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age-based calc of sel_dead_num and bio is repaired#663

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Rick-Methot-NOAA merged 2 commits intomainfrom
repair-age-discard-#662
Apr 1, 2025
Merged

age-based calc of sel_dead_num and bio is repaired#663
Rick-Methot-NOAA merged 2 commits intomainfrom
repair-age-discard-#662

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@Rick-Methot-NOAA
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Concisely describe what has been changed/addressed in the pull request.

What tests have been done?

when use age-based selectivity, retention and discard mortality, the results now appear correct with the sel_dead values intermediate between the sel and the sel*ret values

Where are the relevant files?

<-- - [x] No test files are required for this pull request. -->

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. -->

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@iantaylor-NOAA iantaylor-NOAA left a comment

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The code changes look good to me, but I would leave it to @chantelwetzel-noaa to confirm that the results for her model look accurate.

@Rick-Methot-NOAA
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good suggestion Elizabeth to clean up the code comments, some of which were copied between sections.
BTW, I made a comment in another issue about what looks like a non-trivial bit of work to get separate wt-at-age for discarded fish into the wtatage..ss file and used by the code.

@Rick-Methot-NOAA Rick-Methot-NOAA linked an issue Apr 1, 2025 that may be closed by this pull request
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I tested the model and the values in the catch table are as expected.

@Rick-Methot-NOAA Rick-Methot-NOAA merged commit a374f3f into main Apr 1, 2025
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@Rick-Methot-NOAA Rick-Methot-NOAA deleted the repair-age-discard-#662 branch April 1, 2025 22:40
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[Bug]: age discard with discard mortality using wrong vector

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