text:
%%
%% This is file `elsarticle.cls',
%% generated with the docstrip utility.
%%
%% The original source files were:
%%
%% elsarticle.dtx  (with options: `class')
%%
%% Copyright 2007, 2008 Elsevier Ltd.
%%
%% This file is part of the 'Elsarticle Bundle'.
%% -------------------------------------------
%%
%% It may be distributed under the conditions of the LaTeX Project Public
%% License, either version 1.2 of this license or (at your option) any
%% later version.  The latest version of this license is in
%%    http://www.latex-project.org/lppl.txt
%% and version 1.2 or later is part of all distributions of LaTeX
%% version 1999/12/01 or later.
%%
%% The list of all files belonging to the 'Elsarticle Bundle' is
%% given in the file `manifest.txt'.
%%
%% $Id: elsarticle.cls,v 1.18 2008-08-28 06:03:47 cvr Exp $
%%
 \def\RCSfile{elsarticle}%
 \def\RCSversion{1.0.1}%
 \def\RCSdate{2008/05/22}%
 \def\@shortjnl{\relax}
 \def\@journal{Elsevier Science} \def\@company{Elsevier Science}
 \def\@issn{000-0000}
 \def\@shortjid{elsarticle}
\NeedsTeXFormat{LaTeX2e}[1995/12/01]
\ProvidesClass{\@shortjid}[\RCSdate, \RCSversion: \@journal]
\def\ABD{\AtBeginDocument}
\newif\ifpreprint \preprintfalse
\newif\iflongmktitle \longmktitlefalse

\def\@blstr{1}
\newdimen\@bls
\@bls=\baselineskip

\def\@finalWarning{%
  *****************************************************\MessageBreak
   This document is typeset in the CRC style which\MessageBreak
   is not suitable for submission.\MessageBreak
   \MessageBreak
   Please typeset again using 'preprint' option\MessageBreak
   for creating PDF suitable for submission.\MessageBreak
  ******************************************************\MessageBreak
}

\DeclareOption{preprint}{\global\preprinttrue
  \gdef\@blstr{1}\xdef\jtype{0}%
   \AtBeginDocument{\@twosidefalse\@mparswitchfalse}}
\DeclareOption{final}{\gdef\@blstr{1}\global\preprintfalse}
\DeclareOption{review}{\global\preprinttrue\gdef\@blstr{1.5}}
\DeclareOption{authoryear}{\xdef\@biboptions{authoryear}}
\DeclareOption{number}{\xdef\@biboptions{square,numbers}}
\DeclareOption{numbers}{\xdef\@biboptions{square,numbers}}
\DeclareOption{longtitle}{\global\longmktitletrue}
\DeclareOption{5p}{\xdef\jtype{5}\global\preprintfalse
  \ExecuteOptions{twocolumn}}
  \def\jtype{0}
\DeclareOption{3p}{\xdef\jtype{3}\global\preprintfalse}
\DeclareOption{1p}{\xdef\jtype{1}\global\preprintfalse
  \AtBeginDocument{\@twocolumnfalse}}
\DeclareOption{times}{\IfFileExists{txfonts.sty}%
  {\AtEndOfClass{\RequirePackage{txfonts}%
  \gdef\ttdefault{cmtt}%
   \let\iint\relax
  \let\iiint\relax
  \let\iiiint\relax
  \let\idotsint\relax
  \let\openbox\relax}}{\RequirePackage{times}}}
\ExecuteOptions{a4paper,10pt,oneside,onecolumn,number,preprint}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
\ProcessOptions
\LoadClass{article}
\RequirePackage{graphicx}
\let\comma\@empty
\let\tnotesep\@empty
\def\title#1{\gdef\@title{#1}}
\let\@title\@empty

\def\elsLabel#1{\@bsphack\protected@write\@auxout{}%
         {\string\Newlabel{#1}{\@currentlabel}}\@esphack}
\def\Newlabel#1#2{\expandafter\xdef\csname X@#1\endcsname{#2}}

\def\Ref#1{\@ifundefined{X@#1}{0}{\csname X@#1\endcsname}%
}

\def\tnotemark[#1]{\textsuperscript{\@for\@@tmark:=#1\do{%
      \edef\tnotenum{\@ifundefined{X@\@@tmark}{1}{\Ref{\@@tmark}}}%
      \ifcase\tnotenum\or\ding{73}\or,\ding{73}\ding{73}\fi}}%
}
\let\@tnotemark\@empty

\let\@tnotes\@empty
\RequirePackage{pifont}
\newcounter{tnote}
\def\tnotetext[#1]#2{\g@addto@macro\@tnotes{%
  \refstepcounter{tnote}\elsLabel{#1}%
   \def\thefootnote{\ifcase\c@tnote\or\ding{73}\or\ding{73}\ding{73}\fi}%
    \footnotetext{#2}}}

