Add function to create output files in format required by U.S. Species Information System (SIS) database

[iantaylor-NOAA]

Attached files are in the format required by the SIS database which is used by the Stock SMART web tool and other NOAA purposes. The files were created by @andi-stephens-NOAA in 2022 using a clunky process that Andi and I developed years ago which relies on the files in output-csv-files. It should be straightforward and much more efficient to just create these files directly within the hake assessment workflow.

I would be happy to help with this in fall 2023 (after U.S. west coast groundfish assessments and summer breaks, but before hake gets too busy), but it could happen any time before Spring 2024 when the files should be submitted.

Hake_2022_SIS_info_timeseries.csv
Hake_2022_SIS_info_values.csv

Checklist of next steps added 12 March 2024:

• @iantaylor-NOAA to merge branch of r4ss with improvements to get_SIS_info() (example use of the modified function for 2023 PFMC groundfish is shown in https://github.com/pfmc-assessments/PFMC-SIS/blob/main/R/pfmc-assessments_to_SIS_2023.R)
• @kellijohnson-NOAA to explore adding an mcmc = TRUE/FALSE switch to that function to work for hake

[aaronmberger-nwfsc]

At the same time, I would like to automate our annual NWFSC TSC groundfish reporting document (i.e., text already largely taken from the stock assessment directly, with one additional summary figure) as standard workflow output.

[iantaylor-NOAA]

The attached file Hake_to_SIS.R.txt is the most recently used script that I can find for converting a combination of median-population-estimates.csv and the model output as read by r4ss::SS_output(). Dates in the file are a few years old, but I can't find a more recent version and don't recall any changes other than the dates. That script may be useful to understand what quantities were being used where in the status-quo workflow for producing SIS input.

Recent changes to the r4ss::get_SIS_info() function (as referenced in the checklist added to the first comment of this thread) have now been merged into the main branch so that function is available for further edits as needed.