Test for Inf in covariate columns #408

Author: seananderson

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.6.0.9028
+Version: 0.6.0.9029
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "sean@seananderson.ca",
            role = c("aut", "cre"),

NEWS.md

@@ -1,5 +1,7 @@
 # sdmTMB (development version)
 
+* Add check for `Inf`/`-Inf` values before fitting. #408
+
 * Add priors for `breakpt()` and `logistic()` parameters. #403
 
 * Add linear component of smoothers to `tidy()`. #90

R/fit.R

@@ -859,6 +859,12 @@ sdmTMB <- function(
     formula_no_bars_no_sm <- remove_s_and_t2(formula_no_bars)
     X_ij[[ii]] <- model.matrix(formula_no_bars_no_sm, data)
     mf[[ii]] <- model.frame(formula_no_bars_no_sm, data)
+    vars <- colnames(mf[[ii]])
+    for (g in seq_along(vars)) {
+      if (any(is.infinite(mf[[ii]][, g, drop = TRUE]))) {
+        cli_abort("Column `{vars[g]}` had an Inf/-Inf value. Please remove this before fitting the model.")
+      }
+    }
 
     mt[[ii]] <- attr(mf[[ii]], "terms")
     # parse everything mgcv + smoothers:

tests/testthat/test-index.R

@@ -187,3 +187,17 @@ test_that("get_index works", {
 #
 # })
 
+# https://github.com/pbs-assess/sdmTMB/issues/408
+test_that("Models error our nicely with Inf or -Inf covariates before get_index()", {
+  d <- pcod
+  d$depth_scaled[1] <- -Inf
+  expect_error(m <- sdmTMB(
+    data = d,
+    formula = density ~ 0 + as.factor(year) + depth_scaled,
+    spatiotemporal = "off", # speed
+    spatial = "off", # speed
+    time = "year",
+    family = delta_gamma(type = "poisson-link")
+  ), regexp = "Inf")
+})
+