\newcounter{fnote}
\def\fnmark[#1]{\let\comma\@empty
    \def\@fnmark{\@for\@@fnmark:=#1\do{%
    \edef\fnotenum{\@ifundefined{X@\@@fnmark}{1}{\Ref{\@@fnmark}}}%
  \unskip\comma\fnotenum\let\comma,}}%
}

\let\@fnotes\@empty\let\@fnmark\@empty
\def\fntext[#1]#2{\g@addto@macro\@fnotes{%
     \refstepcounter{fnote}\elsLabel{#1}%
   \def\thefootnote{\thefnote}%
   \global\setcounter{footnote}{\thefnote}%
   \footnotetext{#2}}}

\def\cormark[#1]{\edef\cnotenum{\Ref{#1}}\unskip%
   \textsuperscript{\sep\ifcase\cnotenum\or
       $\ast$\or$\ast\ast$\fi\hspace{-1pt}}\let\sep=,}

\let\@cormark\@empty
\let\@cornotes\@empty
\newcounter{cnote}
\def\cortext[#1]#2{\g@addto@macro\@cornotes{%
    \refstepcounter{cnote}\elsLabel{#1}%
    \def\thefootnote{\ifcase\thecnote\or$\ast$\or
    $\ast\ast$\fi}%
    \footnotetext{#2}}}

\def\corref#1{\cormark[#1]}
\def\fnref#1{\fnmark[#1]}
\def\tnoteref#1{\tnotemark[#1]}

\def\resetTitleCounters{\c@cnote=0
   \c@fnote=0 \c@tnote=0 \c@footnote=0}

\let\eadsep\@empty
\let\@elseads\@empty
\let\@elsuads\@empty
\let\@cormark\@empty
\def\ead{\@ifnextchar[{\@uad}{\@ead}}
\gdef\@ead#1{\bgroup\def\_{\string\_}\def\{{\string\{}%
   \def\}{\string\}}%
   \edef\tmp{\the\@eadauthor}
   \immediate\write\@auxout{\string\emailauthor
     {#1}{\expandafter\strip@prefix\meaning\tmp}}%
  \egroup
}
\newcounter{ead}
\gdef\emailauthor#1#2{\stepcounter{ead}%
     \g@addto@macro\@elseads{\raggedright%
      \let\corref\@gobble
      \eadsep\texttt{#1} (#2)\def\eadsep{\unskip,\space}}%
}
\gdef\@uad[#1]#2{\bgroup
   \edef\tmp{\the\@eadauthor}
   \immediate\write\@auxout{\string\urlauthor
     {#2}{\expandafter\strip@prefix\meaning\tmp}}%
  \egroup
}
\def\urlauthor#1#2{\g@addto@macro\@elsuads{\let\corref\@gobble%
     \raggedright\eadsep\texttt{#1}\space(#2)%
     \def\eadsep{\unskip,\space}}%
}

\def\elsauthors{}
\def\pprinttitle{}
\let\authorsep\@empty
\let\sep\@empty
\newcounter{author}
\def\author{\@ifnextchar[{\@@author}{\@author}}

\newtoks\@eadauthor
\def\@@author[#1]#2{\g@addto@macro\elsauthors{%
    \def\baselinestretch{1}%
    \authorsep#2\unskip\textsuperscript{%#1%
      \@for\@@affmark:=#1\do{%
       \edef\affnum{\@ifundefined{X@\@@affmark}{1}{\Ref{\@@affmark}}}%
     \unskip\sep\affnum\let\sep=,}%
      \ifx\@fnmark\@empty\else\unskip\sep\@fnmark\let\sep=,\fi}%
    \def\authorsep{\unskip,\space}%
    \global\let\sep\@empty
    \global\let\@fnmark\@empty}%
    \@eadauthor={#2}
}

\def\@author#1{\g@addto@macro\elsauthors{\normalsize%
    \def\baselinestretch{1}%
    \upshape\authorsep#1\unskip\textsuperscript{%
      \ifx\@fnmark\@empty\else\unskip\sep\@fnmark\let\sep=,\fi}%
    \def\authorsep{\unskip,\space}%
    \global\let\@fnmark\@empty
    \global\let\sep\@empty}%
    \@eadauthor={#1}
}

\def\elsaddress{}
\def\addsep{\par\vskip6pt}
\def\address{\@ifnextchar[{\@@address}{\@address}}

\newcounter{affn}
\renewcommand\theaffn{\alph{affn}}

\long\def\@@address[#1]#2{\g@addto@macro\elsaddress{%
    \def\baselinestretch{1}%
     \refstepcounter{affn}\elsLabel{#1}%
    \textsuperscript{\theaffn}#2\par}}

