Allow NAs in prepare_mcmc_array

NEWS.md

@@ -1,5 +1,6 @@
 # bayesplot (development version)
 
+* `prepare_mcmc_array()` now warns instead of erroring on `NA`s in the input.
 * `ppc_ecdf_overlay()`, `ppc_ecdf_overlay_grouped()`, and `ppd_ecdf_overlay()` now always use `geom_step()`. The `discrete` argument is deprecated.
 * Fixed missing `drop = FALSE` in `nuts_params.CmdStanMCMC()`.
 * Replace `apply()` with `storage.mode()` for integer-to-numeric matrix conversion in `validate_predictions()`.

R/helpers-mcmc.R

@@ -29,7 +29,9 @@ prepare_mcmc_array <- function(x,
     abort("Arrays should have 2 or 3 dimensions. See help('MCMC-overview').")
   }
   if (anyNA(x)) {
-    abort("NAs not allowed in 'x'.")
+    warn(
+      "NAs were found in 'x'. `prepare_mcmc_array()` does not remove them; some plots may render with missing values dropped, while summary functions (e.g. intervals, densities, diagnostics) may produce misleading results or error. Consider removing NAs before plotting or summarizing."
+    )
   }
 
   if (rlang::is_quosures(pars)) {

tests/testthat/test-helpers-mcmc.R

@@ -240,9 +240,12 @@ test_that("transformations recycled properly if not a named list", {
 
 
 # prepare_mcmc_array ------------------------------------------------------
-test_that("prepare_mcmc_array errors if NAs", {
-  arr[1,1,1] <- NA
-  expect_error(prepare_mcmc_array(arr), "NAs not allowed")
+test_that("prepare_mcmc_array warns but does not error if NAs", {
+  arr_na <- arr
+  arr_na[1,1,1] <- NA
+  expect_warning(out <- prepare_mcmc_array(arr_na), "NAs were found")
+  expect_s3_class(out, "mcmc_array")
+  expect_true(anyNA(out))
 })
 test_that("prepare_mcmc_array processes non-array input types correctly", {
   # errors are mostly covered by tests of the many internal functions above