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e-perl-NOAA merged 6 commits into from
May 19, 2025
Merged

Improve selex pattern age size bin description #288

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e97c19e
Improve description and example text of age and size bin selectivitie…
e-perl-NOAA May 13, 2025
6ec416d
add concurrency stipulation to github actions
e-perl-NOAA May 15, 2025
33a25b3
fix multicolumn
e-perl-NOAA May 15, 2025
6ea9042
fix spelling of multicolumn
e-perl-NOAA May 15, 2025
c7100d0
address issue #289; also add part about bin-specific params
e-perl-NOAA May 16, 2025
79dc693
update wording
e-perl-NOAA May 19, 2025
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4 changes: 4 additions & 0 deletions .github/workflows/build-ss3-manual-html.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,10 @@ on:
required: false
type: string

concurrency:
group: ${{ github.workflow}}-${{ github.ref }}
cancel-in-progress: true

jobs:
build-html:
runs-on: ubuntu-latest
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4 changes: 4 additions & 0 deletions .github/workflows/build-ss3-manual-pdf.yml
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Expand Up @@ -16,6 +16,10 @@ on:
default: ${{ github.ref }}
required: false
type: string

concurrency:
group: ${{ github.workflow}}-${{ github.ref }}
cancel-in-progress: true

jobs:
build-pdf:
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35 changes: 25 additions & 10 deletions 9control.tex
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Expand Up @@ -1721,7 +1721,7 @@ \subsubsection{Predator Fleet Mortality}
\item Option = 2: program will read 4 retention parameters and 4 discard mortality parameters.
\item Option = 3: no additional parameters are read and all fish are assumed discarded and dead.
\item Option = 4: program will read 7 retention parameters for dome-shaped retention and 4 discard mortality parameters.
\item Option = negative fleet number: will mirror the retention and discard mortality pattern of the lower numbered fleet.
\item Option = negative value: mirror the retention and discard mortality pattern of a lower numbered fleet identified as abs(value)
\end{itemize}

\myparagraph{Male}
Expand Down Expand Up @@ -2180,7 +2180,11 @@ \subsubsection{Predator Fleet Mortality}

\hypertarget{RandomWalkScaling}{}
\myparagraph{Pattern 41 (age) - Random Walk Selectivity with User-Defined Scaling}
Selectivity pattern 17 with two additional parameters. The two additional parameters are the bin numbers to define the range of bins for scaling. All the selectivity values will be scaled (divided) by the mean value over this range. The low and high bin numbers are defined before the other selectivity parameters.
Selectivity pattern 17 with two additional parameters. The two additional parameters are the bin numbers to define the age range of bins for scaling. All the selectivity values will be scaled (divided) by the mean value over this age range. \textbf{The low and high bin numbers are defined BEFORE the bin-specific parameters for that fleet.}
\begin{itemize}
\item p1 (AgeSel\_ScaleAgeLo)- low age
\item p2 (AgeSel\_ScaleAgeHi)- high age
\end{itemize}

\begin{longtable}{p{1cm} p{1cm} p{1cm} p{2.9cm} p{1.9cm} p{4.2cm}}
\hline
Expand All @@ -2193,14 +2197,19 @@ \subsubsection{Predator Fleet Mortality}
\hline
\endhead

0 & 20 & 10 & \multicolumn{1}{c}{...} & 0 & \#AgeSel\_ScaleAgeLo \Tstrut\\
0 & 20 & 20 & \multicolumn{1}{c}{...} & 0 & \#AgeSel\_ScaleAgeHi \Bstrut\\
0 & 15 & 10 & \multicolumn{1}{c}{...} & 0 & \#AgeSel\_ScaleAgeLo \Tstrut\\
0 & 20 & 20 & \multicolumn{1}{c}{...} & 0 & \#AgeSel\_ScaleAgeHi \Tstrut\\
\multicolumn{6}{l}{... other selectivity parameters as in Pattern 17} \Bstrut\\
\hline
\end{longtable}

\hypertarget{CubicSplineScaling}{}
\myparagraph{Pattern 42 (size or age) - Cubic Spline Selectivity with User-Defined Scaling}
Selectivity pattern 27 with two additional parameters. The two additional parameters are the bin numbers to define the range of bins for scaling. All the selectivity values will be scaled (divided) by the mean value over this range. The low and high bin numbers are defined before the other selectivity parameters.
Selectivity pattern 27 with two additional parameters. The two additional parameters are the bin numbers to define the age range of bins for scaling. All the selectivity values will be scaled (divided) by the mean value over this age range. \textbf{The low and high bin numbers are defined BEFORE the bin-specific parameters for that fleet.}
\begin{itemize}
\item p1 (AgeSel\_ScaleAgeLo)- low age
\item p2 (AgeSel\_ScaleAgeHi)- high age
\end{itemize}

\begin{longtable}{p{1cm} p{1cm} p{1cm} p{2.9cm} p{1.9cm} p{4.2cm}}
\hline
Expand All @@ -2213,15 +2222,20 @@ \subsubsection{Predator Fleet Mortality}
\hline
\endhead

0 & 20 & 10 & \multicolumn{1}{c}{...} & 0 & \#AgeSpline\_ScaleAgeLo \Tstrut\\
0 & 20 & 20 & \multicolumn{1}{c}{...} & 0 & \#AgeSpline\_ScaleAgeHi \Bstrut\\
0 & 15 & 10 & \multicolumn{1}{c}{...} & 0 & \#AgeSpline\_ScaleAgeLo \Tstrut\\
0 & 20 & 20 & \multicolumn{1}{c}{...} & 0 & \#AgeSpline\_ScaleAgeHi \Tstrut\\
\multicolumn{6}{l}{... other selectivity parameters as in Pattern 27} \Bstrut\\
\hline
\end{longtable}

\hypertarget{NonParamScaling}{}
\myparagraph{Pattern 43 (size) - Non-parametric Selectivity with User-Defined Scaling}
Selectivity pattern 6 with two additional parameters. The two additional parameters are the bin numbers to define the range of bins for scaling. All the selectivity values will be scaled (divided) by the mean value over this range. The low and high bin numbers are defined before the other selectivity parameters.

Selectivity pattern 6 with two additional parameters. The two additional parameters are the size bin numbers to define the range of bins for scaling. All the selectivity values will be scaled (divided) by the mean value over this size range. \textbf{The low and high bin numbers are defined BEFORE the bin-specific parameters for that fleet.}
\begin{itemize}
\item p1 (SizeSel\_ScaleBinLo)- low size
\item p2 (SizeSel\_ScaleBinHi)- high size
\end{itemize}

\begin{longtable}{p{1cm} p{1cm} p{1cm} p{2.9cm} p{1.9cm} p{4.2cm}}
\hline
LO \Tstrut & HI & INIT & <other entries> & Block Fxn & Parameter Label \Bstrut\\
Expand All @@ -2234,7 +2248,8 @@ \subsubsection{Predator Fleet Mortality}
\endhead

1 & 80 & 50 & \multicolumn{1}{c}{...} & 0 & \#SizeSel\_ScaleBinLo \Tstrut\\
1 & 80 & 70 & \multicolumn{1}{c}{...} & 0 & \#SizeSel\_ScaleBinHi \Bstrut\\
1 & 80 & 70 & \multicolumn{1}{c}{...} & 0 & \#SizeSel\_ScaleBinHi \Tstrut\\
\multicolumn{6}{l}{... other selectivity parameters as in Pattern 6} \Bstrut\\
\hline
\end{longtable}

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