\long\def\@address#1{\g@addto@macro\elsauthors{%
    \def\baselinestretch{1}%
    \addsep\footnotesize\itshape#1\def\addsep{\par\vskip6pt}%
    \def\authorsep{\par\vskip8pt}}}

\newbox\absbox
\renewenvironment{abstract}{\global\setbox\absbox=\vbox\bgroup
  \hsize=\textwidth\def\baselinestretch{1}%
  \noindent\unskip\textbf{Abstract}
 \par\medskip\noindent\unskip\ignorespaces}
 {\egroup}

\newbox\keybox
\def\keyword{%
  \def\sep{\unskip, }%
 \def\MSC{\@ifnextchar[{\@MSC}{\@MSC[2000]}}
  \def\@MSC[##1]{\par\leavevmode\hbox {\it ##1~MSC:\space}}%
  \def\PACS{\par\leavevmode\hbox {\it PACS:\space}}%
  \def\JEL{\par\leavevmode\hbox {\it JEL:\space}}%
  \global\setbox\keybox=\vbox\bgroup\hsize=\textwidth
  \normalsize\normalfont\def\baselinestretch{1}
  \parskip\z@
  \noindent\textit{Key words: }
  \raggedright                         % Keywords are not justified.
  \ignorespaces}
\def\endkeyword{\par \egroup}

\newdimen\Columnwidth
\Columnwidth=\columnwidth

\def\printFirstPageNotes{%
  \iflongmktitle
   \let\columnwidth=\textwidth\fi
  \ifx\@tnotes\@empty\else\@tnotes\fi
  \ifx\@cornotes\@empty\else\@cornotes\fi
  \ifx\@elseads\@empty\relax\else
   \let\thefootnote\relax
   \footnotetext{\ifnum\theead=1\relax
      \textit{Email address:\space}\else
      \textit{Email addresses:\space}\fi
     \@elseads}\fi
  \ifx\@elsuads\@empty\relax\else
   \let\thefootnote\relax
   \footnotetext{\textit{URL:\space}%
     \@elsuads}\fi
  \ifx\@fnotes\@empty\else\@fnotes\fi
  \iflongmktitle\if@twocolumn
   \let\columnwidth=\Columnwidth\fi\fi
}

\long\def\pprintMaketitle{\clearpage
  \iflongmktitle\if@twocolumn\let\columnwidth=\textwidth\fi\fi
  \resetTitleCounters
  \def\baselinestretch{1}%
  \printFirstPageNotes
  \begin{center}%
 \thispagestyle{pprintTitle}%
   \def\baselinestretch{1}%
    \Large\@title\par\vskip18pt
    \normalsize\elsauthors\par\vskip10pt
    \footnotesize\itshape\elsaddress\par\vskip36pt
    %\hrule\vskip12pt
    \ifvoid\absbox\else\unvbox\absbox\par\vskip10pt\fi
    \ifvoid\keybox\else\unvbox\keybox\par\vskip10pt\fi
    %\hrule\vskip12pt
    \end{center}%
  \gdef\thefootnote{\arabic{footnote}}%
  }

\def\printWarning{%
     \mbox{}\par\vfill\par\bgroup
     \fboxsep12pt\fboxrule1pt
     \hspace*{.18\textwidth}
     \fcolorbox{gray50}{gray10}{\box\warnbox}
     \egroup\par\vfill\thispagestyle{empty}
     \setcounter{page}{0}
     \clearpage}

\long\def\finalMaketitle{%
  \resetTitleCounters
  \def\baselinestretch{1}%
   \MaketitleBox
   \thispagestyle{pprintTitle}%
  \gdef\thefootnote{\arabic{footnote}}%
  }

\long\def\MaketitleBox{%
  \resetTitleCounters
  \def\baselinestretch{1}%
  \begin{center}%
   \def\baselinestretch{1}%
    \Large\@title\par\vskip18pt
    \normalsize\elsauthors\par\vskip10pt
    \footnotesize\itshape\elsaddress\par\vskip36pt
    %\hrule\vskip12pt
    \ifvoid\absbox\else\unvbox\absbox\par\vskip10pt\fi
    \ifvoid\keybox\else\unvbox\keybox\par\vskip10pt\fi
    %\hrule\vskip12pt
    \end{center}%
  }

\def\FNtext#1{\par\bgroup\footnotesize#1\egroup}
\newdimen\space@left
\def\alarm#1{\typeout{******************************}%
             \typeout{#1}%
             \typeout{******************************}%
}
\long\def\getSpaceLeft{%\global\@twocolumnfalse%
   \global\setbox0=\vbox{\hsize=\textwidth\MaketitleBox}%
   \global\setbox1=\vbox{\hsize=\textwidth
    \let\footnotetext\FNtext
    \printFirstPageNotes}%
    \xdef\noteheight{\the\ht1}%
    \xdef\titleheight{\the\ht0}%
    \@tempdima=\vsize
    \advance\@tempdima-\noteheight
    \advance\@tempdima-1\baselineskip
}

