From c7290bbf239b7a170768d41a859d856eb39181c3 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Tue, 27 Oct 2026 09:08:25 -0400
Subject: [PATCH] Remove global environment objects as per
 https://github.com/nmfs-ost/stockplotr/issues/421

---
 R/extract_sis_data.R       | 4 ++++
 R/plot_biomass.R           | 5 +++++
 R/plot_fishing_mortality.R | 7 ++++++-
 3 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/R/extract_sis_data.R b/R/extract_sis_data.R
index 9176af07..16a7f291 100644
--- a/R/extract_sis_data.R
+++ b/R/extract_sis_data.R
@@ -394,4 +394,8 @@ extract_sis_data <- function(sis_data_dir = getwd(),
     write.csv(ts_dat_filled, ts_dat_path, row.names = FALSE)
     cli::cli_alert_success("Files saved successfully in {sis_data_dir}.")
   }
+  
+  # remove global variables
+  c("biomass", "spawning_biomass", "recruitment", "fishing_mortality", "index", "catch") |>
+    purrr::walk(~ if (exists(.x, envir = .GlobalEnv)) rm(list = .x, envir = .GlobalEnv))
 }
diff --git a/R/plot_biomass.R b/R/plot_biomass.R
index 724649ed..0045c54c 100644
--- a/R/plot_biomass.R
+++ b/R/plot_biomass.R
@@ -325,6 +325,11 @@ plot_biomass <- function(
       scale_amount = scale_amount
     )
   }
+  
+  # remove global variable "selected_module"
+  if (exists("selected_module", envir = .GlobalEnv)) rm("selected_module", envir = .GlobalEnv)  
+  
   # Output final plot
   final
+
 }
diff --git a/R/plot_fishing_mortality.R b/R/plot_fishing_mortality.R
index bf67a4e2..deabfb69 100644
--- a/R/plot_fishing_mortality.R
+++ b/R/plot_fishing_mortality.R
@@ -198,6 +198,11 @@ plot_fishing_mortality <- function(
       scale_amount = 1
     )
   }
+  
+  # remove global variable "selected_module"
+  if (exists("selected_module", envir = .GlobalEnv)) rm("selected_module", envir = .GlobalEnv) 
+  
   # Output final plot
-  final
+  final  
+
 }