SAMfromSA_taf_template

TAF template for the SAMfromSA method: a SAM assessment on stockassessment.org brought into TAF.

The example is the Faroe Plateau cod assessment, Cod_27_5b1 on stockassessment.org.

• boot/sam_data.R and boot/sam_config.R: download the data files and the model configuration of the assessment from stockassessment.org. The assessment is set by sam_assessment at the top of each.
• data.R: reads the data files and writes them as TAF tables, and sets up the SAM data.
• model.R: fits SAM with the configuration (model_fit.R), with retrospective and leave-one-out fits and residuals, and runs the forecast scenarios (model_forecast.R).
• output.R: the tables of the fit, Mohn's rho, and an FLStock object made with FLfse.
• report.R: the plots of stockassessment.org (report_plots_saorg.R), the plots and tables of the template (report_plots.R, report_tables.R), and the reports (report_doc.R): a Word and HTML report from report.Rmd and a quality report from report_quality_report.qmd.

Copied from ices-taf-dev/wiki-example-stockassessment at commit 32e0b43.