tests/testthat/test-random_effects_ci.R

In parameters: Processing of Model Parameters

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

skip_on_cran()


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"
    )
  )
})