test-glmmTMB.R
In parameters: Processing of Model Parameters

skip_on_cran()

skip_if_not_installed("withr")
skip_if_not_installed("glmmTMB")
skip_if_not(getRversion() >= "4.0.0")

data("fish", package = "parameters")
data("Salamanders", package = "glmmTMB")

withr::with_options(list(parameters_exponentiate = FALSE), {
  m1 <- suppressWarnings(glmmTMB::glmmTMB(
    count ~ child + camper + (1 | persons),
    ziformula = ~ child + camper + (1 | persons),
    data = fish,
    family = glmmTMB::truncated_poisson()
  ))

  m2 <- suppressWarnings(glmmTMB::glmmTMB(
    count ~ child + camper + (1 | persons),
    data = fish,
    family = poisson()
  ))

  m3 <- suppressWarnings(glmmTMB::glmmTMB(
    count ~ spp + mined + (1 | site),
    ziformula = ~ spp + mined,
    family = glmmTMB::nbinom2,
    data = Salamanders
  ))

  test_that("ci", {
    expect_equal(
      ci(m1)$CI_low,
      c(0.33067, -1.32402, 0.55037, -1.66786, 1.44667, -1.64177),
      tolerance = 1e-3
    )
    expect_equal(
      ci(m1, component = "cond")$CI_low,
      c(0.33067, -1.32402, 0.55037),
      tolerance = 1e-3
    )
    expect_equal(
      ci(m1, component = "zi")$CI_low,
      c(-1.66786, 1.44667, -1.64177),
      tolerance = 1e-3
    )

    expect_equal(ci(m2)$CI_low, c(-0.47982, -1.85096, 0.76044), tolerance = 1e-3)
    expect_equal(
      ci(m2, component = "cond")$CI_low,
      c(-0.47982, -1.85096, 0.76044),
      tolerance = 1e-3
    )

    expect_message(expect_null(ci(m2, component = "zi")), "no zero-inflation component")
  })

  test_that("se", {
    expect_equal(
      standard_error(m1)$SE,
      c(0.47559, 0.09305, 0.09346, 0.65229, 0.3099, 0.32324),
      tolerance = 1e-3
    )
    expect_equal(
      standard_error(m1, effects = "random")$persons$`(Intercept)`,
      c(0.69856, 0.68935, 0.68749, 0.68596),
      tolerance = 1e-3
    )
    expect_equal(
      standard_error(m1, component = "cond")$SE,
      c(0.47559, 0.09305, 0.09346),
      tolerance = 1e-3
    )
    expect_equal(
      standard_error(m1, component = "zi")$SE,
      c(0.65229, 0.3099, 0.32324),
      tolerance = 1e-3
    )

    expect_equal(standard_error(m2)$SE, c(0.62127, 0.08128, 0.08915), tolerance = 1e-3)
    expect_equal(
      standard_error(m2, component = "cond")$SE,
      c(0.62127, 0.08128, 0.08915),
      tolerance = 1e-3
    )

    expect_message(
      expect_null(standard_error(m2, component = "zi")),
      "no zero-inflation component"
    )
  })

  test_that("p_value", {
    expect_equal(p_value(m1)$p, c(0.00792, 0, 0, 0.55054, 0, 0.00181), tolerance = 1e-3)
    expect_equal(p_value(m1, component = "cond")$p, c(0.00792, 0, 0), tolerance = 1e-3)
    expect_equal(
      p_value(m1, component = "zi")$p,
      c(0.55054, 0, 0.00181),
      tolerance = 1e-3
    )

    expect_equal(p_value(m2)$p, c(0.23497, 0, 0), tolerance = 1e-3)
    expect_equal(p_value(m2, component = "cond")$p, c(0.23497, 0, 0), tolerance = 1e-3)

    expect_message(
      expect_null(p_value(m2, component = "zi")),
      "no zero-inflation component"
    )
  })

