tests/testthat/test-model_parameters_df_method.R

In parameters: Processing of Model Parameters

skip_if_not_installed("lmerTest")
skip_if_not_installed("pbkrtest")
skip_if_not_installed("lme4")
skip_if_not_installed("glmmTMB", minimum_version = "1.1.13")
skip_if_not_installed("insight", minimum_version = "1.4.3")

mtcars$cyl <- as.factor(mtcars$cyl)
model <- suppressMessages(lme4::lmer(
  mpg ~ as.factor(gear) * hp + as.factor(am) + wt + (1 | cyl),
  data = mtcars
))
model2 <- suppressMessages(lmerTest::lmer(
  mpg ~ as.factor(gear) * hp + as.factor(am) + wt + (1 | cyl),
  data = mtcars
))
model3 <- suppressMessages(glmmTMB::glmmTMB(
  mpg ~ as.factor(gear) * hp + as.factor(am) + wt + (1 | cyl),
  data = mtcars,
  REML = TRUE
))
model4 <- suppressMessages(glmmTMB::glmmTMB(
  mpg ~ as.factor(gear) * hp + as.factor(am) + wt + (1 | cyl),
  data = mtcars,
  REML = FALSE
))

mp0 <- model_parameters(model, digits = 5, effects = "fixed")
mp1 <- model_parameters(model, digits = 5, ci_method = "normal", effects = "fixed")
mp2 <- model_parameters(model, digits = 5, ci_method = "s", effects = "fixed")
mp3 <- model_parameters(model, digits = 5, ci_method = "kr", effects = "fixed")
mp4 <- model_parameters(model, digits = 5, ci_method = "wald", effects = "fixed")
mp5 <- model_parameters(model3, digits = 5, ci_method = "kr", effects = "fixed")
mp6 <- model_parameters(
  model3,
  digits = 5,
  ci_method = "satterthwaite",
  effects = "fixed"
)

test_that("model_parameters, ci_method default (residual)", {
  expect_equal(
    mp0$SE,
    c(2.77457, 3.69574, 3.521, 0.01574, 1.58514, 0.86316, 0.02973, 0.01668),
    tolerance = 1e-3
  )
  expect_equal(mp0$df, c(22, 22, 22, 22, 22, 22, 22, 22), tolerance = 1e-3)
  expect_equal(
    mp0$p,
    c(0, 0.00258, 0.14297, 0.17095, 0.84778, 0.00578, 0.00151, 0.32653),
    tolerance = 1e-3
  )
  expect_equal(
    mp0$CI_low,
    c(24.54722, 4.89698, -1.95317, -0.05493, -2.97949, -4.42848, -0.16933, -0.05133),
    tolerance = 1e-3
  )
})

test_that("model_parameters, ci_method normal", {
  expect_equal(
    mp1$SE,
    c(2.77457, 3.69574, 3.521, 0.01574, 1.58514, 0.86316, 0.02973, 0.01668),
    tolerance = 1e-3
  )
  expect_equal(mp1$df, c(22, 22, 22, 22, 22, 22, 22, 22), tolerance = 1e-3)
  expect_equal(
    mp1$p,
    c(0, 0.00068, 0.12872, 0.15695, 0.846, 0.00224, 0.00029, 0.31562),
    tolerance = 1e-3
  )
  expect_equal(
    mp1$CI_low,
    c(24.86326, 5.31796, -1.5521, -0.05313, -2.79893, -4.33015, -0.16595, -0.04943),
    tolerance = 1e-3
  )
})

test_that("model_parameters, ci_method satterthwaite", {
  expect_equal(
    mp2$SE,
    c(2.77457, 3.69574, 3.521, 0.01574, 1.58514, 0.86316, 0.02973, 0.01668),
    tolerance = 1e-3
  )
  expect_equal(mp2$df, c(24, 24, 24, 24, 24, 24, 24, 24), tolerance = 1e-3)
  expect_equal(
    mp2$p,
    c(0, 0.00236, 0.14179, 0.16979, 0.84763, 0.00542, 0.00136, 0.32563),
    tolerance = 1e-3
  )
  expect_equal(
    mp2$CI_low,
    c(24.57489, 4.93385, -1.91805, -0.05477, -2.96368, -4.41987, -0.16904, -0.05117),
    tolerance = 1e-3
  )
  expect_equal(mp2$SE, mp6$SE, tolerance = 1e-3)
  expect_equal(mp2$df_error, mp6$df_error, tolerance = 1e-3)
})