  \skip\footins=24pt

\newbox\els@boxa
\newbox\els@boxb

\ifpreprint
  \def\maketitle{\pprintMaketitle}
  \else
   \ifnum\jtype=1
    \def\maketitle{%
      \iflongmktitle\getSpaceLeft
       \global\setbox\els@boxa=\vsplit0 to \@tempdima
       \box\els@boxa\par\resetTitleCounters
       \thispagestyle{pprintTitle}%
       \printFirstPageNotes
       \box0%
      \else
       \finalMaketitle\printFirstPageNotes
      \fi
    \gdef\thefootnote{\arabic{footnote}}}%
  \else
 \ifnum\jtype=5
    \def\maketitle{%
      \iflongmktitle\getSpaceLeft
       \global\setbox\els@boxa=\vsplit0 to \@tempdima
       \box\els@boxa\par\resetTitleCounters
       \thispagestyle{pprintTitle}%
       \printFirstPageNotes
       \twocolumn[\box0]%\printFirstPageNotes
      \else
       \twocolumn[\finalMaketitle]\printFirstPageNotes
     \fi
     \gdef\thefootnote{\arabic{footnote}}}
  \else
  \if@twocolumn
    \def\maketitle{%
      \iflongmktitle\getSpaceLeft
       \global\setbox\els@boxa=\vsplit0 to \@tempdima
       \box\els@boxa\par\resetTitleCounters
       \thispagestyle{pprintTitle}%
       \printFirstPageNotes
       \twocolumn[\box0]%
      \else
       \twocolumn[\finalMaketitle]\printFirstPageNotes
      \fi
     \gdef\thefootnote{\arabic{footnote}}}%
   \else
    \def\maketitle{%
      \iflongmktitle\getSpaceLeft
       \global\setbox\els@boxa=\vsplit0 to \@tempdima
       \box\els@boxa\par\resetTitleCounters
       \thispagestyle{pprintTitle}%
       \printFirstPageNotes
       \box0%
     \else
       \finalMaketitle\printFirstPageNotes
      \fi
    \gdef\thefootnote{\arabic{footnote}}}%
   \fi
  \fi
 \fi
\fi
\def\ps@pprintTitle{%
     \let\@oddhead\@empty
     \let\@evenhead\@empty
     \def\@oddfoot{\footnotesize\itshape
       Preprint submitted to \ifx\@journal\@empty Elsevier
       \else\@journal\fi\hfill\today}%
     \let\@evenfoot\@oddfoot}

\def\@seccntDot{.}
\def\@seccntformat#1{\csname the#1\endcsname\@seccntDot\hskip 0.5em}

\renewcommand\section{\@startsection {section}{1}{\z@}%
           {18\p@ \@plus 6\p@ \@minus 3\p@}%
           {9\p@ \@plus 6\p@ \@minus 3\p@}%
           {\normalsize\bfseries\boldmath}}
\renewcommand\subsection{\@startsection{subsection}{2}{\z@}%
           {12\p@ \@plus 6\p@ \@minus 3\p@}%
           {3\p@ \@plus 6\p@ \@minus 3\p@}%
           {\normalfont\normalsize\itshape}}
\renewcommand\subsubsection{\@startsection{subsubsection}{3}{\z@}%
           {12\p@ \@plus 6\p@ \@minus 3\p@}%
           {\p@}%
           {\normalfont\normalsize\itshape}}

\def\paragraph{\secdef{\els@aparagraph}{\els@bparagraph}}
\def\els@aparagraph[#1]#2{\elsparagraph[#1]{#2.}}
\def\els@bparagraph#1{\elsparagraph*{#1.}}