  test_that("model_parameters", {
    expect_equal(
      model_parameters(m1, effects = "fixed")$Coefficient,
      c(1.2628, -1.14165, 0.73354, -0.38939, 2.05407, -1.00823),
      tolerance = 1e-3
    )
    expect_equal(
      model_parameters(m1, effects = "all")$Coefficient,
      c(1.2628, -1.14165, 0.73354, -0.38939, 2.05407, -1.00823, 0.9312, 1.17399),
      tolerance = 1e-3
    )
    expect_equal(
      model_parameters(m2, effects = "fixed")$Coefficient,
      c(0.73785, -1.69166, 0.93516),
      tolerance = 1e-3
    )
    expect_equal(
      model_parameters(m3, effects = "fixed")$Coefficient,
      c(
        -0.61038,
        -0.9637,
        0.17068,
        -0.38706,
        0.48795,
        0.58949,
        -0.11327,
        1.42935,
        0.91004,
        1.16141,
        -0.93932,
        1.04243,
        -0.56231,
        -0.893,
        -2.53981,
        -2.56303,
        1.51165
      ),
      tolerance = 1e-2
    )
    expect_identical(
      model_parameters(m1)$Component,
      c(
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "conditional",
        "zero_inflated"
      )
    )
    expect_null(model_parameters(m2, effects = "fixed")$Component)
    expect_identical(
      model_parameters(m2)$Component,
      c("conditional", "conditional", "conditional", "conditional")
    )
    expect_identical(
      model_parameters(m3, effects = "fixed")$Component,
      c(
        "conditional",
        "conditional",
        "conditional",
        "conditional",
        "conditional",
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "dispersion"
      )
    )
    expect_equal(
      model_parameters(m3, effects = "fixed")$SE,
      c(
        0.4052,
        0.6436,
        0.2353,
        0.3424,
        0.2383,
        0.2278,
        0.2439,
        0.3666,
        0.6279,
        1.3346,
        0.8005,
        0.714,
        0.7263,
        0.7535,
        2.1817,
        0.6045,
        NA
      ),
      tolerance = 1e-2
    )
  })

  test_that("model_parameters.mixed-random", {
    params <- model_parameters(m1, effects = "random", group_level = TRUE)
    expect_identical(c(nrow(params), ncol(params)), c(8L, 10L))
    expect_named(
      params,
      c(
        "Parameter",
        "Level",
        "Coefficient",
        "SE",
        "CI",
        "CI_low",
        "CI_high",
        "Component",
        "Effects",
        "Group"
      )
    )
    expect_identical(
      as.vector(params$Parameter),
      c(
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)"
      )
    )
    expect_identical(
      params$Component,
      c(
        "conditional",
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated"
      )
    )
    expect_equal(
      params$Coefficient,
      c(-1.24, -0.3456, 0.3617, 1.2553, 1.5719, 0.3013, -0.3176, -1.5665),
      tolerance = 1e-2
    )
  })

  test_that("model_parameters.mixed-random grouplevel", {
    params <- model_parameters(m1, effects = "grouplevel")
    expect_identical(c(nrow(params), ncol(params)), c(8L, 10L))
    expect_named(
      params,
      c(
        "Parameter",
        "Level",
        "Coefficient",
        "SE",
        "CI",
        "CI_low",
        "CI_high",
        "Component",
        "Effects",
        "Group"
      )
    )
    expect_identical(
      as.vector(params$Parameter),
      c(
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)"
      )
    )
    expect_identical(
      params$Component,
      c(
        "conditional",
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated"
      )
    )
    expect_equal(
      params$Coefficient,
      c(-1.24, -0.3456, 0.3617, 1.2553, 1.5719, 0.3013, -0.3176, -1.5665),
      tolerance = 1e-2
    )
  })

  test_that("model_parameters.mixed-random total", {
    params <- model_parameters(m1, effects = "total")
    expect_identical(c(nrow(params), ncol(params)), c(8L, 6L))
    expect_named(
      params,
      c("Group", "Level", "Parameter", "Coefficient", "Component", "Effects")
    )
    expect_identical(
      as.vector(params$Parameter),
      c(
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)"
      )
    )
    expect_identical(
      params$Component,
      c(
        "conditional",
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated"
      )
    )
    expect_equal(
      params$Coefficient,
      c(0.02278, 0.91717, 1.62455, 2.51811, 1.18248, -0.08808, -0.70703, -1.95584),
      tolerance = 1e-2
    )
  })

