From 1418f42a2b905f1fcd9febf235103133161a5b2b Mon Sep 17 00:00:00 2001
From: Eric Ward <5046884+ericward-noaa@users.noreply.github.com>
Date: Fri, 13 Sep 2024 07:58:26 -0700
Subject: [PATCH] Add warning messages when components are collapsing to 0

---
 R/tmb-sim.R | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/R/tmb-sim.R b/R/tmb-sim.R
index 08cc8e7a..a95d0a07 100644
--- a/R/tmb-sim.R
+++ b/R/tmb-sim.R
@@ -271,6 +271,21 @@ sdmTMB_simulate <- function(formula,
   d[["omega_s"]] <- if (all(s$omega_s_A != 0)) s$omega_s_A
   d[["epsilon_st"]] <- if (all(s$epsilon_st_A_vec != 0)) s$epsilon_st_A_vec
   d[["zeta_s"]] <- if (all(s$zeta_s_A != 0)) s$zeta_s_A
+  
+    # Warnings for pieces collapsing to 0. The sum() > 0 piece is needed because parameters that are input are turned to 0x0 matrices
+  if (sum(sigma_O) > 0) {
+    if(is.null(d[["omega_s"]])) cli::cli_alert_info(paste("Warning: spatial field is collapsing to 0 but sigma_O was specified.",
+                                                        "Please check the spatial range and cutoff distance used to construct the mesh."))
+  }
+  if (sum(sigma_E) > 0) {
+    if(is.null(d[["epsilon_st"]])) cli::cli_alert_info(paste("Warning: spatiotemporal field is collapsing to 0 but sigma_E was specified.",
+                                                        "Please check the spatial range and cutoff distance used to construct the mesh."))
+  }
+  if (sum(sigma_Z) > 0) {
+    if(is.null(d[["zeta_s"]])) cli::cli_alert_info(paste("Warning: spatially varying coefficient field is collapsing to 0 but sigma_Z was specified.",
+                                                               "Please check the spatial range and cutoff distance used to construct the mesh."))
+  }
+  
   if (any(family$family %in% c("truncated_nbinom1", "truncated_nbinom2"))) {
     d[["mu"]] <- family$linkinv(s$eta_i, phi = phi)
   } else {