\newcommand\elsparagraph{\@startsection{paragraph}{4}{0\z@}%
           {10\p@ \@plus 6\p@ \@minus 3\p@}%
           {-6\p@}%
           {\normalfont\itshape}}
\newdimen\leftMargin
\leftMargin=2em
\newtoks\@enLab  %\newtoks\@enfont
\def\@enQmark{?}
\def\@enLabel#1#2{%
  \edef\@enThe{\noexpand#1{\@enumctr}}%
  \@enLab\expandafter{\the\@enLab\csname the\@enumctr\endcsname}%
  \@enloop}
\def\@enSpace{\afterassignment\@enSp@ce\let\@tempa= }
\def\@enSp@ce{\@enLab\expandafter{\the\@enLab\space}\@enloop}
\def\@enGroup#1{\@enLab\expandafter{\the\@enLab{#1}}\@enloop}
\def\@enOther#1{\@enLab\expandafter{\the\@enLab#1}\@enloop}
\def\@enloop{\futurelet\@entemp\@enloop@}
\def\@enloop@{%
  \ifx A\@entemp         \def\@tempa{\@enLabel\Alph  }\else
  \ifx a\@entemp         \def\@tempa{\@enLabel\alph  }\else
  \ifx i\@entemp         \def\@tempa{\@enLabel\roman }\else
  \ifx I\@entemp         \def\@tempa{\@enLabel\Roman }\else
  \ifx 1\@entemp         \def\@tempa{\@enLabel\arabic}\else
  \ifx \@sptoken\@entemp \let\@tempa\@enSpace         \else
  \ifx \bgroup\@entemp   \let\@tempa\@enGroup         \else
  \ifx \@enum@\@entemp   \let\@tempa\@gobble          \else
                         \let\@tempa\@enOther
             \fi\fi\fi\fi\fi\fi\fi\fi
  \@tempa}
\newlength{\@sep} \newlength{\@@sep}
\setlength{\@sep}{.5\baselineskip plus.2\baselineskip
            minus.2\baselineskip}
\setlength{\@@sep}{.1\baselineskip plus.01\baselineskip
            minus.05\baselineskip}
\providecommand{\sfbc}{\rmfamily\upshape}
\providecommand{\sfn}{\rmfamily\upshape}
\def\@enfont{\ifnum \@enumdepth >1\let\@nxt\sfn \else\let\@nxt\sfbc \fi\@nxt}
\def\enumerate{%
   \ifnum \@enumdepth >3 \@toodeep\else
      \advance\@enumdepth \@ne
      \edef\@enumctr{enum\romannumeral\the\@enumdepth}\fi
   \@ifnextchar[{\@@enum@}{\@enum@}}
\def\@@enum@[#1]{%
  \@enLab{}\let\@enThe\@enQmark
  \@enloop#1\@enum@
  \ifx\@enThe\@enQmark\@warning{The counter will not be printed.%
   ^^J\space\@spaces\@spaces\@spaces The label is: \the\@enLab}\fi
  \expandafter\edef\csname label\@enumctr\endcsname{\the\@enLab}%
  \expandafter\let\csname the\@enumctr\endcsname\@enThe
  \csname c@\@enumctr\endcsname7
  \expandafter\settowidth
            \csname leftmargin\romannumeral\@enumdepth\endcsname
            {\the\@enLab\hskip\labelsep}%
  \@enum@}
\def\@enum@{\list{{\@enfont\csname label\@enumctr\endcsname}}%
           {\usecounter{\@enumctr}\def\makelabel##1{\hss\llap{##1}}%
     \ifnum \@enumdepth>1\setlength{\topsep}{\@@sep}\else
           \setlength{\topsep}{\@sep}\fi
     \ifnum \@enumdepth>1\setlength{\itemsep}{0pt plus1pt minus1pt}%
      \else \setlength{\itemsep}{\@@sep}\fi
     %\setlength\leftmargin{\leftMargin}%%%{1.8em}
     \setlength{\parsep}{0pt plus1pt minus1pt}%
     \setlength{\parskip}{0pt plus1pt minus1pt}
                   }}

\def\endenumerate{\par\ifnum \@enumdepth >1\addvspace{\@@sep}\else
           \addvspace{\@sep}\fi \endlist}

