About

This repository contains the code and models used for the 2023 American Samoa BMUS Stock Assessment.

Repository Structure

The folder structure is as follows:

/Data: contains all raw data files, not available in the repository for confidentiality reasons but available in the "02_Assessment Report/Data folder image" folder on Google Drive (unzip content in /Data folder). Please contact Marc Nadon for permisions.

/Scripts:

• /01_Data scripts: data processing scripts, all called by 01_Run data scripts.R
• /02_SS scripts: scripts to create SS files and run bootstraps, diagnostics, forecasts, and alternate models
• /03_Report scripts: scripts to create figures and tables for the assessment report
• /04_Other scripts: scripts for extra analyses

/SS3 models: contains history of model runs during development by species. Model runs include the 4 SS input files, the executable ss_opt_win.exe can be found in the TEMPLATE_FILES directory.

/SS3 final models: contains the final model runs (base and alternates) discussed in the assessment report by species.

/Images: high resolution .jpg images of BMUS species used in report and presentations.

To use this repo

1. Clone repository onto personal laptop.
2. Open /Scripts/01_Run data scripts.R
3. Run script and login and give full permission to Google Drive when prompted (click bottom option to read and write to files).
4. Open /Scripts/02_Run SS models.R and adjust settings as needed. For first run, it is recommended to set the following options:
   • runmodels = T
   • Specify DirName as the name of the folder you want to create (e.g. 01_Base)
   • printreport = F
   • Create_species_report_figs = F
   • N_boot = 0
   • N_foreyrs = 0
   • RD = F
   • Begin = 1967
   • DeleteForecastFiles = T (inside Build_All_SS function)
   • write_files = T (inside Build_All_SS function)
   • readGoogle = T (inside Build_All_SS function)
5. Create list of species and settings (Lt)
6. To run 1 species, set i to the number that species is in the list (e.g. i = 1 for APRU) and run line 20 (lapply(list(Lt[[i]]),function(x) {...}).
7. To run all species use line 19 to run for loop.
8. Once model runs, to run diagnostics and print diagnostic report, set:
   • runmodels = F
   • printreport = T
   • RD = T (make sure do_retro, do_profile, and do_jitter are set to RD)
   • ProfRes = 0.1 (or however small you want the resolution of the profile)
   • profile = "SR_LN(R0)" (name of the parameter you are profiling over as recognized by r4ss::profile())
   • write_files = F (inside Build_All_SS function)
   • Njitter = 100 (inside Build_All_SS function)
   • jitterFraction = 0.1
9. Once diagnostics are run on the single model, run bootstraps by setting N_boot = 30, keeping write_files = F, runmodels = F, and setting RD = F and printreport = F.
10. To run projections, set N_boot back to 0 and N_foreyrs = 7. Projections will be run based on the specified catch range in Lt$FixedCatchSeq.
11. Alternate models can be run by /Scripts/02_SS scripts/09_Run_Alt_Models.R. Note that alternate life history scenarios were changed and run manually. Figures and tables for alternate model runs can be created with /Scripts/03_Report scripts/Create_AltMods_Figs_Tables.R.
12. Once all models and figures are created, formatted figures and tables for the report can be created with 02_Run SS models.R by turning all model runs off and only creating the species report figures:
    • runmodels = F
    • printreport = F
    • Create_species_report_figs = T
    • N_boot = 0
    • N_foreyrs = 0
    • RD = F
    • write_files = F

Github Disclaimer

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