revise code and change VBK_seas usage

[Rick-Methot-NOAA]

Concisely describe what has been changed/addressed in the pull request.

• Resolves [Bug]: growth discrepancy when season duration is < 1.0 (months < 12) and growth type is Gompertz-Richards #735
• [Question]: Code review for growth #156
  The issue "code review for growth" contains several tasks to be resolved.

What tests have been done?

Where are the relevant files?

<-- - [x] Test files are in the issue. --> See repo with growth test files (https://github.com/e-perl-NOAA/growth-test-models)

What tests/review still need to be done?

Is there an input change for users to Stock Synthesis?

<-- - [x] No, there was no input change. -->

Additional information (optional).

[Rick-Methot-NOAA]

I will test with big skate locally to diagnose the run failure

[Copilot]

Pull request overview

This pull request refactors the growth calculation code in Stock Synthesis, focusing on improving variable naming clarity and revising how seasonal growth adjustments (VBK_seas) are applied. The changes address issues #735 and #156.

Key changes:

• Renamed growth-related variables for clarity (VBK_temp → VBK_work, VBK_temp2 → VBK_by_seas)
• Restructured growth type handling with improved switch statement organization
• Modified VBK_seas usage by removing seasdur(s) multipliers in growth calculations
• Added documentation comments explaining VBK variable purposes
• Removed preprocessor conditionals (#ifdef DO_ONCE) in favor of runtime checks

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[e-perl-NOAA]

@Rick-Methot-NOAA I had copilot review the PR in case there was anything that it might be able to easily identify anything the that might cause the big skate model to fail. There were some suggestions it gave which didn't matter and I closed those but it might be worth looking at some of the other suggestions it made. If they are wrong or you don't agree, feel free to just click the "Resolve conversation" button and they will go away.

[Rick-Methot-NOAA]

now investigating the failure with growth time-vary

[e-perl-NOAA]

This looks good to me in that the tests are now passing. Copilot seems to think that the logic of everything is more consistent than it was.

[Rick-Methot-NOAA]

@e-perl-NOAA The Richards and age-specific null values are each 1.0, per the manual.

Cessation model (8) is giving unexpected results that need separate attention. Let's leave it out of the current test.

[e-perl-NOAA]

@Rick-Methot-NOAA I have all the run models with growth plots in each of the respective folders (aside from cessation) in this repository. The only thing that I don't have is any sort of table. The values used to make the growth plots are Age_Beg and Len_Beg. I can grab these for males and females or just one sex, etc. or any other values you would like. I just don't know what values and what sort of structure of table would be most useful for you.

[Rick-Methot-NOAA]

I think we need in one text file the following lines from each report.sso file. So all the results that we need will be in one file. I added a line to be the identifier for each run.

Growth-1-annual
MEAN_SIZE_TIMESERIES report:49
Morph Yr Seas SubSeas 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
1 1971 1 1 20 20.5 21 21.5 22 22.5 23 23.5 24 24.5 25 25.5 26 26.5 27 27.5 28 28.5 29 29.5 30 30.5 31 31.5 32 32.5 33 33.5 34 34.5 35 35.5 36 36.5 37 37.5 38 38.5 39 39.5 43.379
1 1971 1 2 20.25 20.75 21.25 21.75 22.25 22.75 23.25 23.75 24.25 24.75 25.25 25.75 26.25 26.75 27.25 27.75 28.25 28.75 29.25 29.75 30.25 30.75 31.25 31.75 32.25 32.75 33.25 33.75 34.25 34.75 35.25 35.75 36.25 36.75 37.25 37.75 38.25 38.75 39.25 39.75 43.629
1 2011 1 1 20 20.5 21 21.5 22 22.5 23 23.5 24 24.5 25 25.5 26 26.5 27 27.5 28 28.5 29 29.5 30 30.5 31 31.5 32 32.5 33 33.5 34 34.5 35 35.5 36 36.5 37 37.5 38 38.5 39 39.5 43.379
1 2011 1 2 20.25 20.75 21.25 21.75 22.25 22.75 23.25 23.75 24.25 24.75 25.25 25.75 26.25 26.75 27.25 27.75 28.25 28.75 29.25 29.75 30.25 30.75 31.25 31.75 32.25 32.75 33.25 33.75 34.25 34.75 35.25 35.75 36.25 36.75 37.25 37.75 38.25 38.75 39.25 39.75 43.629

[e-perl-NOAA]

@Rick-Methot-NOAA And you want this in a text file, not a csv for excel sheet?

[Rick-Methot-NOAA]

space delimited text is read by excel just as easily as csv.

[e-perl-NOAA]

Okay, that output from the report file (as r4ss grabs it) is now in this text file for all of the models.

[Rick-Methot-NOAA]

Growth test models and commentary found in this repo: https://github.com/e-perl-NOAA/growth-test-models

[Rick-Methot-NOAA]

commit ab2ae43
adds output table mean_size by cohort and demonstrates match of midseason in one season model to the beginning of season 2 in a two season model

[Rick-Methot-NOAA]

run failure probably due to the new table, which is in same section as the current table MEAN_SIZE_TIMESERIES report:49.
The new table starts with:
#_Mean_size_by_cohort
Morph YearClass Seas SubSeas 0 1 2

New table is omitted if growth is not time-varying

Let me know what changes would ease reading by r4ss. @iantaylor-NOAA

[iantaylor-NOAA]

I'll take a look at adding the new table to the r4ss parsing. I'm guessing it will be fine as you've created it.

[iantaylor-NOAA]

I made a minor change in 3557ff7 to the format of the new table header to match the format of the following tables that start "mean_size_Jan_1_for_sex...". This allowed a more trivial change to the r4ss code which I pushed right away. The r4ss function doesn't yet read the new table but the ss3 test should now play through without crashing. I can then add the read of the new table next.