\def\sitem{\@noitemargtrue\@item[\@itemlabel *]}

\def\itemize{\@ifnextchar[{\@Itemize}{\@Itemize[]}}

\def\@Itemize[#1]{\def\next{#1}%
  \ifnum \@itemdepth >\thr@@\@toodeep\else
   \advance\@itemdepth\@ne
  \ifx\next\@empty\else\expandafter\def\csname
   labelitem\romannumeral\the\@itemdepth\endcsname{#1}\fi%
  \edef\@itemitem{labelitem\romannumeral\the\@itemdepth}%
  \expandafter\list\csname\@itemitem\endcsname
  {\def\makelabel##1{\hss\llap{##1}}}%
 \fi}
\def\newdefinition#1{%
  \@ifnextchar[{\@odfn{#1}}{\@ndfn{#1}}}%]
\def\@ndfn#1#2{%
  \@ifnextchar[{\@xndfn{#1}{#2}}{\@yndfn{#1}{#2}}}
\def\@xndfn#1#2[#3]{%
  \expandafter\@ifdefinable\csname #1\endcsname
    {\@definecounter{#1}\@newctr{#1}[#3]%
     \expandafter\xdef\csname the#1\endcsname{%
       \expandafter\noexpand\csname the#3\endcsname \@dfncountersep
          \@dfncounter{#1}}%
     \global\@namedef{#1}{\@dfn{#1}{#2}}%
     \global\@namedef{end#1}{\@enddefinition}}}
\def\@yndfn#1#2{%
  \expandafter\@ifdefinable\csname #1\endcsname
    {\@definecounter{#1}%
     \expandafter\xdef\csname the#1\endcsname{\@dfncounter{#1}}%
     \global\@namedef{#1}{\@dfn{#1}{#2}}%
     \global\@namedef{end#1}{\@enddefinition}}}
\def\@odfn#1[#2]#3{%
  \@ifundefined{c@#2}{\@nocounterr{#2}}%
    {\expandafter\@ifdefinable\csname #1\endcsname
    {\global\@namedef{the#1}{\@nameuse{the#2}}
  \global\@namedef{#1}{\@dfn{#2}{#3}}%
  \global\@namedef{end#1}{\@enddefinition}}}}
\def\@dfn#1#2{%
  \refstepcounter{#1}%
  \@ifnextchar[{\@ydfn{#1}{#2}}{\@xdfn{#1}{#2}}}
\def\@xdfn#1#2{%
  \@begindefinition{#2}{\csname the#1\endcsname}\ignorespaces}
\def\@ydfn#1#2[#3]{%
  \@opargbegindefinition{#2}{\csname the#1\endcsname}{#3}\ignorespaces}
\def\@dfncounter#1{\noexpand\arabic{#1}}
\def\@dfncountersep{.}
\def\@begindefinition#1#2{\trivlist
   \item[\hskip\labelsep{\bfseries #1\ #2.}]\upshape}
\def\@opargbegindefinition#1#2#3{\trivlist
      \item[\hskip\labelsep{\bfseries #1\ #2\ (#3).}]\upshape}
\def\@enddefinition{\endtrivlist}

\def\@begintheorem#1#2{\trivlist
  \let\baselinestretch\@blstr
   \item[\hskip \labelsep{\bfseries #1\ #2.}]\itshape}
\def\@opargbegintheorem#1#2#3{\trivlist
  \let\baselinestretch\@blstr
      \item[\hskip \labelsep{\bfseries #1\ #2\ (#3).}]\itshape}

\def\newproof#1{%
  \@ifnextchar[{\@oprf{#1}}{\@nprf{#1}}}
\def\@nprf#1#2{%
  \@ifnextchar[{\@xnprf{#1}{#2}}{\@ynprf{#1}{#2}}}
\def\@xnprf#1#2[#3]{%
  \expandafter\@ifdefinable\csname #1\endcsname
    {\@definecounter{#1}\@newctr{#1}[#3]%
     \expandafter\xdef\csname the#1\endcsname{%
       \expandafter\noexpand\csname the#3\endcsname \@prfcountersep
          \@prfcounter{#1}}%
     \global\@namedef{#1}{\@prf{#1}{#2}}%
     \global\@namedef{end#1}{\@endproof}}}
\def\@ynprf#1#2{%
  \expandafter\@ifdefinable\csname #1\endcsname
    {\@definecounter{#1}%
     \expandafter\xdef\csname the#1\endcsname{\@prfcounter{#1}}%
     \global\@namedef{#1}{\@prf{#1}{#2}}%
     \global\@namedef{end#1}{\@endproof}}}
\def\@oprf#1[#2]#3{%
  \@ifundefined{c@#2}{\@nocounterr{#2}}%
    {\expandafter\@ifdefinable\csname #1\endcsname
    {\global\@namedef{the#1}{\@nameuse{the#2}}%
  \global\@namedef{#1}{\@prf{#2}{#3}}%
  \global\@namedef{end#1}{\@endproof}}}}
\def\@prf#1#2{%
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text:
@book{Mangel2006,
  author = {Mangel, Marc},
  file = {:home/cboettig/Documents/Mendeley/Unknown/2006/Mangel - 2006 - Unknown.pdf:pdf},
  isbn = {9780521830454},
  mendeley-groups = {Math Methods and Model Inference},
  publisher = {Cambridge University Press},
  title = {{The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology}},
  year = {2006},
  doi = {10.1017/cbo9780511819872}
}

@Online{Boettiger_2014,
    doi = {10.5281/zenodo.12669},
    url = {http://dx.doi.org/10.5281/zenodo.12669},
    author = {Boettiger, Carl and Mangel, Marc and Munch, Steve},
    publisher = {ZENODO},
    title = {nonparametric-bayes v0.1.0},
    year = {2014},
}

@book{Gardiner2009,
  author = {Gardiner, Crispin},
  isbn = {3540707123},
  mendeley-groups = {Math Methods and Model Inference},
  pages = {447},
  publisher = {Springer},
  title = {{Stochastic Methods: A Handbook for the Natural and Social Sciences (Springer Series in Synergetics)}},
  url = {http://www.amazon.com/Stochastic-Methods-Handbook-Sciences-Synergetics/dp/3540707123},
  year = {2009}
}

