implement depletion survey as a parameter for XSSS

[k-doering-NOAA]

Imported from redmine, Issue #47209 Opened by @RickMethot on 2018-03-01 Status when imported: On Hold

from Jason Cope: If it is a parameter, we are able to access the MCMC machinery for estimation for SSS (we have a way of putting all the draws in the .pin file, which makes calculation really fast) and allows us to bypass AIS and use MCMC, which makes the integration and ultimate processing of output much better. If it is a parameter, then if can have a prior. I would create another SRR function (or 2 if you are currently using 2) and add one more parameter to be read. That parameter would be the depletion (hate that word; it really is escapement) level. Because it is a parameter, it can have a prior. Then I would create a new survey type to make the correct logL calculation between this parameter and the expected value for escapement in the right year. Trying to think through how this will work in MCMC

A MCMC parameter draw will create: value for this new parameter, P value for the prior likelihood from P-Pprior value for escapement' from R0 and other model parameters value for the survey likelihood from P-escapement'

so it will be critical to be smart about the specified prior se relative to the se used for the survey logL so if the prior se is small, then either the MLE or the MCMC will move R0 and other parameters towards producing escapement values that are close to the prior for P.