From 005d9c58df8295eea61a5e7a35c8bb3c00a236c4 Mon Sep 17 00:00:00 2001
From: Sarah Gaichas <sarah.gaichas@noaa.gov>
Date: Sat, 7 Oct 2023 17:27:43 -0400
Subject: [PATCH] appends biomass pools if they exist for surveys

---
 R/om_index.R | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/R/om_index.R b/R/om_index.R
index 167ca6a..d99cb08 100644
--- a/R/om_index.R
+++ b/R/om_index.R
@@ -49,9 +49,16 @@ om_index <- function(usersurvey = usersurvey_file,
   {
     source(s, local = TRUE)
 
+    # add in biomass pools if they exist
+    if("truebiopool_ss" %in% names(omlist_ss)){
+      truebio_ss <- rbind(omlist_ss$truebio_ss, omlist_ss$truebiopool_ss)
+    }else{
+      truebio_ss <- omlist_ss$truebio_ss
+    }
+
     #biomass based fishery independent survey index
     # this uses result$biomass_ages to sample biomass directly, no need for wt@age est
-    survey_B <- atlantisom::create_survey(dat = omlist_ss$truebio_ss,
+    survey_B <- atlantisom::create_survey(dat = truebio_ss,
                                           time = survtime,
                                           species = survspp,
                                           boxes = survboxes,