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Hyperlink selex patterns (#236)
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* add hyperlinks to rest of selex patterns

* fix

* add words to dictionary; fix hypertargets

* fix dictionary and hyperlink
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e-perl-NOAA authored Jul 19, 2024
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2 changes: 1 addition & 1 deletion 13output.tex
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Before listing the derived quantities reported to the standard deviation report, there are a couple of topics that deserve further explanation.

\hypertarget{VirginUnfished}{}
\subsubsection[Virgin Spawning Biomass vs Unfished Spawning Biomass]{\protect\hyperlink{}{Virgin Spawning Biomass vs Unfished Spawning Biomass}}
\subsubsection[Virgin Spawning Biomass vs Unfished Spawning Biomass]{\protect\hyperlink{VirginUnfished}{Virgin Spawning Biomass vs Unfished Spawning Biomass}}
Unfished is the condition for which reference points (benchmark) are calculated. Virgin Spawning Biomass (B0) is the initial condition on which the start of the time-series depends. If biology or spawner-recruitment parameters are time-varying, then the benchmark year input in the forecast file tells the model which years to average in order to calculate ``unfished''. In this case, virgin recruitment and/or the virgin spawning biomass will differ from their unfished counterparts. Virgin recruitment and spawning biomass are reported in the mgmt\_quant portion of the sd\_report and are now labeled as ``unfished'' for clarity. Note that if ln(R0) is time-varying, then this will cause unfished to differ from virgin. However, if regime shift parameter is time-varying, then unfished will remain the same as virgin because the regime shift is treated as a temporary offset from virgin. Virgin spawning biomass is denoted as SPB\_virgin and spawning biomass unfished is denoted as SPB\_unf in the report file.

Virgin Spawning Biomass (B0) is used in four ways within SS3:
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