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Merged
e-perl-NOAA merged 6 commits into from
Mar 9, 2026
Merged

Lualatex isn't working properly, this is a workaround to at least make the pdf #323

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49deefa
try removing mybox commands to see if it fixes latex creation
e-perl-NOAA Feb 3, 2026
2a2fc08
fix item
e-perl-NOAA Feb 3, 2026
d196e91
try again
e-perl-NOAA Feb 3, 2026
35f83c4
try again
e-perl-NOAA Feb 3, 2026
889349d
try section by section
e-perl-NOAA Feb 3, 2026
5082509
try fix
e-perl-NOAA Mar 9, 2026
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5 changes: 3 additions & 2 deletions 12runningSS3.tex
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Expand Up @@ -12,9 +12,10 @@
\end{verbatim}
\end{quote}

\begin{mybox}{Note}
% \begin{mybox}{Note}
\textbf{Note:}
If you are on a Windows system and get a warning about the Microsoft Defender SmartScreen preventing an unrecognized app from starting, follow \href{https://answers.microsoft.com/en-us/windows/forum/all/how-to-change-the-mode-of-smart-app-control-from/399a276f-5585-40fe-b72d-c014cac82b32}{these instructions} to turn the Smart App Control off. If you don't have permissions to do so, either contact your IT department to have them change the setting or use \texttt{r4ss::get\_ss3\_exe()} which seems to work in this case too.
\end{mybox}
% \end{mybox}

On Mac and Linux computers, the executable name must be preceded by a period and slash (unless its location has been added to the user's PATH). Note that the user may need to change permissions for Stock Synthesis to be executable before running SS3 for the first time:

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9 changes: 5 additions & 4 deletions 15special.tex
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Expand Up @@ -139,9 +139,10 @@
\item 1 \#\_months/season
\item \# resultant season duration = 0.08333
\end{itemize}
\begin{mybox}{\textbf{With continuous season option 1, the user will see this warning}} \\
Warning: Season durations sum to < 11.9, so SS3 assumes you are doing years as pseudo-seasons. There can be only 1 season in this time-step and SS3 will ignore month input and assume all observation occur at middle of this pseudo-year. Mortality, growth, and movement rates are per annum, so will get multiplied by the duration of this time-step as they are used. What gets reported as age is now age in time-steps; and input of age-specific $M$ or $K$ requires one entry per time-step. Similarly, output of age-specific quantities is in terms of number of time-steps, not real years. Spawn\_month and settlement\_month in control file are best set to 1.0 when doing years as pseudo-seasons.
\end{mybox}
% \begin{mybox}{}
\item \textbf{With continuous season option 1, the user will see this warning} \\
Warning: Season durations sum to < 11.9, so SS3 assumes you are doing years as pseudo-seasons. There can be only 1 season in this time-step and SS3 will ignore month input and assume all observation occur at middle of this pseudo-year. Mortality, growth, and movement rates are per annum, so will get multiplied by the duration of this time-step as they are used. What gets reported as age is now age in time-steps; and input of age-specific $M$ or $K$ requires one entry per time-step. Similarly, output of age-specific quantities is in terms of number of time-steps, not real years. Spawn\_month and settlement\_month in control file are best set to 1.0 when doing years as pseudo-seasons.
% \end{mybox}
\item \textbf{Option 3: Manual season duration adjustment} \hypertarget{option3}{} \\
This creates a continuous stream of seasons and each is treated as if it is a logical year of \underline{full} (12 month) duration. SS3 will not be able to detect that you are intending to use these years as seasons. All rate parameters will need to be divided by 12.0 by the user because the season duration is not being internally adjusted.
\begin{itemize}
Expand Down Expand Up @@ -184,7 +185,7 @@
\item Edit the recruitment deviation (rec\_dev) start and end years to be in terms of the model time steps.
\item Parameters:
\begin{itemize}
\item If using \hyperlink{option3}{option 3}, growth rate and any other rate parameters will need manual adjustment to be in terms of the duration of the season.
\item If using \hyperlink{option2}{option 2}, growth rate and any other rate parameters will need manual adjustment to be in terms of the duration of the season.
\item Edit any age selectivity parameters that refer to age, because they are now in terms of quarters.
\item Decrease the $R_{0}$ parameter starting value because it is now the average number of recruitments per quarter year.
\item If there needs to be some degree of seasonality to a parameter, then you could create a cyclic pattern in the environmental input and make the parameter a function of this cyclic pattern.
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112 changes: 43 additions & 69 deletions SS330_User_Manual.tex
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@@ -1,32 +1,31 @@
% Preamble =========================================================================================
%Options added to improve pdf accessibility:
\RequirePackage{pdfmanagement-testphase}
\PassOptionsToPackage{enable-debug}{expl3}
%\DeclareDocumentMetadata { }
\DocumentMetadata{testphase={phase-III,math}}
\ExplSyntaxOn
\pdfmanagement_add:nnn{Catalog}{Lang}{(enUS)}
\ExplSyntaxOff
% \RequirePackage{pdfmanagement-testphase}
% \PassOptionsToPackage{enable-debug}{expl3}
% \DeclareDocumentMetadata {
% \DocumentMetadata{testphase={phase-III,math,table,title}}
\DocumentMetadata{lang=en-US,pdfversion=2.0}

