-
Notifications
You must be signed in to change notification settings - Fork 3
/
SS330_User_Manual.tex
240 lines (215 loc) · 8.46 KB
/
SS330_User_Manual.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
% Preamble =========================================================================================
%Options added to improve pdf accessibility:
\RequirePackage{pdfmanagement-testphase}
\PassOptionsToPackage{enable-debug,check-declarations}{expl3}
%\DeclareDocumentMetadata { }
\DocumentMetadata{testphase={phase-III,math}}
\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{natbib}
\usepackage{lipsum, multicol}
\usepackage[margin=1in, includefoot]{geometry}
\usepackage{graphicx} %allows for impage import
\graphicspath{{images/}}
%\usepackage[hidelinks]{hyper ref} % Allows for clickable links
\usepackage{hyper ref}
\usepackage{ragged2e}
\usepackage{enumerate}
\usepackage{multirow}
\usepackage{booktabs}
\usepackage[T1]{fontenc}
\usepackage{lmodern}
\usepackage[none]{hyphenat}
\usepackage{array}
\usepackage{lscape}
\usepackage{pdflscape}
\usepackage{longtable}
\usepackage[utf8]{inputenc}
%\usepackage[english]{babel}
\usepackage[table]{xcolor}
\usepackage{colortbl}
\usepackage{hhline}
\usepackage{dcolumn}
\usepackage{tocloft}
\setlength{\cftsubsecnumwidth}{3em}
\setlength{\cftsubsubsecnumwidth}{4em}
\usepackage{hypcap}
\usepackage{amsmath}
\usepackage{hyperref}
%\usepackage[pdfborderstyle={/S/U/W 1}]{hyperref}
\usepackage{float}
\usepackage{fancyhdr}
\usepackage[parfill]{parskip}
\usepackage{roboto} % sans serif font for headers
\usepackage{crimson} % serif font
\usepackage[T1]{fontenc} % controls font enconding
\usepackage[nottoc,numbib]{tocbibind}
\usepackage[all]{nowidow} % Widow Control
% For tagging the pdf: https://github.com/jgm/pandoc/issues/5409#issuecomment-770417614
\ifluatex
% \usepackage[luamode]{tagpdf}
\tagpdfsetup{
activate-all=true,
interwordspace=true
}
\fi
% End tagging the pdf
% Set widow and club penalties
\widowpenalty=100000
\clubpenalty=100000
%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}
\parskip = 12pt % space between paragraphs
\setlength{\extrarowheight}{1.5pt}
\setlength{\arraycolsep}{1.5pt}
%Control over how latex wraps text when justified
\tolerance=1
\emergencystretch=\maxdimen
\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?
unicode = false, % non-Latin characters in Acrobat's bookmarks
pdftoolbar = true, % show Acrobat's toolbar?
pdfmenubar = true, % show Acrobat's menu?
pdffitwindow = false, % window fit to page when opened
pdfstartview = {FitH}, % fits the width of the page to the window
pdfnewwindow = false, % links in new window
colorlinks = false, % false: boxed links; true: colored links
linkbordercolor = black, % the color of the link border color (colorlink =false)
linkcolor = blue, % color of internal links (change box color with linkbordercolor)
citecolor = blue, % color of links to bibliography
filecolor = blue, % color of file links
urlcolor = blue, % color of external links
pdfborderstyle = {/S/U/W 1} % border style will be underline of width 1pt
}
\newcommand\Tstrut{\rule{0pt}{3.5ex}} % "top" strut
\newcommand\Bstrut{\rule[-1.7ex]{0pt}{0pt}} % "bottom" strut
\newcommand{\TBstrut}{\Tstrut\Bstrut} % top&bottom struts
\newcolumntype{L}{>{\centering\arraybackslash}m{3in}}
\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
\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}
\xpretocmd{\maketitle}{\TitlePageFont}{}{}
\title{\textcolor[cmyk]{1.00,0.83,0.41,0.36}{Stock Synthesis User Manual\\ Version 3.30.23.1}}
\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}
\date{December 05, 2024}
% ==== Glossary ========================================================
\usepackage[xindy,acronym]{glossaries}
\setacronymstyle{long-short}
\glsdisablehyper
\makenoidxglossaries
\loadglsentries{ss3_glossaries.tex}
\begin{document}
% ====== Title Page ===================================================
\maketitle
\begin{figure}[ht]
\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
% ====== Table of Contents ===================================================
\glsaddall
\pagenumbering{roman}
\tableofcontents
\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
\input{5converting}
% ======== Section 6: Starter File
\input{6starter}
% ======== Section 7: Forecast File
\input{7forecast}
% ======== Section 8: Data File
\input{8data}
% ======== Section 9: Control File
\input{9control}
% ======== Section 10: Optional Inputs
\input{10optional_inputs}
% ======== Section 11: Likelihoods
\input{11likelihoods}
%========= Section 12: Running SS
\input{12runningSS3}
% ======== Section 13: Output Files
\input{13output}
%========= Section 14: R4SS
\input{14r4ss}
%========= Section 15: Special Set-ups
\input{15special}
%========= Section 16: Essays
\input{16essays}
%========= Glossary
\hypertarget{Glossary}{}
\addcontentsline{toc}{section}{Glossary}
\printnoidxglossary[type=main,title=\protect\hyperlink{Glossary}{Glossary},nonumberlist]
\hypertarget{Acronyms}{}
\addcontentsline{toc}{section}{List of Acronyms}
\printnoidxglossary[type=\acronymtype,title=\protect\hyperlink{Acronyms}{List of Acronyms},nonumberlist]
%========= Reference Section
\newpage
\bibliography{SS3}
\bibliographystyle{JournalBiblio/cjfas}
\newpage
\end{document}