  test_that("model_parameters.mixed-ran_pars", {
    params <- model_parameters(m1, effects = "random")
    expect_identical(c(nrow(params), ncol(params)), c(2L, 9L))
    expect_named(
      params,
      c(
        "Parameter",
        "Coefficient",
        "SE",
        "CI",
        "CI_low",
        "CI_high",
        "Effects",
        "Group",
        "Component"
      )
    )
    expect_identical(params$Parameter, c("SD (Intercept)", "SD (Intercept)"))
    expect_identical(params$Component, c("conditional", "zero_inflated"))
    expect_equal(params$Coefficient, c(0.9312, 1.17399), tolerance = 1e-2)
  })

  test_that("model_parameters.mixed-all_pars", {
    params <- model_parameters(m1, effects = "all")
    expect_identical(c(nrow(params), ncol(params)), c(8L, 12L))
    expect_named(
      params,
      c(
        "Parameter",
        "Coefficient",
        "SE",
        "CI",
        "CI_low",
        "CI_high",
        "z",
        "df_error",
        "p",
        "Effects",
        "Group",
        "Component"
      )
    )
    expect_identical(
      params$Parameter,
      c(
        "(Intercept)",
        "child",
        "camper1",
        "(Intercept)",
        "child",
        "camper1",
        "SD (Intercept)",
        "SD (Intercept)"
      )
    )
    expect_identical(
      params$Component,
      c(
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "conditional",
        "zero_inflated"
      )
    )
    expect_equal(
      params$Coefficient,
      c(1.2628, -1.14165, 0.73354, -0.38939, 2.05407, -1.00823, 0.9312, 1.17399),
      tolerance = 1e-2
    )
  })

  test_that("model_parameters.mixed-all", {
    params <- model_parameters(m1, effects = "all", group_level = TRUE)
    expect_identical(c(nrow(params), ncol(params)), c(14L, 13L))
    expect_named(
      params,
      c(
        "Parameter",
        "Level",
        "Coefficient",
        "SE",
        "CI",
        "CI_low",
        "CI_high",
        "z",
        "df_error",
        "p",
        "Component",
        "Effects",
        "Group"
      )
    )
    expect_identical(
      params$Parameter,
      c(
        "(Intercept)",
        "child",
        "camper1",
        "(Intercept)",
        "child",
        "camper1",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)",
        "(Intercept)"
      )
    )
    expect_identical(
      params$Component,
      c(
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "conditional",
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated"
      )
    )
    expect_equal(
      params$Coefficient,
      c(
        1.2628,
        -1.1417,
        0.7335,
        -0.3894,
        2.0541,
        -1.0082,
        -1.24,
        -0.3456,
        0.3617,
        1.2553,
        1.5719,
        0.3013,
        -0.3176,
        -1.5665
      ),
      tolerance = 1e-2
    )
  })

  data(mtcars)
  mdisp <- glmmTMB::glmmTMB(hp ~ 0 + wt / mpg, mtcars)
  test_that("model_parameters, dispersion", {
    mp <- model_parameters(mdisp)
    expect_equal(mp$Coefficient, c(59.50992, -0.80396, 48.97731), tolerance = 1e-2)
    expect_identical(mp$Parameter, c("wt", "wt:mpg", "(Intercept)"))
    expect_identical(mp$Component, c("conditional", "conditional", "dispersion"))
  })

  mdisp <- glmmTMB::glmmTMB(hp ~ 0 + wt / mpg + (1 | gear), mtcars)
  test_that("model_parameters, dispersion", {
    mp <- model_parameters(mdisp)
    expect_equal(
      mp$Coefficient,
      c(58.25869, -0.87868, 47.01676, 36.99492),
      tolerance = 1e-2
    )
    expect_identical(
      mp$Parameter,
      c("wt", "wt:mpg", "SD (Intercept)", "SD (Observations)")
    )
    expect_identical(
      mp$Component,
      c("conditional", "conditional", "conditional", "conditional")
    )
  })

  m4 <- suppressWarnings(glmmTMB::glmmTMB(
    count ~ child + camper + (1 + xb | persons),
    ziformula = ~ child + camper + (1 + zg | persons),
    data = fish,
    family = glmmTMB::truncated_poisson()
  ))

