Document parameter devs approach implemented in 3.30.13

[k-doering-NOAA]

Imported from redmine, Issue #66186
Opened by @k-doering-NOAA on 2019-07-18
Status when imported: In Progress

From the release notes for 3.30.13:

Greetings Stock Synthesis (SS) Users,
In this release of Stock Synthesis 3.30.13.00 we have included some fixes, augmentations and new features.  Thanks to some users
who were pushing the envelope on time-varying parameters for finding some needed fixes to the code.  You can find all the changes 
listed in the Change Log and below.   The fixes were minor and mostly in the output, but there is one big fix affecting the 
calculation of the log likelihood for the parameter deviations.  We will put out a fuller report on that later and encourage you 
to contact us if you need info on this change sooner.

To the best of my knowledge, the fuller report did not get finished, so I am opening this issue as a reminder to the team. Rick, I added you as the assignee for now, but feel free to change.

[k-doering-NOAA]

comment from @k-doering-NOAA on 2020-04-01:
Rick, maybe you could provide a link to the draft or provide a copy of the latest draft here?

[k-doering-NOAA]

comment from @RickMethot on 2020-04-01:
here is the current draft.

Ideally, we would conduct a fuller test of the performance of parameter deviations in MLE and MCMC mode. Another task for another team member I suppose.

[k-doering-NOAA]

comment from @RickMethot on 2020-08-07:
today notice that when rho = 0, the logL of the parmdevs was simply the sum of squared devs. It was missing the multiplication by 0.5.
Add this factor on this date, but it will now produce a different logL than previously. Messy.

[k-doering-NOAA]

comment from @RickMethot on 2020-08-26:
Belay that finding. the logL was ok with the 0.5 factor

[k-doering-NOAA]

comment from @k-doering-NOAA on 2020-08-26:
Document performance of related issues (links included in this issue)

[k-doering-NOAA]

comment from @k-doering-NOAA on 2020-08-26:
Moving this tag to the next release, as there is not much sense in holding up the 3.30.16 for better performance testing of parameter dev approaches. @richard.methot, feel free to change the tags back if this is not what you had in mind.

[Rick-Methot-NOAA]

This issue and issue #20 are the same topic

[k-doering-NOAA]

@RickMethot I think this one assumed that the parameter dev approaches were done and just needed to be communicated better to users. But then more discussion happened on issue #20 , so maybe the best move is to go ahead and close this issue? I think when we close #20 , we should open an issue in https://github.com/nmfs-stock-synthesis/ss-documentation to document better