complete addition of TG_min_recap, and revise compreport

[Rick-Methot-NOAA]

What issue(s) does this PR address? Describe and add issue numbers, if applicable.

This adds capability to exclude from the tag logL tag groups with less than a specified minimum number of recaptures

• [tag-recapture: create user filter to set min number of recaptures for inclusion of a tag-group #280 ] Link issue on pull request

What tests have been done? Upload any model input files created for testing in a zip file, if possible.

works with the IOTC Yellowfin tuna spatial model

What tests/review still need to be done? Who can do it, and by when is it needed (ideally)?

none

Check which is true. This PR requires:

• Changes in r4ss
• Changes to SS3 manual
• Changes to SSI (the SS3 GUI)
• An entry in the stock synthesis change log (new features, bug reports)

Describe any changes in r4ss/SS3 manual/SSI/change log that are needed (if checked):

input of new feature is conditional on TG_mixperiod having a negative value:
1 # do tags (0/1)
121 # N tag groups
769 # N recap events
-4 # TG_mixperiod (latency) is the first period in which logL is calculated for this tag group (0 = release period)

(use negative value for TG_mixperiod to invoke reading TG_min_recap after TG_maxperiods

16 # max periods (seasons) to track recoveries, after which tags are still read into this accumulator period
2 # TG_min_recap: N recaps >= mixperiod must be >= min_recap to include tag group in logL

Additional information (optional):

@jyqalan

[k-doering-NOAA]

@Rick-Methot-NOAA, did you want this to be part of the 3.30.19?

[Rick-Methot-NOAA]

Yes because we still are waiting on the rebuilder revision.
Will need some work on the manual and r4ss.

[k-doering-NOAA]

Looks good! I took a look at the code, then Rick walked me through the changes while screen sharing and explained why they were made. Makes sense to me.

Optional changes:

• ssnew comments for the new conditional input
• using a new 2 option for the do tag flag as the trigger for the conditional input rather than a negative value on the mix period. Rick made the observation that this may be better and I agree it may be more intuitive for users.

[Rick-Methot-NOAA]

revise trigger
2 # do tags (0/1/2); where 2 allows entry of TG_min_recap
instead of negative mixperiod value as trigger.

[k-doering-NOAA]

Looks good @Rick-Methot-NOAA ! I ran a version of the YFT for the spatial project, and it worked well. Attached are the input files for the version with the min recapture option for future.

Running with -stopph 0 -nohess, only the 2 tag likelihoods changed when using the min recapture option, and the likelihoods were reduced, so this checks out.

I also tried running with estimation as well, and the model ran fine.

Something picky: I noticed there was a space in the .ss_new file when printing the # COND line; I will push a small change to get rid of it.

This is ready to merge in once I push the picky change.

use_min_option_inputfiles.zip