  test_that("model_parameters.mixed-ran_pars", {
    expect_message(
      {
        params <- model_parameters(m4, effects = "random")
      },
      regex = "Your model may"
    )
    expect_identical(c(nrow(params), ncol(params)), c(6L, 9L))
    expect_named(
      params,
      c(
        "Parameter",
        "Coefficient",
        "SE",
        "CI",
        "CI_low",
        "CI_high",
        "Effects",
        "Group",
        "Component"
      )
    )
    expect_identical(
      params$Parameter,
      c(
        "SD (Intercept)",
        "SD (xb)",
        "Cor (Intercept~xb)",
        "SD (Intercept)",
        "SD (zg)",
        "Cor (Intercept~zg)"
      )
    )
    expect_identical(
      params$Component,
      c(
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated"
      )
    )
    expect_equal(
      params$Coefficient,
      c(3.40563, 1.21316, -1, 2.73583, 1.56833, 1),
      tolerance = 1e-2
    )
  })

  # exponentiate for dispersion = sigma parameters -----------------------

  set.seed(101)
  ## rbeta() function parameterized by mean and shape
  my_rbeta <- function(n, mu, shape0) {
    rbeta(n, shape1 = mu * shape0, shape2 = (1 - mu) * shape0)
  }
  n <- 100
  ng <- 10
  dd <- data.frame(x = rnorm(n), f = factor(rep(1:(n / ng), ng)))
  dd <- transform(dd, y = my_rbeta(n, mu = plogis(-1 + 2 * x + rnorm(ng)[f]), shape0 = 5))

  m_exp <- glmmTMB::glmmTMB(y ~ x + (1 | f), family = glmmTMB::beta_family(), dd)

  test_that("model_parameters, exp, glmmTMB", {
    mp1 <- model_parameters(m_exp, exponentiate = TRUE)
    mp2 <- model_parameters(m_exp, exponentiate = FALSE)
    expect_equal(mp1$Coefficient, c(0.49271, 6.75824, 5.56294, 1.14541), tolerance = 1e-3)
    expect_equal(mp1$Coefficient[3:4], mp2$Coefficient[3:4], tolerance = 1e-3)
  })

  test_that("model_parameters, no dispersion, glmmTMB", {
    mp1 <- model_parameters(
      m_exp,
      effects = "fixed",
      component = "conditional",
      exponentiate = TRUE
    )
    mp2 <- model_parameters(
      m_exp,
      effects = "fixed",
      component = "conditional",
      exponentiate = FALSE
    )
    expect_equal(
      mp1$Coefficient,
      unname(exp(unlist(glmmTMB::fixef(m_exp)$cond))),
      tolerance = 1e-3
    )
    expect_equal(
      mp2$Coefficient,
      unname(unlist(glmmTMB::fixef(m_exp)$cond)),
      tolerance = 1e-3
    )
  })

  # proper printing ---------------------

  test_that("print-model_parameters glmmTMB", {
    skip_on_os(c("mac", "linux", "solaris"))
    skip_if_not(getRversion() >= "4.3.3")

    mp <- model_parameters(m4, effects = "fixed", component = "conditional")
    out <- utils::capture.output(print(mp))
    expect_snapshot(out[-5])

    mp <- model_parameters(
      m4,
      ci_random = TRUE,
      effects = "random",
      component = "conditional",
      verbose = FALSE
    )
    out <- utils::capture.output(print(mp))
    expect_identical(
      attributes(mp)$pretty_labels,
      c(
        `SD (Intercept)` = "SD (Intercept)",
        `SD (xb)` = "SD (xb)",
        `Cor (Intercept~xb)` = "Cor (Intercept~xb)"
      )
    )
    expect_identical(
      substr(out, 1, 30),
      c(
        "# Random Effects",
        "",
        "Parameter                   | ",
        "------------------------------",
        "SD (Intercept: persons)     | ",
        "SD (xb: persons)            | ",
        "Cor (Intercept~xb: persons) | "
      )
    )
    expect_equal(mp$Coefficient, c(3.40563, 1.21316, -1), tolerance = 1e-3)
    expect_equal(mp$CI_low, c(1.64567, 0.5919, -1), tolerance = 1e-3)

