derby2.tex

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\begin{document}
\vspace*{0.2in}


% Title must be 250 characters or less.
\begin{flushleft}
{\Large
\textbf\newline{Bridge between fishery dependent and fishery independent
data - Design of Fishing Derbies for use in Recreational Fisheries
Management} % Please use "sentence case" for title and headings (capitalize only the first word in a title (or heading), the first word in a subtitle (or subheading), and any proper nouns).
}
\newline
% Insert author names, affiliations and corresponding author email (do not include titles, positions, or degrees).
\\
Trevor Davies\textsuperscript{\getAff{BC
Government}}\textsuperscript{*},
Brett Van Poorten\textsuperscript{\getAff{Ministry of
Forests}, \getAff{Simon Fraser University}}\\
\bigskip
\textbf{\getAff{FLNRORD}}B.C. Ministry of Forests, Fish and Wildlife
Branch, Victoria, British Columbia, Canada\\
\textbf{\getAff{Simon Fraser University}}School of Resource and
Environmental Management, Simon Fraser University, 8888 University
Drive, Burnaby, BC, Canada\\
\bigskip
* Corresponding author: trevor.davies@gov.bc.ca\\
\end{flushleft}
% Please keep the abstract below 300 words
\section*{Abstract}
Abstract is the last thing to write - keep that with line at the
beginning of the code

% Please keep the Author Summary between 150 and 200 words
% Use first person. PLOS ONE authors please skip this step.
% Author Summary not valid for PLOS ONE submissions.
\section*{Author summary}
I don't publish in plos One so I'm not sure why this is here.

\linenumbers

% Use "Eq" instead of "Equation" for equation citations.
\emph{Text based on plos sample manuscript, see
\url{https://journals.plos.org/ploscompbiol/s/latex}}

\hypertarget{introduction}{%
\section{Introduction}\label{introduction}}

Collecting and synthesizing data that are aligned with fishery
management goals is essential for the long term sustainability of
fishery resources. Data used to manage fisheries are derived from two
principle sources: fishery-independent data (scientific surveys) and
fishery-dependent data (collected from active participants in the
fishery). The collection of fishery-independent data for the purpose of
stock assessment and management is generally preferred as it is less
prone to bias and confounding effects that can arise from individual
fisher behavior including skill and gear selection that can be difficult
to correct for. Although preferred, fishery-independent data can be
expensive to collect thus fishery-dependent data as an attractive
alternative despite its shortcomings.

Depending on the value of the fishery, the use of fishery-dependent data
can have dire consequences. Indeed, one of the causes of the worlds
greatest fishery collapse (Atlantic cod) was a result of weighing
commercial fishery catch-and-effort data in the analyses of population
trends (see my thesis for reference for this). There are however, ways
to include fishery independent data and it plays a large role in the
management of large commercial fisheries (Tuna - see Maunder GLM paper).
This is possible for large scale fisheries where catches of individual
vessels can be accounted for in the analysis but this is less practical
for relatively small scale recreational fisheries.

New technologies are allowing for the easy and remote collection of
recreational fishing data. These data are collected by mobile apps where
fishers opportunistically enter their catches and include other
information such as size, species and even location. These apps collect
individual fishing behaviour so that can be controlled in the analysis
but still suffer from gear and effort issues.

See outline

Ways to control for this

\begin{itemize}
\tightlist
\item
  Structure surveys via derbies
\item
  Model individual fisher behaviour (maybe we could use age for
  experience?)
\item
  Use derbies as a way to build catchability effectiveness of gear
  types?
\item
  Data imputation to other fisheries?
\item
  Integrate into stock assessment - combine with fishing effort
  estimates
\item
\end{itemize}

How this paper should proceed

\begin{itemize}
\tightlist
\item
  Simulation?
\item
  make a table of warts of recreational fishery data
\item
\end{itemize}

Here are two sample references: {[}1,2{]}.

