TAF template for the SS3 method: Stock Synthesis, run with the R packages r4ss, ss3diags and ss3om.
The example is a sardine assessment. Its SS3 input files (control, data, starter, forecast and weight at age) are in boot/initial/data/ss3, and the SS3 executables, version 3.30.22.1 for Linux and Windows, in boot/initial/software.
data.R: reads the SS3 input files with r4ss and writes the main data as TAF tables.model.R: runs SS3, refits with the bias ramp adjusted, and runs 50 jitters and a 5-year retrospective analysis.model_forecast.R: the short-term forecast with SS3, over a grid of F multipliers for the catch options table, with its tables and plots.output.R: an FLStock object made with ss3om, and tables of the results.report.R: empty so far.
The scripts were written at the Workshop on TAF Stock Assessment Templates (WKTSAT), and copied from src/SS3 of ices-eg/WKTSAT at commit d343202, without the model results committed there in model/, which TAF makes when the model is run.