    mp <- model_parameters(
      m4,
      ci_random = TRUE,
      effects = "fixed",
      component = "zero_inflated"
    )
    out <- utils::capture.output(print(mp))
    expect_identical(
      attributes(mp)$pretty_labels,
      c(`(Intercept)` = "(Intercept)", child = "child", camper1 = "camper [1]")
    )
    expect_identical(
      substr(out, 1, 12),
      c(
        "# Fixed Effe",
        "",
        "Parameter   ",
        "------------",
        "(Intercept) ",
        "child       ",
        "camper [1]  "
      )
    )
    expect_equal(mp$Coefficient, c(1.88964, 0.15712, -0.17007), tolerance = 1e-3)
    expect_equal(mp$CI_low, c(0.5878, -0.78781, -0.92836), tolerance = 1e-3)

    mp <- model_parameters(
      m4,
      ci_random = TRUE,
      effects = "random",
      component = "zero_inflated",
      verbose = FALSE
    )
    out <- utils::capture.output(print(mp))
    expect_identical(
      attributes(mp)$pretty_labels,
      c(
        `SD (Intercept)` = "SD (Intercept)",
        `SD (zg)` = "SD (zg)",
        `Cor (Intercept~zg)` = "Cor (Intercept~zg)"
      )
    )
    expect_identical(
      substr(out, 1, 30),
      c(
        "# Random Effects (Zero-Inflati",
        "",
        "Parameter                   | ",
        "------------------------------",
        "SD (Intercept: persons)     | ",
        "SD (zg: persons)            | ",
        "Cor (Intercept~zg: persons) | "
      )
    )
    expect_equal(mp$Coefficient, c(2.73583, 1.56833, 1), tolerance = 1e-3)
    expect_equal(mp$CI_low, c(1.16329, 0.64246, -1), tolerance = 1e-3)

    mp <- model_parameters(
      m4,
      ci_random = TRUE,
      effects = "all",
      component = "conditional",
      verbose = FALSE
    )
    out <- utils::capture.output(print(mp))
    expect_identical(
      attributes(mp)$pretty_labels,
      c(
        `(Intercept)` = "(Intercept)",
        child = "child",
        camper1 = "camper [1]",
        `SD (Intercept)` = "SD (Intercept)",
        `SD (xb)` = "SD (xb)",
        `Cor (Intercept~xb)` = "Cor (Intercept~xb)"
      )
    )
    expect_identical(
      substr(out, 1, 30),
      c(
        "# Fixed Effects",
        "",
        "Parameter   | Log-Mean |   SE ",
        "------------------------------",
        "(Intercept) |     2.55 | 0.25 ",
        "child       |    -1.09 | 0.10 ",
        "camper [1]  |     0.27 | 0.10 ",
        "",
        "# Random Effects",
        "",
        "Parameter                   | ",
        "------------------------------",
        "SD (Intercept: persons)     | ",
        "SD (xb: persons)            | ",
        "Cor (Intercept~xb: persons) | "
      )
    )
    expect_equal(
      mp$Coefficient,
      c(2.54713, -1.08747, 0.2723, 3.40563, 1.21316, -1),
      tolerance = 1e-3
    )
    expect_equal(
      mp$CI_low,
      c(2.06032, -1.27967, 0.07461, 1.64567, 0.5919, -1),
      tolerance = 1e-3
    )

    mp <- model_parameters(
      m4,
      effects = "all",
      ci_random = TRUE,
      component = "zero_inflated",
      verbose = FALSE
    )
    out <- utils::capture.output(print(mp))
    expect_identical(
      attributes(mp)$pretty_labels,
      c(
        `(Intercept)` = "(Intercept)",
        child = "child",
        camper1 = "camper [1]",
        `SD (Intercept)` = "SD (Intercept)",
        `SD (zg)` = "SD (zg)",
        `Cor (Intercept~zg)` = "Cor (Intercept~zg)"
      )
    )
    expect_identical(
      substr(out, 1, 30),
      c(
        "# Fixed Effects (Zero-Inflatio",
        "",
        "Parameter   | Log-Mean |   SE ",
        "------------------------------",
        "(Intercept) |     1.89 | 0.66 ",
        "child       |     0.16 | 0.48 ",
        "camper [1]  |    -0.17 | 0.39 ",
        "",
        "# Random Effects (Zero-Inflati",
        "",
        "Parameter                   | ",
        "------------------------------",
        "SD (Intercept: persons)     | ",
        "SD (zg: persons)            | ",
        "Cor (Intercept~zg: persons) | "
      )
    )
    expect_equal(
      mp$Coefficient,
      c(1.88964, 0.15712, -0.17007, 2.73583, 1.56833, 1),
      tolerance = 1e-3
    )
    expect_equal(
      mp$CI_low,
      c(0.5878, -0.78781, -0.92836, 1.16329, 0.64246, -1),
      tolerance = 1e-3
    )

