This repository was made to store the scripts used for testing the implementation of red tide mortality in the Red Grouper stock assessment using SSMSE.
There are 3 main scripts for our SSMSE process. First is the SSMSE_red_grouper_start.R file which defines the scenarios and initiates the SSMSE runs. The diagnostic_ssmse.R file extracts data directly from the stock synthesis runs and summarizes more complex statistics like catch at age and selectivity. Finally, the future_red_tide_results_review or red_tide_2_years_results_review generate all of the results figures and tables for reviewing the summarized outputs. The current project uses the red_tide_2_years_results_review.
Previous runs houses all of the html files of previous runs we chose to highlight throughout the process. For example, the 2025_07_03 runs titled SigmaR, r0_SigmaR, and 2025_07_07_r0 were tests with either SigmaR, R0, or both fixed.
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