test_that("model_parameters, ci_method kenward", {
  expect_equal(
    mp3$SE,
    c(2.97608, 6.10454, 3.98754, 0.02032, 1.60327, 0.91599, 0.05509, 0.01962),
    tolerance = 1e-3
  )
  expect_equal(
    mp3$df,
    c(19.39553, 5.27602, 23.57086, 8.97297, 22.7421, 23.76299, 2.72622, 22.82714),
    tolerance = 1e-3
  )
  expect_equal(
    mp3$p,
    c(0, 0.09176, 0.19257, 0.30147, 0.84942, 0.00828, 0.15478, 0.40248),
    tolerance = 1e-3
  )
  expect_equal(
    mp3$CI_low,
    c(24.08091, -2.887, -2.88887, -0.06828, -3.01082, -4.5299, -0.29339, -0.05735),
    tolerance = 1e-3
  )

  expect_equal(mp5$SE, mp3$SE, tolerance = 1e-3)
  expect_equal(mp5$df_error, mp3$df_error, tolerance = 1e-3)

  expect_warning(expect_warning(expect_warning(
    {
      mp7 <- model_parameters(model4, digits = 5, ci_method = "kr", effects = "fixed")
    },
    regex = "Model was not fitted"
  )))

  expect_equal(mp5$SE, mp7$SE, tolerance = 1e-3)
  expect_equal(mp5$df_error, mp7$df_error, tolerance = 1e-3)
})

test_that("model_parameters, ci_method wald (t)", {
  expect_equal(
    mp4$SE,
    c(2.77457, 3.69574, 3.521, 0.01574, 1.58514, 0.86316, 0.02973, 0.01668),
    tolerance = 1e-3
  )
  expect_equal(mp4$df, c(22, 22, 22, 22, 22, 22, 22, 22), tolerance = 1e-3)
  expect_equal(
    mp4$p,
    c(0, 0.00258, 0.14297, 0.17095, 0.84778, 0.00578, 0.00151, 0.32653),
    tolerance = 1e-3
  )
  expect_equal(
    mp4$CI_low,
    c(24.54722, 4.89698, -1.95317, -0.05493, -2.97949, -4.42848, -0.16933, -0.05133),
    tolerance = 1e-3
  )
})


test_that("model_parameters, satterthwaite compare", {
  s <- summary(model2)
  expect_equal(mp2$df, as.vector(s$coefficients[, "df"]), tolerance = 1e-4)
  expect_equal(mp2$t, as.vector(s$coefficients[, "t value"]), tolerance = 1e-4)
  expect_equal(mp2$p, as.vector(s$coefficients[, "Pr(>|t|)"]), tolerance = 1e-4)
  expect_equal(mp2$SE, as.vector(s$coefficients[, "Std. Error"]), tolerance = 1e-4)
})

test_that("model_parameters, satterthwaite Conf Int-1", {
  ci1 <- ci_satterthwaite(model)
  expect_equal(mp2$CI_low, ci1$CI_low, tolerance = 1e-4)
  ci2 <- ci_satterthwaite(model2)
  expect_equal(mp2$CI_low, ci2$CI_low, tolerance = 1e-4)
})

test_that("model_parameters, satterthwaite Conf Int-2", {
  coef.table <- as.data.frame(summary(model2)$coefficients)
  coef.table$CI_low <- coef.table$Estimate -
    (coef.table$"Std. Error" * qt(0.975, df = coef.table$df))
  coef.table$CI_high <- coef.table$Estimate +
    (coef.table$"Std. Error" * qt(0.975, df = coef.table$df))

  expect_equal(mp2$CI_low, coef.table$CI_low, tolerance = 1e-4)
  expect_equal(mp2$CI_high, coef.table$CI_high, tolerance = 1e-4)
})

test_that("model_parameters, Kenward-Roger compare", {
  s <- summary(model2, ddf = "Kenward-Roger")
  expect_equal(mp3$df, as.vector(s$coefficients[, "df"]), tolerance = 1e-4)
  expect_equal(mp3$t, as.vector(s$coefficients[, "t value"]), tolerance = 1e-4)
  expect_equal(mp3$p, as.vector(s$coefficients[, "Pr(>|t|)"]), tolerance = 1e-4)
  expect_equal(mp3$SE, as.vector(s$coefficients[, "Std. Error"]), tolerance = 1e-4)
})


model <- lm(mpg ~ as.factor(gear) * hp + as.factor(am) + wt, data = mtcars)
test_that("model_parameters, ci_method-lm", {
  expect_s3_class(model_parameters(model), "parameters_model")
  expect_message(model_parameters(model, ci_method = "kenward"))
})