    mp <- model_parameters(
      m4,
      effects = "all",
      component = "all",
      ci_random = TRUE,
      verbose = FALSE
    )
    out <- utils::capture.output(print(mp))
    expect_identical(
      attributes(mp)$pretty_labels,
      c(
        `(Intercept)` = "(Intercept)",
        child = "child",
        camper1 = "camper [1]",
        `(Intercept)` = "(Intercept)",
        child = "child",
        camper1 = "camper1", # nolint
        `SD (Intercept)` = "SD (Intercept)",
        `SD (xb)` = "SD (xb)",
        `Cor (Intercept~xb)` = "Cor (Intercept~xb)",
        `SD (Intercept)` = "SD (Intercept)",
        `SD (zg)` = "SD (zg)", # nolint
        `Cor (Intercept~zg)` = "Cor (Intercept~zg)"
      )
    )
    expect_identical(
      substr(out, 1, 30),
      c(
        "# Fixed Effects (Count Model)",
        "",
        "Parameter   | Log-Mean |   SE ",
        "------------------------------",
        "(Intercept) |     2.55 | 0.25 ",
        "child       |    -1.09 | 0.10 ",
        "camper [1]  |     0.27 | 0.10 ",
        "",
        "# Fixed Effects (Zero-Inflatio",
        "",
        "Parameter   | Log-Odds |   SE ",
        "------------------------------",
        "(Intercept) |     1.89 | 0.66 ",
        "child       |     0.16 | 0.48 ",
        "camper [1]  |    -0.17 | 0.39 ",
        "",
        "# Random Effects Variances",
        "",
        "Parameter                   | ",
        "------------------------------",
        "SD (Intercept: persons)     | ",
        "SD (xb: persons)            | ",
        "Cor (Intercept~xb: persons) | ",
        "",
        "# Random Effects (Zero-Inflati",
        "",
        "Parameter                   | ",
        "------------------------------",
        "SD (Intercept: persons)     | ",
        "SD (zg: persons)            | ",
        "Cor (Intercept~zg: persons) | "
      )
    )
    expect_equal(
      mp$Coefficient,
      c(
        2.54713,
        -1.08747,
        0.2723,
        1.88964,
        0.15712,
        -0.17007,
        3.40563,
        1.21316,
        -1,
        2.73583,
        1.56833,
        1
      ),
      tolerance = 1e-3
    )
    expect_equal(
      mp$CI_low,
      c(
        2.06032,
        -1.27967,
        0.07461,
        0.5878,
        -0.78781,
        -0.92836,
        1.64567,
        0.5919,
        -1,
        1.16329,
        0.64246,
        -1
      ),
      tolerance = 1e-3
    )
  })

  # proper printing of digits ---------------------

  test_that("print-model_parameters glmmTMB digits", {
    skip_on_os(c("mac", "linux", "solaris"))
    skip_if_not(getRversion() >= "4.3.3")

    mp <- model_parameters(m4, ci_random = TRUE, effects = "all", component = "all")
    out <- utils::capture.output(print(mp, digits = 4, ci_digits = 5))
    expect_snapshot(out[-c(5, 14)])

    mp <- model_parameters(
      m4,
      effects = "all",
      component = "all",
      ci_random = TRUE,
      digits = 4,
      ci_digits = 5
    )
    out <- utils::capture.output(print(mp))
    expect_snapshot(out[-c(5, 14)])
  })