@article{Mangel2014,
author = {Mangel, Marc},
journal = {Bulletin of Mathematical Biology},
title = {{Stochastic Dynamic Programming Illuminates the Link Between Environment}},
volume = {in press},
year = {2014}
}
@book{Clark2000,
address = {Oxford},
author = {Clark, Colin W and Mangel, Marc},
mendeley-groups = {Math Methods and Model Inference},
publisher = {Oxford University Press},
title = {{Dynamic state variable models in ecology}},
year = {2000}
}

@incollection{Mangel2001,
address = {Washington DC},
author = {Mangel, Marc and Fiksen, 0yvind and Giske, Jarl},
booktitle = {Modeling in natural resource management, development, interpretation and application.},
editor = {Shenk, T. M. and Franklin, A. B.},
pages = {57--71},
publisher = {Island Press},
title = {{Theoretical and statistical models in natural resource management and research}},
year = {2001}
}
@book{Clark2009,
address = {New York},
author = {Clark, Colin W.},
publisher = {Wiley},
title = {{Mathematical Bioeconomics}},
year = {2009}
}
@book{Clark1976,
address = {New York},
author = {Clark, Colin W.},
publisher = {Wiley},
title = {{Mathematical Bioeconomics}},
year = {1976}
}

@article{Walters1978,
author = {Walters, Carl J and Hilborn, Ray},
doi = {10.1146/annurev.es.09.110178.001105},
file = {:home/cboettig/Documents/Mendeley/Annual Review of Ecology and Systematics/1978/Walters, Hilborn - 1978 - Annual Review of Ecology and Systematics.pdf:pdf},
issn = {0066-4162},
journal = {Annual Review of Ecology and Systematics},
keywords = {parameter uncertainty},
mendeley-groups = {Theoretical Ecology/PDG Control},
mendeley-tags = {parameter uncertainty},
month = nov,
number = {1},
pages = {157--188},
title = {{Ecological Optimization and Adaptive Management}},
url = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.es.09.110178.001105},
volume = {9},
year = {1978}
}

@article{Scheffer2009,
abstract = {Complex dynamical systems, ranging from ecosystems to financial markets and the climate, can have tipping points at which a sudden shift to a contrasting dynamical regime may occur. Although predicting such critical points before they are reached is extremely difficult, work in different scientific fields is now suggesting the existence of generic early-warning signals that may indicate for a wide class of systems if a critical threshold is approaching.},
author = {Scheffer, Marten and Bascompte, Jordi and Brock, William A and Brovkin, Victor and Carpenter, Stephen R and Dakos, Vasilis and Held, Hermann and van Nes, Egbert H and Rietkerk, Max and Sugihara, George},
doi = {10.1038/nature08227},
file = {:home/cboettig/Documents/Mendeley/Nature/2009/Scheffer et al. - 2009 - Nature.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Animals,Asthma,Asthma: physiopathology,Biological,Climate,Economic,Ecosystem,Eutrophication,Extinction,Humans,Models,Seizures,Seizures: physiopathology,Stochastic Processes,critical transition,ecology,regime shifts,stochastic,tipping point,warning signals},
mendeley-groups = {Theoretical Ecology/Early Warning Signs,Theoretical Ecology},
mendeley-tags = {critical transition,ecology,regime shifts,stochastic,tipping point,warning signals},
number = {7260},
pages = {53--9},
pmid = {19727193},
publisher = {Nature Publishing Group},
title = {{Early-warning signals for critical transitions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19727193},
volume = {461},
year = {2009}
}

@book{Gelman2003,
  author = {Gelman, Andrew and Carlin, John B. and Stern, Hal S. and Rubin, Donald B.},
  edition = {2nd},
  mendeley-groups = {Math Methods and Model Inference},
  publisher = {Chapman and Hall/CRC},
  title = {{Bayesian Data Analysis}},
  year = {2003}
}

@article{Sigourney2012,
author = {Sigourney, Douglas B. and Munch, Stephan B. and Letcher, Benjamin H.},
doi = {10.1016/j.ecolmodel.2012.08.009},
file = {:home/cboettig/Documents/Mendeley/Ecological Modelling/2012/Sigourney, Munch, Letcher - 2012 - Ecological Modelling.pdf:pdf},
issn = {03043800},
journal = {Ecological Modelling},
month = dec,
pages = {125--134},
publisher = {Elsevier B.V.},
title = {{Combining a Bayesian nonparametric method with a hierarchical framework to estimate individual and temporal variation in growth}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0304380012004206},
volume = {247},
year = {2012}
}

