From e97c19e2d94001447f376e9001c9a3793ef52c9d Mon Sep 17 00:00:00 2001 From: Elizabeth Perl Date: Tue, 13 May 2025 16:16:55 -0400 Subject: [PATCH 1/6] Improve description and example text of age and size bin selectivities (ss3-source-code#670) --- 9control.tex | 33 ++++++++++++++++++++++++--------- 1 file changed, 24 insertions(+), 9 deletions(-) diff --git a/9control.tex b/9control.tex index f7ab614e..3e9a2c78 100644 --- a/9control.tex +++ b/9control.tex @@ -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 other selectivity parameters.} + \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 @@ -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\\ + \muticolumn{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 other selectivity parameters.} + \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 @@ -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\\ + \muticolumn{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 other selectivity parameters.} + \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 & & Block Fxn & Parameter Label \Bstrut\\ @@ -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\\ + \muticolumn{6}{l}{... other selectivity parameters as in Pattern 6} \Bstrut\\ \hline \end{longtable} From 6ec416d0a7228e87eb7c49524ea183b1b655609d Mon Sep 17 00:00:00 2001 From: Elizabeth Perl Date: Thu, 15 May 2025 10:24:29 -0400 Subject: [PATCH 2/6] add concurrency stipulation to github actions --- .github/workflows/build-ss3-manual-html.yml | 4 ++++ .github/workflows/build-ss3-manual-pdf.yml | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/.github/workflows/build-ss3-manual-html.yml b/.github/workflows/build-ss3-manual-html.yml index b7863199..6cd50491 100644 --- a/.github/workflows/build-ss3-manual-html.yml +++ b/.github/workflows/build-ss3-manual-html.yml @@ -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 diff --git a/.github/workflows/build-ss3-manual-pdf.yml b/.github/workflows/build-ss3-manual-pdf.yml index e889995f..b02f4896 100644 --- a/.github/workflows/build-ss3-manual-pdf.yml +++ b/.github/workflows/build-ss3-manual-pdf.yml @@ -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: From 33a25b34a6c1c102deda92d142d2426b275d34a1 Mon Sep 17 00:00:00 2001 From: Elizabeth Perl Date: Thu, 15 May 2025 10:42:54 -0400 Subject: [PATCH 3/6] fix multicolumn --- 9control.tex | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/9control.tex b/9control.tex index 3e9a2c78..b715131f 100644 --- a/9control.tex +++ b/9control.tex @@ -2199,7 +2199,7 @@ \subsubsection{Predator Fleet Mortality} 0 & 15 & 10 & \multicolumn{1}{c}{...} & 0 & \#AgeSel\_ScaleAgeLo \Tstrut\\ 0 & 20 & 20 & \multicolumn{1}{c}{...} & 0 & \#AgeSel\_ScaleAgeHi \Tstrut\\ - \muticolumn{6}{l}{... other selectivity parameters as in Pattern 17} \Bstrut\\ + \muticolumn{6}{l}{... other selectivity parameters as in Pattern 17} & & & & & \Bstrut\\ \hline \end{longtable} @@ -2224,7 +2224,7 @@ \subsubsection{Predator Fleet Mortality} 0 & 15 & 10 & \multicolumn{1}{c}{...} & 0 & \#AgeSpline\_ScaleAgeLo \Tstrut\\ 0 & 20 & 20 & \multicolumn{1}{c}{...} & 0 & \#AgeSpline\_ScaleAgeHi \Tstrut\\ - \muticolumn{6}{l}{... other selectivity parameters as in Pattern 27} \Bstrut\\ + \muticolumn{6}{l}{... other selectivity parameters as in Pattern 27} & & & & & \Bstrut\\ \hline \end{longtable} @@ -2249,7 +2249,7 @@ \subsubsection{Predator Fleet Mortality} 1 & 80 & 50 & \multicolumn{1}{c}{...} & 0 & \#SizeSel\_ScaleBinLo \Tstrut\\ 1 & 80 & 70 & \multicolumn{1}{c}{...} & 0 & \#SizeSel\_ScaleBinHi \Tstrut\\ - \muticolumn{6}{l}{... other selectivity parameters as in Pattern 6} \Bstrut\\ + \muticolumn{6}{l}{... other selectivity parameters as in Pattern 6} & & & & & \Bstrut\\ \hline \end{longtable} From 6ea9042b79e05fe9fc56521fd3fc1d6f1c4b199e Mon Sep 17 00:00:00 2001 From: Elizabeth Perl Date: Thu, 15 May 2025 11:08:42 -0400 Subject: [PATCH 4/6] fix spelling of multicolumn --- 9control.tex | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/9control.tex b/9control.tex index b715131f..7a006e2f 100644 --- a/9control.tex +++ b/9control.tex @@ -2199,7 +2199,7 @@ \subsubsection{Predator Fleet Mortality} 0 & 15 & 10 & \multicolumn{1}{c}{...