Workshop on TAF Stock Assessment Templates
This repository contains placeholder, initially, for standard template scripts to perform well defined tasks required for a stock assessment using Stock Synthesis or SAM.
Examples include, running a model, running a retropsective, create the SAG output, creating an FLStock object, generating a presentation, generating a basic standard report.
- Start from RDBES / Intercatch files
- Preformed survey indices
- ss ctrl files
- model_SS3.R - Laura
- data_SAM.R - Sofie
- output_SAG.R - Jean-Baptiste
- model_forecast - Klaas
- model_SAM.R - Klaas
- model_retrospective - Jean-Baptiste
- report_wg_presentation - Colin
- data_FLSAM.R - Petur
Additional tasks:
- investigate stockplotr:: convert_output, create_rda
- investigate dev containers
Consider scripts -> functions, candidates are:
- output_SAG.R
####src/SS3/data.R Prepares the data to run the assessment, saved in the src/SS3/data folder as CSV files and RData file.
####src/SS3/model.R RUN SS3 model fit, retrospective and jitter
####src/SS3/model_forecast.R RUN the short-term forecast using SS3 (grid of F-multipliers relative to the Fsq to cover alternative scenarios in the catch option table) and generate default tables and figures for the advice sheet and the report.