% \ExplSyntaxOn
% \pdfmanagement_add:nnn{Catalog}{Lang}{(enUS)}
% \ExplSyntaxOff
% End accessibility options
\documentclass[12pt]{article}
\usepackage{sectsty} % Allows for different fonts for header and body
\usepackage{sectsty} % Allows for different fonts for header and body
\usepackage{natbib}
\usepackage{multicol}
\usepackage[margin=1in, includefoot]{geometry}
\usepackage{graphicx} %allows for impage import
\usepackage{graphicx} % Allows for impage import
\graphicspath{{images/}}
\usepackage{ragged2e}
\usepackage{enumitem}
\usepackage{multirow}
\usepackage{booktabs}
\usepackage{fontspec}
% \usepackage{lmodern}
\usepackage[none]{hyphenat}
\usepackage{array}
% \usepackage{lscape}
\usepackage{pdflscape}
\usepackage{longtable}
% \usepackage[utf8]{inputenc}
\usepackage[table]{xcolor}
\usepackage{colortbl}
\usepackage{hhline}
Expand All @@ -47,31 +46,33 @@
\usepackage[most]{tcolorbox} % callout box

% callout box controls
\tcbuselibrary{skins,breakable}
\newtcolorbox{mybox}[2][]{
breakable,
sharp corners,
skin=enhancedmiddle jigsaw,
parbox=false,
boxrule=0mm,
leftrule=2mm,
boxsep=0mm,
arc=0mm,
outer arc=0mm,
attach title to upper,
after title={:\ },
coltitle=black,
colback=gray!10,
colframe=black,
title={#2},
fonttitle=\bfseries,#1}
% \tcbuselibrary{skins,breakable}
% \newtcolorbox{mybox}[2][]{
% breakable,
% sharp corners,
% skin=enhancedmiddle jigsaw,
% parbox=false,
% boxrule=0mm,
% leftrule=2mm,
% boxsep=0mm,
% arc=0mm,
% outer arc=0mm,
% attach title to upper,
% after title={:\ },
% coltitle=black,
% colback=gray!10,
% colframe=black,
% title={#2},
% fonttitle=\bfseries,#1}


% For tagging the pdf: https://github.com/jgm/pandoc/issues/5409#issuecomment-770417614
\ifluatex
\usepackage{tagpdf}
\tagpdfsetup{
activate-all=true,
interwordspace=true
}
activate-all=true,
interwordspace=true
}
\fi
% End tagging the pdf

Expand All @@ -81,22 +82,17 @@

%sectsty commands
% all section headers use the same sans serif family - roboto
%\allsectionsfont{\sffamily\selectfont\roboto\mdseries\bfseries}
\allsectionsfont{\sffamily\selectfont\roboto\mdseries\bfseries}
% Set size and color of section header AL's H1
%\sectionfont{\LARGE\nohang\centering\roboto\textcolor[cmyk]{0.90, 0.54, 0.28, 0.12}}
\sectionfont{\LARGE\nohang\centering\roboto\textcolor[cmyk]{0.90, 0.54, 0.28, 0.12}}
% Set size and color of subsection header AL's H2
%\subsectionfont{\fontsize{18pt}{20pt}\selectfont\roboto\nohang\centering\textcolor[cmyk]{0.90, 0.54, 0.28, 0.12}}
\subsectionfont{\fontsize{18pt}{20pt}\selectfont\roboto\nohang\centering\textcolor[cmyk]{0.90, 0.54, 0.28, 0.12}}
% Set size and color of subsubsection header AL's H3
\subsubsectionfont{\hspace{0pt}\nohang\fontsize{16pt}{18pt}\selectfont\roboto\raggedright\textcolor[cmyk]{0.50, 0.05, 0.0, 0.40}}
% Set size and color of paragraph header AL's H4
%\paragraphfont{\fontsize{14pt}{16pt}\selectfont\robotocondensed\fontseries{bl}\selectfont\textcolor[cmyk]{0.50, 0.05, 0.0, 0.40}}
\paragraphfont{\fontsize{14pt}{16pt}\selectfont\robotocondensed\fontseries{bl}\selectfont\textcolor[cmyk]{0.50, 0.05, 0.0, 0.40}}
\newcolumntype{R}{>{\raggedright\arraybackslash}p{3cm}}

