tests/testthat/test-model_parameters_std_mixed.R

In parameters: Processing of Model Parameters

skip_if_not_installed("effectsize")
skip_if_not_installed("lme4")
skip_on_cran()


data(iris)
set.seed(1234)
iris$grp <- as.factor(sample(1:3, nrow(iris), replace = TRUE))

# fit example model
model <- lme4::lmer(
  Sepal.Length ~ Species * Sepal.Width + Petal.Length + (1 | grp),
  data = iris
)

test_that("model_parameters, standardize-refit, wald-normal", {
  params <- model_parameters(
    model,
    ci_method = "normal",
    standardize = "refit",
    verbose = FALSE,
    effects = "fixed"
  )
  expect_equal(c(nrow(params), ncol(params)), c(7, 10))
  expect_equal(
    params$Coefficient,
    c(
      0.96949,
      -1.28631,
      -1.81461,
      0.34791,
      1.74252,
      -0.25421,
      -0.18834
    ),
    tolerance = 1e-3
  )
  expect_equal(
    params$SE,
    c(0.2045, 0.2619, 0.34035, 0.05968, 0.13914, 0.09762, 0.0945),
    tolerance = 1e-3
  )
  expect_equal(
    params$CI_high,
    c(
      1.37031,
      -0.77301,
      -1.14754,
      0.46488,
      2.01523,
      -0.06287,
      -0.00312
    ),
    tolerance = 1e-3
  )
})

test_that("model_parameters, standardize-refit, wald-t", {
  params <- model_parameters(
    model,
    ci_method = "wald",
    standardize = "refit",
    verbose = FALSE,
    effects = "fixed"
  )
  expect_equal(
    params$CI_high,
    c(
      1.37378,
      -0.76856,
      -1.14177,
      0.4659,
      2.01759,
      -0.06121,
      -0.00151
    ),
    tolerance = 1e-3
  )
})

test_that("model_parameters, standardize-refit", {
  params <- model_parameters(
    model,
    standardize = "refit",
    verbose = FALSE,
    effects = "fixed"
  )
  expect_equal(c(nrow(params), ncol(params)), c(7, 10))
  expect_equal(
    params$Coefficient,
    c(
      0.96949,
      -1.28631,
      -1.81461,
      0.34791,
      1.74252,
      -0.25421,
      -0.18834
    ),
    tolerance = 1e-3
  )
  expect_equal(params$SE,
    c(0.2045, 0.2619, 0.34035, 0.05968, 0.13914, 0.09762, 0.0945),
    tolerance = 1e-3
  )
  expect_equal(
    params$CI_high,
    c(
      1.37378,
      -0.76856,
      -1.14177,
      0.4659,
      2.01759,
      -0.06121,
      -0.00151
    ),
    tolerance = 1e-3
  )

  params <- model_parameters(
    model,
    standardize = "refit",
    verbose = FALSE,
    effects = "all"
  )
  paramsZ <- model_parameters(
    effectsize::standardize(model),
    effects = "all",
    verbose = FALSE
  )
  expect_equal(paramsZ, params, ignore_attr = TRUE)
})

test_that("model_parameters, standardize-posthoc", {
  params <- model_parameters(model,
    standardize = "posthoc",
    verbose = FALSE,
    effects = "fixed"
  )
  expect_equal(c(nrow(params), ncol(params)), c(7, 10))
  expect_equal(
    params$Std_Coefficient,
    c(0, 0.49679, -0.49355, 0.34791, 1.74252, -0.25421, -0.18834),
    tolerance = 1e-3
  )
  expect_equal(params$SE,
    c(0, 0.66228, 0.70202, 0.05968, 0.13914, 0.09762, 0.0945),
    tolerance = 1e-3
  )
  expect_equal(
    params$CI_high,
    c(0, 1.80607, 0.8943, 0.4659, 2.01759, -0.06121, -0.00151),
    tolerance = 1e-3
  )
})

