tests/testthat/test-random_effects_ci.R

In parameters: Processing of Model Parameters

skip_on_cran()

skip_on_os("mac")
skip_if_not_installed("lme4")

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

m1 <- suppressMessages(lme4::lmer(
  angle ~ temperature + (temperature | recipe) + (temperature | replicate),
  data = cake
))
m2 <- suppressMessages(lme4::lmer(Reaction ~ Days + (Days | Subject), data = sleepstudy))
m3 <- suppressMessages(lme4::lmer(
  angle ~ temperature + (temperature | recipe),
  data = cake
))
m4 <- suppressMessages(lme4::lmer(
  angle ~ temperature + (temperature | replicate),
  data = cake
))
m5 <- suppressMessages(lme4::lmer(
  Reaction ~ Days + (Days + Months | Subject),
  data = sleepstudy
))

## TODO also check messages for profiled CI

expect_message(
  {
    mp1 <- model_parameters(m1, ci_random = TRUE)
  },
  regex = "meaningful"
)
mp2 <- model_parameters(m2, ci_random = TRUE)
expect_message(
  {
    mp3 <- model_parameters(m3, ci_random = TRUE)
  },
  regex = "meaningful"
)
expect_message(
  {
    mp4 <- model_parameters(m4, ci_random = TRUE)
  },
  regex = "meaningful"
)
expect_message(
  {
    mp5 <- model_parameters(m5, ci_random = TRUE)
  },
  regex = "meaningful"
)


# model 1 ---------------------

test_that("random effects CIs, two slopes, categorical", {
  expect_equal(
    mp1$CI_low,
    c(
      28.75568,
      4.97893,
      -1.95002,
      -2.69995,
      -3.62201,
      -2.69102,
      4.28558,
      0.21474,
      0.40062,
      0.10169,
      0.04953,
      1e-05,
      0.55398,
      0,
      2e-05,
      0.6333,
      1.09851,
      0.00944,
      -0.65406,
      -0.69103,
      -1,
      -0.95271,
      -0.90617,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -0.99802,
      -1,
      -0.75274,
      -0.99836,
      -1,
      -0.96895,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      4.07985
    ),
    tolerance = 1e-3,
    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(
      "",
      "",
      "",
      "",
      "",
      "",
      "replicate",
      "recipe",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "replicate",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "Residual"
    )
  )
})


# model 2 ---------------------

test_that("random effects CIs, simple slope", {
  expect_equal(
    mp2$CI_low,
    c(237.93546, 7.41637, 15.5817, 3.91828, -0.50907, 22.80044),
    tolerance = 1e-3,
    ignore_attr = TRUE
  )

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

  expect_identical(mp2$Group, c("", "", "Subject", "Subject", "Subject", "Residual"))
})


# model 3 ---------------------

test_that("random effects CIs, categorical slope-1", {
  expect_equal(
    mp3$CI_low[14:28],
    c(-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 7.09933),
    tolerance = 1e-2,
    ignore_attr = TRUE
  )

  expect_equal(
    mp3$CI_low[1:12],
    c(
      30.91139,
      4.33247,
      -2.6798,
      -3.20703,
      -4.07681,
      -3.27237,
      0.06301,
      0,
      0,
      0.1192,
      0.32213,
      0
    ),
    tolerance = 1e-2,
    ignore_attr = TRUE
  )
  expect_identical(
    mp3$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"
    )
  )
})


# model 4 ---------------------

test_that("random effects CIs, categorical slope-2", {
  expect_equal(
    mp4$CI_low,
    c(
      28.88523,
      4.96796,
      -1.93239,
      -1.98597,
      -2.68858,
      -2.5524,
      4.27899,
      0.35378,
      0.08109,
      0.03419,
      0,
      0.49982,
      -0.68893,
      -0.71984,
      -1,
      -0.96725,
      -0.92158,
      -1,
      -0.99894,
      -1,
      -0.80378,
      -0.99924,
      -1,
      -0.9778,
      -1,
      -1,
      -1,
      4.21143
    ),
    tolerance = 1e-3,
    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"
    )
  )
})


