[feat]: table_derived_quantities

[Schiano-NOAA]

One of the high priority tables for development in {stockplotr} is a derived quantity table. This is a table of derived quantities to help guide management. We do not have a current example for this so the developer for this table has some free rein to choose the design and quantities. It would be helpful to have members of the stock assessment workflows steering committee meeting commenting on this table design and decide on which values to include.

Start: the developer of this table should create a list of quantities for this table. These could include MSST, MFMT, Ftarg, Btarg, M, Rcurr, R0, h, SBC, fraction unfished, recruitment.

Next: work on setting up a branch and a new function called table_derived_quantities() for this table. Please follow the branch and PR indicators. There are instructions in the CONTRIBUTING.md that describe how each table or figure are set up and the steps/related functions that can create it.

Last: set up a testing framework using {testthat} to test the function.

@Schiano-NOAA or @sbreitbart-NOAA can run tests on the function to ensure it is compatible with all models that are compatible in the convert_output function. (We are planning on adding test data sets to the package for all models in the future.)

Please complete what you are able to do and the package maintainers can pick up where you left off whether it be getting together the quantities for the table or completing the table code and not yet setting up the tests.

[okenk]

I'm not 100% sure what a derived quantity table is, as we report too many derived quantities to put them all in one table. I think you might mean reference points. Assuming that is the case, on the west coast we report values based on three different targets: the biomass target, the SPR target, and MSY. This is what our terms of reference currently require (though they are in flux):

Here is an example table:

In general, because assessments in our region usually do not assume spawning output is directly proportional to spawning biomass, it is important to report both spawning output and some sort of population biomass.

The generic {r4ss} code that was used to produce the table is here

Separately from the reference points table, we have a 1) table of every model parameter (this includes M and h) and 2) several tables of various time series (including recruitment, SPR, fraction unfished, and spawning output). In the executive summary, the time series are only for the last ten years. In the main document, they cover the full modeled period.