  # proper alignment of CIs ---------------------
  test_that("print-model_parameters glmmTMB CI alignment", {
    skip_if_not_installed("curl")
    skip_if_offline()
    skip_on_os(c("mac", "linux", "solaris"))
    skip_if_not(getRversion() >= "4.3.3")

    model_pr <- tryCatch(
      {
        load(url(
          "https://github.com/d-morrison/parameters/raw/glmmTMB/data/pressure_durations.RData"
        ))
        glmmTMB::glmmTMB(
          formula = n_samples ~ Surface + Side + Jaw + (1 | Participant / Session),
          ziformula = ~ Surface + Side + Jaw + (1 | Participant / Session),
          dispformula = ~1,
          family = glmmTMB::nbinom2(),
          data = pressure_durations
        )
      },
      error = function(e) {
        NULL
      }
    )

    mp <- model_parameters(
      model_pr,
      effects = "random",
      component = "all",
      ci_random = TRUE
    )
    expect_snapshot(print(mp))

    mp <- model_parameters(model_pr, effects = "fixed", component = "all")
    expect_snapshot(print(mp))
  })

  test_that("model_parameters.mixed-all", {
    skip_on_os(c("mac", "linux", "solaris"))
    skip_if_not(getRversion() >= "4.3.3")

    params <- model_parameters(m4, effects = "all")
    expect_identical(c(nrow(params), ncol(params)), c(12L, 12L))
    expect_identical(
      colnames(params),
      c(
        "Parameter",
        "Coefficient",
        "SE",
        "CI",
        "CI_low",
        "CI_high",
        "z",
        "df_error",
        "p",
        "Effects",
        "Group",
        "Component"
      )
    )
    expect_identical(
      params$Parameter,
      c(
        "(Intercept)",
        "child",
        "camper1",
        "(Intercept)",
        "child",
        "camper1",
        "SD (Intercept)",
        "SD (xb)",
        "Cor (Intercept~xb)",
        "SD (Intercept)",
        "SD (zg)",
        "Cor (Intercept~zg)"
      )
    )
    expect_identical(
      params$Component,
      c(
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated",
        "conditional",
        "conditional",
        "conditional",
        "zero_inflated",
        "zero_inflated",
        "zero_inflated"
      )
    )
    expect_equal(
      params$Coefficient,
      c(
        2.54713,
        -1.08747,
        0.2723,
        1.88964,
        0.15712,
        -0.17007,
        3.40563,
        1.21316,
        -1,
        2.73583,
        1.56833,
        1
      ),
      tolerance = 1e-2
    )
  })

  test_that("print-model_parameters", {
    skip_on_os(c("mac", "linux", "solaris"))
    skip_if_not(getRversion() >= "4.3.3")

    mp <- model_parameters(m1, effects = "fixed", verbose = FALSE)
    expect_snapshot(mp)

    mp <- model_parameters(m1, effects = "fixed", exponentiate = TRUE, verbose = FALSE)
    expect_snapshot(mp)

    mp <- model_parameters(m1, effects = "all", verbose = FALSE)
    expect_snapshot(mp)
  })

  test_that("print-model_parameters, random dispersion", {
    data(Salamanders, package = "glmmTMB")
    m <- glmmTMB::glmmTMB(
      count ~ spp + cover + mined + (1 | site),
      ziformula = ~ spp + mined,
      dispformula = ~ DOY + (1 | site),
      data = Salamanders,
      family = glmmTMB::nbinom1()
    )
    out <- as.data.frame(model_parameters(m, effects = "fixed", component = "all"))
    expect_identical(nrow(out), 19L)
    out <- as.data.frame(model_parameters(m, effects = "random", component = "all"))
    expect_identical(nrow(out), 1L)
    out <- as.data.frame(model_parameters(
      m,
      effects = "random",
      component = "all",
      group_level = TRUE
    ))
    expect_identical(nrow(out), 46L)
    expect_equal(
      out$Coefficient,
      unlist(glmmTMB::ranef(m)),
      ignore_attr = TRUE,
      tolerance = 1e-4
    )
  })

  test_that("robust SE/VCOV", {
    skip_if_not_installed("sandwich")
    skip_if(packageVersion("insight") <= "1.4.0")

    out1 <- standard_error(m1)
    out2 <- sqrt(diag(insight::get_varcov(m1, component = "all")))
    expect_equal(out1$SE, out2[1:6], ignore_attr = TRUE, tolerance = 1e-4)

    out1 <- standard_error(m1, vcov = "HC0")
    out2 <- sqrt(diag(insight::get_varcov(m1, vcov = "HC0", component = "all")))
    expect_equal(out1$SE, out2[1:6], ignore_attr = TRUE, tolerance = 1e-4)

    out <- model_parameters(m1, vcov = "HC0")
    expect_snapshot(print(out, table_width = Inf))
  })
})