check_model() and other functions not working with only post-"hurdle" glmmTMB model (#782)

Author: strengejacke

NEWS.md

@@ -21,6 +21,9 @@
 * `check_outliers()` did not warn that no numeric variables were found when only
   the response variable was numeric, but all relevant predictors were not.
 
+* `check_collinearity()` did not work for glmmTMB models when zero-inflation
+  component was set to `~0`.
+
 # performance 0.12.4
 
 ## Changes

R/check_collinearity.R

@@ -414,7 +414,7 @@ check_collinearity.zerocount <- function(x,
 
 
 .check_collinearity <- function(x, component, ci = 0.95, verbose = TRUE) {
-  v <- insight::get_varcov(x, component = component, verbose = FALSE)
+  v <- .safe(insight::get_varcov(x, component = component, verbose = FALSE))
 
   # sanity check
   if (is.null(v)) {

tests/testthat/test-check_collinearity.R

@@ -222,5 +222,19 @@ test_that("check_collinearity, hurdle/zi models w/o zi-formula", {
 test_that("check_collinearity, invalid data", {
   dd <- data.frame(y = as.difftime(0:5, units = "days"))
   m1 <- lm(y ~ 1, data = dd)
-  expect_error(check_collinearity(m1), "Can't extract variance-covariance matrix")
+  expect_message(check_collinearity(m1), "Could not extract the variance-covariance")
+})
+
+test_that("check_collinearity, glmmTMB hurdle w/o zi", {
+  skip_if_not_installed("glmmTMB")
+  data(Salamanders, package = "glmmTMB")
+  mod_trunc_error <- glmmTMB::glmmTMB(
+    count ~ spp + mined + (1 | site),
+    data = Salamanders[Salamanders$count > 0, , drop = FALSE],
+    family = glmmTMB::truncated_nbinom2(),
+    ziformula = ~ 0,
+    dispformula = ~ 1
+  )
+  out <- check_collinearity(mod_trunc_error)
+  expect_equal(out$VIF, c(1.03414, 1.03414), tolerance = 1e-3)
 })

tests/testthat/test-check_model.R

@@ -40,7 +40,7 @@ test_that("`check_outliers()` works if convergence issues", {
 test_that("`check_model()` for invalid models", {
   dd <- data.frame(y = as.difftime(0:5, units = "days"))
   m1 <- lm(y ~ 1, data = dd)
-  expect_error(check_model(m1))
+  expect_message(check_model(m1), regex = "Date variables are not")
 })
 
 test_that("`check_model()` works for quantreg", {