} & 0 & \#AgeSel\_ScaleAgeLo \Tstrut\\ 0 & 20 & 20 & \multicolumn{1}{c}{...} & 0 & \#AgeSel\_ScaleAgeHi \Tstrut\\ - \muticolumn{6}{l}{... other selectivity parameters as in Pattern 17} & & & & & \Bstrut\\ + \multicolumn{6}{l}{... other selectivity parameters as in Pattern 17} \Bstrut\\ \hline \end{longtable} @@ -2224,7 +2224,7 @@ \subsubsection{Predator Fleet Mortality} 0 & 15 & 10 & \multicolumn{1}{c}{...} & 0 & \#AgeSpline\_ScaleAgeLo \Tstrut\\ 0 & 20 & 20 & \multicolumn{1}{c}{...} & 0 & \#AgeSpline\_ScaleAgeHi \Tstrut\\ - \muticolumn{6}{l}{... other selectivity parameters as in Pattern 27} & & & & & \Bstrut\\ + \multicolumn{6}{l}{... other selectivity parameters as in Pattern 17} \Bstrut\\ \hline \end{longtable} @@ -2249,7 +2249,7 @@ \subsubsection{Predator Fleet Mortality} 1 & 80 & 50 & \multicolumn{1}{c}{...} & 0 & \#SizeSel\_ScaleBinLo \Tstrut\\ 1 & 80 & 70 & \multicolumn{1}{c}{...} & 0 & \#SizeSel\_ScaleBinHi \Tstrut\\ - \muticolumn{6}{l}{... other selectivity parameters as in Pattern 6} & & & & & \Bstrut\\ + \multicolumn{6}{l}{... other selectivity parameters as in Pattern 17} \Bstrut\\ \hline \end{longtable} From c7100d07db0398dee01742e1079c62a48cf7c852 Mon Sep 17 00:00:00 2001 From: Elizabeth Perl Date: Fri, 16 May 2025 12:59:01 -0400 Subject: [PATCH 5/6] address issue #289; also add part about bin-specific params --- 9control.tex | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/9control.tex b/9control.tex index 7a006e2f..981ed964 100644 --- a/9control.tex +++ b/9control.tex @@ -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} @@ -2180,7 +2180,7 @@ \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 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 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 and other selectivity parameters.} \begin{itemize} \item p1 (AgeSel\_ScaleAgeLo)- low age \item p2 (AgeSel\_ScaleAgeHi)- high age @@ -2205,7 +2205,7 @@ \subsubsection{Predator Fleet Mortality} \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 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 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 and other selectivity parameters.} \begin{itemize} \item p1 (AgeSel\_ScaleAgeLo)- low age \item p2 (AgeSel\_ScaleAgeHi)- high age @@ -2230,7 +2230,7 @@ \subsubsection{Predator Fleet Mortality} \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 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 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 and other selectivity parameters.} \begin{itemize} \item p1 (SizeSel\_ScaleBinLo)- low size \item p2 (SizeSel\_ScaleBinHi)- high size From 79dc693d16d18a507979c90abb586015df935ea1 Mon Sep 17 00:00:00 2001 From: Elizabeth Perl Date: Mon, 19 May 2025 15:22:15 -0400 Subject: [PATCH 6/6] update wording --- 9control.tex | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/9control.tex b/9control.tex index 981ed964..dc6d01df 100644 --- a/9control.tex +++ b/9control.tex @@ -2180,7 +2180,7 @@ \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 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 and 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 @@ -2205,7 +2205,7 @@ \subsubsection{Predator Fleet Mortality} \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 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 and 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 @@ -2224,13 +2224,13 @@ \subsubsection{Predator Fleet Mortality} 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 17} \Bstrut\\ + \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 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 and 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 @@ -2249,7 +2249,7 @@ \subsubsection{Predator Fleet Mortality} 1 & 80 & 50 & \multicolumn{1}{c}{...} & 0 & \#SizeSel\_ScaleBinLo \Tstrut\\ 1 & 80 & 70 & \multicolumn{1}{c}{...} & 0 & \#SizeSel\_ScaleBinHi \Tstrut\\ - \multicolumn{6}{l}{... other selectivity parameters as in Pattern 17} \Bstrut\\ + \multicolumn{6}{l}{... other selectivity parameters as in Pattern 6} \Bstrut\\ \hline \end{longtable}