test_that("model_parameters, standardize-posthoc", {
  params <- model_parameters(
    model,
    ci_method = "normal",
    standardize = "posthoc",
    verbose = FALSE,
    effects = "fixed"
  )
  expect_equal(c(nrow(params), ncol(params)), c(7, 10))
  expect_equal(
    params$Std_Coefficient,
    c(0, 0.49679, -0.49355, 0.34791, 1.74252, -0.25421, -0.18834),
    tolerance = 1e-3
  )
  expect_equal(
    params$SE,
    c(0, 0.66228, 0.70202, 0.05968, 0.13914, 0.09762, 0.0945),
    tolerance = 1e-3
  )
  expect_equal(
    params$CI_high,
    c(0, 1.79483, 0.88238, 0.46488, 2.01523, -0.06287, -0.00312),
    tolerance = 1e-3
  )
})

test_that("model_parameters, standardize-posthoc, wald-t", {
  params <- model_parameters(
    model,
    ci_method = "wald",
    standardize = "posthoc",
    verbose = FALSE,
    effects = "fixed"
  )
  expect_equal(
    params$CI_high,
    c(0, 1.80607, 0.8943, 0.4659, 2.01759, -0.06121, -0.00151),
    tolerance = 1e-3
  )
})

test_that("model_parameters, standardize-basic", {
  params <- model_parameters(
    model,
    ci_method = "normal",
    standardize = "basic",
    verbose = FALSE,
    effects = "fixed"
  )
  expect_equal(c(nrow(params), ncol(params)), c(7, 10))
  expect_equal(
    params$Std_Coefficient,
    c(0, 0.23497, -0.23344, 0.34791, 1.74252, -0.77129, -0.61304),
    tolerance = 1e-3
  )
  expect_equal(params$SE,
    c(0, 0.31325, 0.33204, 0.05968, 0.13914, 0.2962, 0.30761),
    tolerance = 1e-3
  )
  expect_equal(
    params$CI_high,
    c(0, 0.84893, 0.41735, 0.46488, 2.01523, -0.19075, -0.01014),
    tolerance = 1e-3
  )
})

test_that("model_parameters, standardize-basic", {
  params <- model_parameters(
    model,
    ci_method = "residual",
    standardize = "basic",
    verbose = FALSE,
    effects = "fixed"
  )
  expect_equal(c(nrow(params), ncol(params)), c(7, 10))
  expect_equal(
    params$Std_Coefficient,
    c(0, 0.23497, -0.23344, 0.34791, 1.74252, -0.77129, -0.61304),
    tolerance = 1e-3
  )
  expect_equal(
    params$SE,
    c(0, 0.31325, 0.33204, 0.05968, 0.13914, 0.2962, 0.30761),
    tolerance = 1e-3
  )
  expect_equal(
    params$CI_high,
    c(0, 0.85424, 0.42299, 0.4659, 2.01759, -0.18572, -0.00492),
    tolerance = 1e-3
  )
})

test_that("model_parameters, standardize-basic", {
  params <- model_parameters(model,
    standardize = "basic",
    verbose = FALSE,
    effects = "fixed"
  )
  expect_equal(
    params$CI_high,
    c(0, 0.85424, 0.42299, 0.4659, 2.01759, -0.18572, -0.00492),
    tolerance = 1e-3
  )
})

test_that("model_parameters, standardize-refit robust", {
  skip_if_not_installed("clubSandwich")
  params <- model_parameters(
    model,
    standardize = "refit",
    effects = "fixed",
    robust = TRUE,
    vcov_estimation = "CR",
    vcov_type = "CR1",
    vcov_args = list(cluster = iris$grp),
    verbose = FALSE
  )
  expect_equal(c(nrow(params), ncol(params)), c(7, 10))
  expect_equal(
    params$Coefficient,
    c(
      0.96949,
      -1.28631,
      -1.81461,
      0.34791,
      1.74252,
      -0.25421,
      -0.18834
    ),
    tolerance = 1e-3
  )
  expect_equal(
    params$SE,
    c(0.07726, 0.33406, 0.22647, 0.0524, 0.10092, 0.18537, 0.05552),
    tolerance = 1e-3
  )
  expect_equal(
    params$CI_high,
    c(
      1.12224,
      -0.6259,
      -1.36691,
      0.45151,
      1.94204,
      0.11227,
      -0.07858
    ),
    tolerance = 1e-3
  )
})