Improvements to do_index = TRUE/get_index errors

#276

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.4.1.9001
+Version: 0.4.1.9002
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "sean@seananderson.ca",
            role = c("aut", "cre"),

NEWS.md

@@ -1,5 +1,8 @@
 # sdmTMB (development version)
 
+* Improve warnings/errors around use of `do_index = TRUE` and `get_index()`
+  if `newdata = NULL`. #276
+
 * Fix prediction with `offset` when `newdata` is `NULL` but `offset` is
   specified. #274
 

R/fit.R

@@ -124,11 +124,13 @@ NULL
 #'   the TMB object doesn't have to be rebuilt with [predict.sdmTMB()] and
 #'   [get_index()]. If `TRUE`, then `predict_args` must have a `newdata` element
 #'   supplied and `area` can be supplied to `index_args`.
-#' @param predict_args A list of arguments to pass to [predict.sdmTMB()] if
-#'   `do_index = TRUE`.
-#' @param index_args A list of arguments to pass to [get_index()] if
+#'   Most users can ignore this option.
+#' @param predict_args A list of arguments to pass to [predict.sdmTMB()] **if**
+#'   `do_index = TRUE`. Most users can ignore this option.
+#' @param index_args A list of arguments to pass to [get_index()] **if**
 #'   `do_index = TRUE`. Currently, only `area` is supported. Bias correction
 #'   can be done when calling [get_index()] on the resulting fitted object.
+#'   Most users can ignore this option.
 #' @param bayesian Logical indicating if the model will be passed to
 #'   \pkg{tmbstan}. If `TRUE`, Jacobian adjustments are applied to account for
 #'   parameter transformations when priors are applied.
@@ -1384,6 +1386,10 @@ sdmTMB <- function(
     version    = utils::packageVersion("sdmTMB")),
     class      = "sdmTMB")
 
+  if ((!is.null(predict_args) || !is.null(index_args)) && isFALSE(do_index)) {
+    cli_abort(c("`predict_args` and/or `index_args` were set but `do_index` was FALSE.",
+      "`do_index` must be TRUE for these arguments to take effect.")) #276
+  }
   if (do_index) {
     args <- list(object = out_structure, return_tmb_data = TRUE)
     args <- c(args, predict_args)

R/index.R

@@ -110,6 +110,11 @@ get_generic <- function(obj, value_name, bias_correct = FALSE, level = 0.95,
       cli_abort(paste0("`obj` needs to be created with ",
         "`predict(..., return_tmb_object = TRUE).`"))
     }
+
+    if (!"report" %in% names(obj$obj)) {
+      cli_abort(c("It looks like the predict function was run without `newdata` specified.",
+        "Re-run the predict function with `newdata` specified.")) #276
+    }
     test <- suppressWarnings(tryCatch(obj$obj$report(obj$obj$env$last.par),
       error = function(e) NA))
     if (all(is.na(test)))

tests/testthat/test-4-index-calculation.R

@@ -55,3 +55,36 @@ test_that("get_index(), get_index_sims(), and get_cog() work", {
   expect_equal(cog$est[which(cog$coord=="X")], cog_wide$est_x)
 })
 
+test_that("index errors are returned as needed", {
+  skip_on_ci()
+  skip_on_cran()
+
+  g <- replicate_df(qcs_grid, "year", unique(pcod_2011$year))
+
+  expect_error(
+  fit <- sdmTMB(
+    density ~ 1,
+    data = pcod_2011,
+    spatial = "off", spatiotemporal = "off",
+    family = tweedie(link = "log"),
+    time = "year",
+    predict_args = list(newdata = g),
+    index_args = list(area = 1)
+  ), regexp = "do_index" # missing!
+  )
+
+  fit <- sdmTMB(
+    density ~ 1,
+    data = pcod_2011, spatial = "off", spatiotemporal = "off",
+    family = tweedie(link = "log"),
+    time = "year"
+  )
+  p1 <- predict(fit, newdata = NULL, return_tmb_object = TRUE)
+  expect_error(get_index(p1), "newdata") # missing!
+
+  p2 <- predict(fit, newdata = g, return_tmb_object = TRUE)
+  suppressMessages(
+    i <- get_index(p2)
+  )
+  expect_s3_class(i, "data.frame")
+})