Test_figures_tables.tex

\documentclass[12pt,]{article}
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% This file contains all of the LaTeX packages you may need to compile the document
% Documentation for each package can be found onlines
\usepackage{tabularx}                                             % table environment providing flexibility
\usepackage{caption}                                              % for creating captions  
\usepackage{longtable}                                            % allows tables to span multiple pages
\usepackage{rotating}                                             % allows for sideways tables
\usepackage{float}                                                % floating environments; may not need in rmarkdown
\usepackage{placeins}                                             % keeps floats from moving
\usepackage{indentfirst}                                          % indents first paragraph of a section
\usepackage{mdwtab}                                               % continued float multi-page figure
\usepackage{enumerate}                                            % create lists
\usepackage{hyperref}                                             % highlight cross references
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%\usepackage{makebox}                                             % make boxes around text
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\usepackage{enumitem}                                             % numbered lists
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\usepackage{verbatim}                                             % produces verbatim results
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\usepackage[inline]{showlabels}                                   % show table and figure labels; comment out for final
%\usepackage{draftwatermark}                                      % places Draft watermark in background; comment out for final
\usepackage{textcomp}                                             % fixes error with packages interfering
\usepackage{lscape}                                               % rotate pages - to allow for landscape longtables
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\RequirePackage[linewidth = 1]{pdfcomment}                        %pdf comments
\RequirePackage[l2tabu, orthodox]{nag}                            %checks packages related to the accessibility?
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\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
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\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi

\begin{document}

{
\setcounter{tocdepth}{4}
\tableofcontents
}
USE THIS .Rmd TO TEST R CODE CHUNKS, FIGURES AND PLOTS BEFORE INSERTING
INTO THE MAIN TEXT OR TO DEBUG

\begin{verbatim}
OFL_mod1 = mod1$derived_quants[grep('OFL',mod1$derived_quants$LABEL),]
      OFL_mod1 = OFL_mod1[c(-1,-2),2]
      
      #Turn into a dataframe and get the total
      OFL = as.data.frame(OFL_mod1)
      OFL$Year=seq(Project_firstyr+2,Project_lastyr,1)
      OFL$Year = as.factor(OFL$Year)
      OFL = OFL[,c(2,1)]
      colnames(OFL) = c('Year','OFL') 

# Create the table
      OFL.table = xtable(OFL, caption=c('Projections of potential OFL (mt) for each model, using the base model forecast.'),
                  label = 'tab:OFL_projection')}
\end{verbatim}

\begin{table}[ht]
\centering
\caption{Projections of potential OFL (mt) for each model, using the base model forecast.} 
\label{tab:OFL_projection}
\begin{tabular}{lr}
  \hline
Year & OFL \\ 
  \hline
2015 & 9.51 \\ 
  2016 & 9.57 \\ 
  2017 & 9.63 \\ 
  2018 & 9.29 \\ 
  2019 & 8.98 \\ 
  2020 & 8.69 \\ 
  2021 & 8.43 \\ 
  2022 & 8.20 \\ 
  2023 & 7.99 \\ 
  2024 & 7.80 \\ 
  2025 & 7.64 \\ 
  2026 & 7.49 \\ 
   \hline
\end{tabular}
\end{table}

\begin{table}[ht]
\centering
\caption{Summary of the biomass/abundance
                                              time series used in the stock
                                              assessment.} 
\label{tab:Index_summary}
\begin{tabular}{>{\centering}p{.4in}>{\centering}p{.3in}>{\centering}p{.3in}>{\centering}p{.3in}>{\centering}p{.6in}>{\centering}p{.5in}>{\centering}p{.2in}>{\centering}p{.8in}>{\centering}p{.3in}>{\centering}p{.5in}}
  \hline
Region & ID & Fleet & Years & Name & Fishery ind. & Filtering & Method & Rank & Endorsed \\ 
  \hline
WA & 1 & 4 & 1981-2014 & Dockside CPUE & No & trip, area, month, Stephens-MacCall & delta-GLM (bin-gamma) & 1 & SSC \\ 
  - & - & - & - & - & - & - & - & - & - \\ 
  - & - & - & - & - & - & - & - & - & - \\ 
  - & - & - & - & - & - & - & - & - & - \\ 
   \hline
\end{tabular}
\end{table}

\hypertarget{refs}{}

\end{document}