# model 5 ---------------------

test_that("random effects CIs, double slope", {
  expect_equal(
    mp5$CI_low,
    c(237.99863, 7.4022, 12.63814, 0.58664, 0, -0.58599, -1, -1, 22.65226),
    tolerance = 1e-3,
    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)"
    )
  )

  expect_identical(
    mp5$Group,
    c(
      "",
      "",
      "Subject",
      "Subject",
      "Subject",
      "Subject",
      "Subject",
      "Subject",
      "Residual"
    )
  )
})


# no random intercept --------------------------
test_that("random effects CIs, simple slope", {
  data(sleepstudy, package = "lme4")
  set.seed(123)
  sleepstudy$Months <- sample.int(4, nrow(sleepstudy), TRUE)

  m2 <- lme4::lmer(Reaction ~ Days + (0 + Days | Subject), data = sleepstudy)
  m5 <- lme4::lmer(Reaction ~ Days + (0 + Days + Months | Subject), data = sleepstudy)

  mp2 <- model_parameters(m2)
  mp5 <- model_parameters(m5)
  expect_equal(
    mp2$CI_low,
    c(243.47155, 6.77765, 5.09041, 26.01525),
    tolerance = 1e-3,
    ignore_attr = TRUE
  )

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

  expect_equal(
    mp5$CI_low,
    c(241.61021, 7.43503, 4.11446, 2.69857, -0.40595, 24.632),
    tolerance = 1e-3,
    ignore_attr = TRUE
  )

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


# poly random slope --------------------------
test_that("random effects CIs, poly slope", {
  data(cake, package = "lme4")
  suppressMessages({
    m <- lme4::lmer(
      angle ~ poly(temp, 2) + (poly(temp, 2) | replicate) + (1 | recipe),
      data = cake
    )
  })
  mp <- model_parameters(m, ci_random = TRUE)

  expect_equal(
    mp$CI_low,
    c(
      28.7884,
      33.56318,
      -12.84259,
      4.27435,
      0.16222,
      7.78988,
      0.87668,
      -0.8172,
      -1,
      -1,
      4.32855
    ),
    tolerance = 1e-3,
    ignore_attr = TRUE
  )

  expect_identical(
    mp$Parameter,
    c(
      "(Intercept)",
      "poly(temp, 2)1",
      "poly(temp, 2)2",
      "SD (Intercept)",
      "SD (Intercept)",
      "SD (poly(temp, 2)1)",
      "SD (poly(temp, 2)2)",
      "Cor (Intercept~poly(temp, 2)1)",
      "Cor (Intercept~poly(temp, 2)2)",
      "Cor (poly(temp, 2)1~poly(temp, 2)2)",
      "SD (Observations)"
    )
  )
})


# poly and categorical random slope --------------------------

test_that("random effects CIs, poly categorical slope", {
  ## NOTE check back every now and then and see if tests still work
  skip("works interactively")

  m <- lme4::lmer(
    angle ~ poly(temp, 2) + (poly(temp, 2) | replicate) + (temperature | recipe),
    data = cake
  )
  mp <- model_parameters(m, effects = "random")

  expect_equal(
    mp$CI_low,
    c(
      4.27846,
      0.22005,
      8.22659,
      1.17579,
      0,
      5e-05,
      0.37736,
      1.24258,
      0,
      -0.77207,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      -1,
      4.22056
    ),
    tolerance = 1e-3,
    ignore_attr = TRUE
  )

  expect_identical(
    mp$Parameter,
    c(
      "SD (Intercept)",
      "SD (Intercept)",
      "SD (poly(temp, 2)1)",
      "SD (poly(temp, 2)2)",
      "SD (temperature.L)",
      "SD (temperature.Q)",
      "SD (temperature.C)",
      "SD (temperature^4)",
      "SD (temperature^5)",
      "Cor (Intercept~poly(temp, 2)1)",
      "Cor (Intercept~poly(temp, 2)2)",
      "Cor (Intercept~temperature.L)",
      "Cor (Intercept~temperature.Q)",
      "Cor (Intercept~temperature.C)",
      "Cor (Intercept~temperature^4)",
      "Cor (Intercept~temperature^5)",
      "Cor (poly(temp, 2)1~poly(temp, 2)2)",
      "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(
    mp$Group,
    c(
      "replicate",
      "recipe",
      "replicate",
      "replicate",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "replicate",
      "replicate",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "replicate",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "recipe",
      "Residual"
    )
  )
})