From 56d9ea88ec1ba26038492fe3dee51c64eaed449a Mon Sep 17 00:00:00 2001
From: Eric Ward <5046884+ericward-noaa@users.noreply.github.com>
Date: Wed, 14 Feb 2024 05:29:01 -0800
Subject: [PATCH 1/3] Add new message about time

See this discussion: https://github.com/pbs-assess/sdmTMB/discussions/298
---
 R/fit.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/fit.R b/R/fit.R
index 326e642ae..3545eea7b 100644
--- a/R/fit.R
+++ b/R/fit.R
@@ -709,6 +709,7 @@ sdmTMB <- function(
   if (!is.null(time)) {
     assert_that(time %in% names(data),
       msg = "Specified `time` column is missing from `data`.")
+    assert_that(length(is.na(as.numeric(data[[time]]))) == 0), msg = "Specified `time` column can't be coerced to a numeric value")
   }
   if (is.null(time)) {
     time <- "_sdmTMB_time"

From d1d8efc3e1a2e7e7a19c98c31352c06877ee56d5 Mon Sep 17 00:00:00 2001
From: Sean Anderson <sean@seananderson.ca>
Date: Wed, 14 Feb 2024 10:30:55 -0800
Subject: [PATCH 2/3] Remove extra `)`; length -> sum?

---
 R/fit.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/fit.R b/R/fit.R
index 3545eea7b..aa51c4d38 100644
--- a/R/fit.R
+++ b/R/fit.R
@@ -709,7 +709,8 @@ sdmTMB <- function(
   if (!is.null(time)) {
     assert_that(time %in% names(data),
       msg = "Specified `time` column is missing from `data`.")
-    assert_that(length(is.na(as.numeric(data[[time]]))) == 0), msg = "Specified `time` column can't be coerced to a numeric value")
+    assert_that(sum(is.na(as.numeric(data[[time]]))) == 0L,
+      msg = "Specified `time` column can't be coerced to a numeric value")
   }
   if (is.null(time)) {
     time <- "_sdmTMB_time"

From 8af542742d7811af7684c2a62a2a81d5bbbb5f2c Mon Sep 17 00:00:00 2001
From: Sean Anderson <sean@seananderson.ca>
Date: Wed, 14 Feb 2024 10:45:20 -0800
Subject: [PATCH 3/3] Enhance error msg; add test

---
 R/fit.R                                |  2 +-
 tests/testthat/test-2-fit-less-basic.R | 12 ++++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/R/fit.R b/R/fit.R
index aa51c4d38..c59da9479 100644
--- a/R/fit.R
+++ b/R/fit.R
@@ -710,7 +710,7 @@ sdmTMB <- function(
     assert_that(time %in% names(data),
       msg = "Specified `time` column is missing from `data`.")
     assert_that(sum(is.na(as.numeric(data[[time]]))) == 0L,
-      msg = "Specified `time` column can't be coerced to a numeric value")
+      msg = "Specified `time` column can't be coerced to a numeric value or contains NAs. Please remove any NAs in the time column.")
   }
   if (is.null(time)) {
     time <- "_sdmTMB_time"
diff --git a/tests/testthat/test-2-fit-less-basic.R b/tests/testthat/test-2-fit-less-basic.R
index 00adf561e..40d0d2944 100644
--- a/tests/testthat/test-2-fit-less-basic.R
+++ b/tests/testthat/test-2-fit-less-basic.R
@@ -507,3 +507,15 @@ test_that("sdmTMB throws error on AR1/RW with non-numeric time", {
       mesh = pcod_mesh_2011
     ))
 })
+
+test_that("Time with an NA gets flagged", {
+  skip_on_cran()
+  d <- pcod_2011
+  d$yr <- as.character(d$year)
+  d$yr[2] <- NA
+  expect_error({
+    m <- sdmTMB(density ~ 1, time = "yr", spatial = "off", spatiotemporal = "off", data = d)
+  }, regexp = "time")
+})
+
+