%\definecolor{lightgray}{gray}{0.92}
\fancyhead{}
\pagestyle{fancy}

Expand All @@ -110,14 +106,6 @@
\hyphenpenalty=10000
\hbadness=10000

%\hypersetup{%
% colorlinks=false,% hyperlinks will be black
% linkbordercolor=red,% hyperlink borders will be red
% pdfborderstyle={/S/U/W 1}% border style will be underline of width 1pt
%}



%%The following sets up how the pdf displays links and functions in Acrobat.
\hypersetup{
bookmarks = true, % show bookmarks bar?
Expand All @@ -143,24 +131,17 @@

\newcommand{\myparagraph}[1]{\paragraph{#1}\mbox{}\\}

% Define a term for SS3 abbreviation to use across document
% \newcommand{\SS}{SS3}

% Create custom font title of document
% note the use of:
%% \textcolor in the title itself
%% \maketitle BEFORE resetting the \fontfamily
%% \maketitle BEFORE resetting the \fontfamily
\usepackage{xparse}
\usepackage{xpatch}
\NewDocumentCommand{\TitlePageFont}{}{%
\sffamily\bfseries%
\fontsize{22pt}{24pt}%
\selectfont%
}%
% sets title for pdf reader
%\usepackage[pdftitle={Stock Synthesis User Manual},
% pdfauthor={Richard D. Methot Jr., Chantel R. Wetzel, Ian G. Taylor, and Kathryn Doering},
% pdfdisplaydoctitle=true]{hyperref}
\NewDocumentCommand{\TitlePageFont}{}{
\sffamily\bfseries
\fontsize{22pt}{24pt}
\selectfont
}
\xpretocmd{\maketitle}{\TitlePageFont}{}{}
\title{\textcolor[cmyk]{1.00,0.83,0.41,0.36}{Stock Synthesis User Manual\\ Version 3.30.24.1}}
\author{Richard D. Methot Jr., Chantel R. Wetzel, Ian G. Taylor, Kathryn L. Doering,\\Elizabeth F. Perl, and Kelli F. Johnson\\\\\\NOAA Fisheries\\Seattle, WA}
Expand All @@ -180,17 +161,13 @@
\begin{center}
\includegraphics[alt={Logo of the National Oceanic and Atmospheric Administration (NOAA)},height=2in]{noaalogo.jpg}
\end{center}
%\caption{Logo of the National Oceanic and Atmospheric Administration (NOAA)}
\label{fig:logo}
\end{figure}

\thispagestyle{empty}
\newpage
\normalfont % this sets the main font to crimson
\normalsize %% return the text to 12 point font - otherwise you end up with 22 point font!
% Set base font as serif
%\fontfamily{crimson}\selectfont

\normalsize % return the text to 12 point font - otherwise you end up with 22 point font!

% ====== Table of Contents ===================================================
\glsaddall
Expand All @@ -199,18 +176,15 @@
\thispagestyle{empty}
\cleardoublepage
\setcounter{secnumdepth}{0}
%\setcounter{page}{1}
\newpage
\raggedright
% ==== List of figures ========================================================
\renewcommand{\headrulewidth}{0pt} % removes the top line across each page
%\listoffigures
%\addcontentsline{toc}{section}{\numberline{}List of Figures}
\cleardoublepage
% ====== Section 1 - 4 =============================================================
\pagenumbering{arabic}
\input{1_4sections}
% ======== Section 5: Converting
======== Section 5: Converting
\input{5converting}
% ======== Section 6: Starter File
\input{6starter}
Expand Down Expand Up @@ -247,7 +221,7 @@
\newpage
\bibliography{SS3}
\bibliographystyle{JournalBiblio/cjfas}
\newpage
\newpage

\end{document}

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