tests/testthat/test-glmmTMB.R

In easystats/estimate: Estimation of Model-Based Predictions, Contrasts and Means

skip_if_not_installed("glmmTMB")
skip_if_not_installed("emmeans")

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

model2 <- suppressWarnings(glmmTMB::glmmTMB(
  count ~ cover + mined + (1 | site),
  ziformula = ~ cover + mined,
  family = glmmTMB::truncated_poisson,
  data = data
))

test_that("estimate_means - glmmTMB", {
  estim <- suppressMessages(estimate_means(model))
  estim2 <- as.data.frame(emmeans::emmeans(model, ~mined, type = "response"))
  expect_equal(estim$rate, estim2$rate, tolerance = 1e-3)

  estim <- suppressMessages(estimate_means(model, component = "zi"))
  estim2 <- as.data.frame(emmeans::emmeans(model, ~mined, component = "zi", type = "response"))
  expect_equal(estim$rate, estim2$rate, tolerance = 1e-3)
})

test_that("estimate_contrasts - glmmTMB", {
  estim <- suppressMessages(estimate_contrasts(model))
  expect_equal(dim(estim), c(1, 9))
  expect_equal(estim$Difference, -1.141923, tolerance = 1e-1)
  expect_equal(c(estim$Level1[1], estim$Level2[1]), c("yes", "no"))

  estim <- suppressMessages(estimate_contrasts(model, component = "zi"))
  expect_equal(dim(estim), c(1, 9))
  expect_equal(estim$Difference, 1.736067, tolerance = 1e-1)
  expect_equal(c(estim$Level1[1], estim$Level2[1]), c("yes", "no"))
})

test_that("estimate_slope - glmmTMB", {
  estim <- suppressMessages(estimate_slopes(model2,
    trend = "cover",
    at = "mined", regrid = "response"
  ))
  estim2 <- as.data.frame(emmeans::emtrends(model2, "mined", var = "cover", regrid = "response"))
  expect_equal(estim$Coefficient, estim2$cover.trend, tolerance = 1e-2)
})


test_that("estimate_response - glmmTMB", {
  estim <- suppressMessages(estimate_expectation(model2))
  expect_equal(dim(estim), c(nrow(data), 8))
})

test_that("estimate_link - glmmTMB", {
  estim <- suppressMessages(estimate_link(model2, preserve_range = FALSE))
  expect_equal(dim(estim), c(20, 7))
})

test_that("estimate_response - glmmTMB", {
  estim <- suppressMessages(estimate_expectation(model2))
  expect_equal(dim(estim), c(644, 8))
})