\#Bridge between fishery dependent and fishery independent data

\hypertarget{structure-of-the-paper}{%
\section{Structure of the paper}\label{structure-of-the-paper}}

\hypertarget{recreational-fishing-derbies-angling-data-alone}{%
\section{Recreational fishing derbies Angling data
alone}\label{recreational-fishing-derbies-angling-data-alone}}

\begin{itemize}
\item
  truncated measure of size structure
\item
  relative abundance
\item
  Table of common fishery metrics - fishery independent - fishery
  independent
\end{itemize}

limitations of fish independent - expensive, high effort

limitations of fishery dependent - more effort

Fixed gear - choice of single or multiple lures

increased power using both methods

\hypertarget{confounding-factors}{%
\subsection{\#Confounding factors}\label{confounding-factors}}

\hypertarget{mark-recapture-monitoring}{%
\subsection{Mark recapture monitoring}\label{mark-recapture-monitoring}}

\hypertarget{equations}{%
\section{Equations}\label{equations}}

Here is an equation: \[ 
  f_{X}(x) = \left(\frac{\alpha}{\beta}\right)
  \left(\frac{x}{\beta}\right)^{\alpha-1}
  e^{-\left(\frac{x}{\beta}\right)^{\alpha}}; 
  \alpha,\beta,x > 0 .
\]

Here is another: \begin{align}
  a^2+b^2=c^2.
\end{align}

Inline equations: \(\sum_{i = 2}^\infty\{\alpha_i^\beta\}\)

\hypertarget{figures-and-tables}{%
\section{Figures and tables}\label{figures-and-tables}}

Figure \ref{fig2} is generated using an R chunk.

\begin{figure}

{\centering \includegraphics[width=0.5\linewidth]{derby2_files/figure-latex/fig2-1} 

}

\caption{\label{fig2}A meaningless scatterplot.}\label{fig:fig2}
\end{figure}

\hypertarget{tables-coming-from-r}{%
\section{Tables coming from R}\label{tables-coming-from-r}}

Tables can also be generated using R chunks, as shown in Table
\ref{tab1} for example.

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{knitr}\SpecialCharTok{::}\FunctionTok{kable}\NormalTok{(}\FunctionTok{head}\NormalTok{(mtcars)[,}\DecValTok{1}\SpecialCharTok{:}\DecValTok{4}\NormalTok{], }
    \AttributeTok{caption =} \StringTok{"}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{label\{tab1\}Caption centered above table"}
\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\begin{longtable}[]{@{}lrrrr@{}}
\caption{\label{tab1}Caption centered above table}\tabularnewline
\toprule()
& mpg & cyl & disp & hp \\
\midrule()
\endfirsthead
\toprule()
& mpg & cyl & disp & hp \\
\midrule()
\endhead
Mazda RX4 & 21.0 & 6 & 160 & 110 \\
Mazda RX4 Wag & 21.0 & 6 & 160 & 110 \\
Datsun 710 & 22.8 & 4 & 108 & 93 \\
Hornet 4 Drive & 21.4 & 6 & 258 & 110 \\
Hornet Sportabout & 18.7 & 8 & 360 & 175 \\
Valiant & 18.1 & 6 & 225 & 105 \\
\bottomrule()
\end{longtable}

\hypertarget{references}{%
\section*{References}\label{references}}
\addcontentsline{toc}{section}{References}

\hypertarget{refs}{}
\begin{CSLReferences}{0}{0}
\leavevmode\vadjust pre{\hypertarget{ref-Feynman1963118}{}}%
\CSLLeftMargin{1. }%
\CSLRightInline{Feynman RP, Vernon Jr. FL. The theory of a general
quantum system interacting with a linear dissipative system. Annals of
Physics. 1963;24: 118--173.
doi:\href{https://doi.org/10.1016/0003-4916(63)90068-X}{10.1016/0003-4916(63)90068-X}}

\leavevmode\vadjust pre{\hypertarget{ref-Dirac1953888}{}}%
\CSLLeftMargin{2. }%
\CSLRightInline{Dirac PAM. The lorentz transformation and absolute time.
Physica. 1953;19: 888--896.
doi:\href{https://doi.org/10.1016/S0031-8914(53)80099-6}{10.1016/S0031-8914(53)80099-6}}

\end{CSLReferences}

\nolinenumbers


\end{document}