temperature.L~temperature.Q)",
      "Cor (temperature.L~temperature.C)", "Cor (temperature.L~temperature^4)",
      "Cor (temperature.L~temperature^5)", "Cor (temperature.Q~temperature.C)",
      "Cor (temperature.Q~temperature^4)", "Cor (temperature.Q~temperature^5)",
      "Cor (temperature.C~temperature^4)", "Cor (temperature.C~temperature^5)",
      "Cor (temperature^4~temperature^5)", "SD (Observations)"
    )
  )

  expect_identical(
    mp4$Group,
    c(
      "", "", "", "", "", "", "replicate", "replicate", "replicate",
      "replicate", "replicate", "replicate", "replicate", "replicate",
      "replicate", "replicate", "replicate", "replicate", "replicate",
      "replicate", "replicate", "replicate", "replicate", "replicate",
      "replicate", "replicate", "replicate", "Residual"
    )
  )
})


test_that("random effects CIs, double slope", {
  expect_equal(
    mp5$CI_low,
    c(238.40606, 7.52296, 15.0171, 3.80547, 0, -0.48781, NaN, NaN, 22.80045),
    tolerance = 1e-2,
    ignore_attr = TRUE
  )

  expect_identical(
    mp5$Parameter,
    c(
      "(Intercept)", "Days", "SD (Intercept)", "SD (Days)", "SD (Months)",
      "Cor (Intercept~Days)", "Cor (Intercept~Months)",
      "Cor (Days~Months)", "SD (Observations)"
    )
  )
})


test_that("random effects CIs, simple slope", {
  data(sleepstudy, package = "lme4")
  set.seed(123)
  sleepstudy$Months <- sample.int(4, nrow(sleepstudy), TRUE)

  set.seed(123)
  m2 <- glmmTMB::glmmTMB(Reaction ~ Days + (0 + Days | Subject), data = sleepstudy)
  m5 <- suppressWarnings(glmmTMB::glmmTMB(Reaction ~ Days + (0 + Days + Months | Subject), data = sleepstudy))

  set.seed(123)
  mp2 <- model_parameters(m2, ci_random = TRUE)
  expect_message(
    {
      mp5 <- model_parameters(m5, ci_random = TRUE)
    },
    "singularity"
  ) # no SE/CI
  expect_equal(
    mp2$CI_low,
    c(243.55046, 6.89554, 4.98429, 25.94359),
    tolerance = 1e-2,
    ignore_attr = TRUE
  )

  expect_identical(
    mp2$Parameter,
    c("(Intercept)", "Days", "SD (Days)", "SD (Observations)")
  )

  ## FIXME: Results differ across R versions, no idea why...
  # expect_equal(
  #   mp5$CI_low,
  #   c(237.03695, 9.04139, NaN, 8.95755, NaN, 30.67054),
  #   tolerance = 1e-2,
  #   ignore_attr = TRUE
  # )

  expect_identical(
    mp5$Parameter,
    c(
      "(Intercept)", "Days", "SD (Days)", "SD (Months)", "Cor (Days~Months)",
      "SD (Observations)"
    )
  )
})


# messages for profiled CI
test_that("profiled CI messages", {
  mp2 <- model_parameters(m2, ci_method = "profile")
  expect_message(utils::capture.output(print(mp2)), regexp = "(.*)profile-likelihood(.*)z-distribution(.*)")
})