From 6cb86b64df8a52f9c288355f7278636ff21d5de7 Mon Sep 17 00:00:00 2001
From: kellijohnson-NOAA <kelli.johnson@noaa.gov>
Date: Thu, 19 May 2022 17:50:06 -0700
Subject: [PATCH] Changes upper bounds of logkappa2

using VAST_3.9.0 the upper bound of logkappa2 is reached
using the default settings b/c of the small number of mesh points.
This commit changes the upper bound to 10 using
run_model = FALSE to get the correct map.
This trick can be found in
https://github.com/James-Thorson-NOAA/VAST/issues/300
which was started by @kellijohnson-NOAA b/c of similar issues
when running the model for West Coast species.

Former-commit-id: 1c9d08baa2e2077ec0530cea5858564697dfad5a
---
 sandbox/pcod_delta_gamma.R | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/sandbox/pcod_delta_gamma.R b/sandbox/pcod_delta_gamma.R
index 5e00a3a..2221a5d 100644
--- a/sandbox/pcod_delta_gamma.R
+++ b/sandbox/pcod_delta_gamma.R
@@ -67,7 +67,21 @@ fit_vast <- fit_model(
   b_i = pcod[, "density"],
   a_i = pcod[, "effort"],
   input_grid = input_grid,
-  working_dir = paste0(here("doc", "appendix-VAST"), "/")
+  working_dir = paste0(here("doc", "appendix-VAST"), "/"),
+  run_model = FALSE
+)
+upperbounds <- fit_vast$Upper
+upperbounds["logkappa2"] <- 10
+fit_vast <- fit_model(
+  settings = settings,
+  Lat_i = pcod[, "lat"],
+  Lon_i = pcod[, "lon"],
+  t_i = pcod[, "year"],
+  b_i = pcod[, "density"],
+  a_i = pcod[, "effort"],
+  input_grid = input_grid,
+  working_dir = paste0(here("doc", "appendix-VAST"), "/"),
+  upper = upperbounds
 )
 #   saveRDS(fit_vast, file = f)
 # } else {