Add message on offset newdata prediction #372

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.6.0.9005
+Version: 0.6.0.9006
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "[email protected]",
            role = c("aut", "cre"),

NEWS.md

@@ -1,5 +1,8 @@
 # sdmTMB (development version)
 
+* Add informative message if fitting with an offset but predicting with offset
+  argument left at NULL on newdata. #372
+
 * Fix passing of `offset` argument through in `sdmTMB_cv()`. Before it was being
   omitted in the prediction (i.e., set to 0). #372
 

R/predict.R

@@ -495,6 +495,15 @@ predict.sdmTMB <- function(object, newdata = NULL,
       cli_abort("`area` should be of the same length as `nrow(newdata)` or of length 1.")
     }
 
+    # newdata, null offset in predict, and non-null in fit #372
+    if (isFALSE(nd_arg_was_null) && is.null(offset) && !all(object$offset == 0)) {
+      msg <- c(
+        "Fitted object contains an offset but the offset is `NULL` in `predict.sdmTMB()`.",
+        "Prediction will proceed assuming the offset vector is 0 in the prediction.",
+        "Specify an offset vector in `predict.sdmTMB()` to override this.")
+      cli_inform(msg)
+    }
+
     if (!is.null(offset)) {
       if (nrow(proj_X_ij[[1]]) != length(offset))
         cli_abort("Prediction offset vector does not equal number of rows in prediction dataset.")

tests/testthat/test-offset.R

@@ -160,6 +160,22 @@ test_that("offset gets passed through cross validation as expected #372", {
   expect_true(length(unique(y$cv_predicted)) == 684L)
 })
 
+test_that("predicting on newdata with a non-null offset in fit but a null offset in predict informs the user appropriately", {
+  dat <- subset(dogfish, catch_weight > 0)
+  fit <- sdmTMB(
+    catch_weight ~ 1,
+    data = dat,
+    family = Gamma("log"),
+    offset = "area_swept",
+    spatial = "off"
+  )
+  pred <- predict(fit)
+  pred <- predict(fit, offset = rep(0, nrow(dat)))
+  pred <- predict(fit, newdata = qcs_grid, offset = rep(0, nrow(qcs_grid)))
+  pred <- predict(fit, newdata = qcs_grid)
+  expect_message({pred <- predict(fit, newdata = qcs_grid)}, regexp = "offset")
+})
+
 # #
 # # offset/prediction setting checks:
 #