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@Rick-Methot-NOAA Rick-Methot-NOAA commented Sep 4, 2025

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

What tests have been done?

Where are the relevant files?

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

What tests/review still need to be done?

Be sure that r4ss is happy

Is there an input change for users to Stock Synthesis?

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

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@e-perl-NOAA
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@Rick-Methot-NOAA the error in the GitHub action for the test models is the following

Finished calculating benchmarks
Writing wtatage.ss_new
Finished posteriors
Error: Error: Invalid index 1965 used for array range [1, 2] in "dvar_vector& dvar4_array::operator() (int i, int j, int k)".
hslice index out of bounds

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Rick-Methot-NOAA commented Sep 5, 2025

@e-perl-NOAA @chantelwetzel-noaa
Let's add something about this to the manual:
The age-selex table in report.sso provides two versions of F. The first, which has been in existence for a long time, is simply labelled "F". It is based on selectivity and is the F-at-age that selects, i.e. catches the fish. The new line is labelled "Fdead" and is the mortality rate caused by fishing. If there is no discarding or if all discarded fish are dead, these two values will be identical. However, if there is discarding and some discarded fish survive, then Fdead will be less that F. F creates the total catch (retained and discarded dead and discarded alive). Fdead is used in the survival calculations, so Z = M + Fdead.

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I think I will do one more push to rename F+ to be F-dead

@Rick-Methot-NOAA Rick-Methot-NOAA linked an issue Sep 5, 2025 that may be closed by this pull request
@Rick-Methot-NOAA Rick-Methot-NOAA merged commit 5313b29 into main Sep 9, 2025
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@Rick-Methot-NOAA Rick-Methot-NOAA deleted the F_report_augment branch September 9, 2025 18:06
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[Feature]: Add F_dead-at-age to output

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