@book{Lehmann1975,
address = {San Francisco},
author = {Lehmann, E. L.},
booktitle = {ZAMM - Zeitschrift f\"{u}r Angewandte Mathematik und Mechanik},
issn = {00442267},
mendeley-groups = {Math Methods and Model Inference},
number = {9},
publisher = {Holden-Day, Inc},
title = {{Nonparametrics: Statistical Methods Based on Ranks}},
volume = {57},
year = {1975}
}

@article{Thorson2014,
abstract = {State-space estimation methods are increasingly used in ecology to estimate productivity and abundance of natural populations while accounting for variability in both population dynamics and measurement processes. However, functional forms for population dynamics and density dependence often will not match the true biological process, and this may degrade the performance of state-space methods. We therefore developed a Bayesian semiparametric state-space model, which uses a Gaussian process (GP) to approximate the population growth function. This offers two benefits for population modeling. First, it allows data to update a specified "prior" on the population growth function, while reverting to this prior when data are uninformative. Second, it allows variability in population dynamics to be decomposed into random errors around the population growth function ("process error") and errors due to the mismatch between the specified prior and estimated growth function ("model error"). We used simulation modeling to illustrate the utility of GP methods in state-space population dynamics models. Results confirmed that the GP model performs similarly to a conventional state-space model when either (1) the prior matches the true process or (2) data are relatively uninformative. However, GP methods improve estimates of the population growth function when the function is misspecified. Results also demonstrated that the estimated magnitude of "model error" can be used to distinguish cases of model misspecification. We conclude with a discussion of the prospects for GP methods in other state-space models, including age and length-structured, meta-analytic, and individual-movement models.},
author = {Thorson, James T and Ono, Kotaro and Munch, Stephan B},
file = {:home/cboettig/Documents/Mendeley/Ecology/2014/Thorson, Ono, Munch - 2014 - Ecology.pdf:pdf},
issn = {0012-9658},
journal = {Ecology},
keywords = {bayesian models,gaussian process,model misspecification,population dynamics model,semiparametric models,state-space models},
mendeley-groups = {Theoretical Ecology},
month = feb,
number = {2},
pages = {329--41},
pmid = {24669727},
title = {{A Bayesian approach to identifying and compensating for model misspecification in population models.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24669727},
volume = {95},
year = {2014}
}

@article{Sugeno2013a,
  abstract = {The importance of Allee effects has long been recognized both in theoretical studies of population dynamics and in conservation sciences. Although the necessary conditions for Allee effects to occur (e.g., difficulty in finding mates and mortality driven by generalist predators at low density) would seem to apply to many species, evidence for Allee effects in natural populations is equivocal at best. This apparent scarcity might be an artifact driven by poor power to detect them with traditional parametric models. To circumvent this potential problem, we developed a semiparametric Bayesian method based on a Gaussian process prior. We validated the method using simulated data sets and applied it to three herring data sets.},
  author = {Sugeno, Masatoshi and Munch, Stephan B},
  doi = {10.1890/12-0454.1},
  file = {:home/cboettig/Documents/Mendeley/Ecology/2013/Sugeno, Munch - 2013 - Ecology.pdf:pdf},
  issn = {0012-9658},
  journal = {Ecology},
  keywords = {Animals,Bayes Theorem,Biological,Biomass,Computer Simulation,Fishes,Models,Population Dynamics},
  month = may,
  number = {5},
  pages = {1196--1204},
  pmid = {23858659},
  title = {{A semiparametric Bayesian method for detecting Allee effects}},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/23858659 http://www.esajournals.org/doi/abs/10.1890/12-0454.1},
  volume = {94},
  year = {2013}
}

@article{Sugeno2013b,
abstract = {The maximum annual reproductive rate (i.e., the slope at the origin in a stock-recruitment relationship) is one of the most important biological reference points in fisheries; it sets the upper limit to sustainable fishing mortality. Estimating the maximum reproductive rate by fitting parametric models to stock-recruitment data may not be a robust approach because two statistically indistinguishable models can generate radically different estimates. To mitigate this issue, we developed a flexible, semiparametric Bayesian approach based on a conditional Gaussian process prior specifically designed to estimate the maximum annual reproductive rate, and applied it to analyze simulated stock-recruitment data sets. Compared with results based on other Gaussian process priors, we found that the conditional Gaussian process prior provided superior results: the accuracy and precision of estimates were enhanced without increasing model complexity. Moreover, compared with parametric alternatives, performance of the conditional Gaussian process prior was comparable to that of the data-generating model and always better than the wrong model.},
author = {Sugeno, Masatoshi and Munch, Stephan B},
file = {:home/cboettig/Documents/Mendeley/Ecological applications a publication of the Ecological Society of America/2013/Sugeno, Munch - 2013 - Ecological applications a publication of the Ecological Society of America.pdf:pdf},
issn = {1051-0761},
journal = {Ecological applications : a publication of the Ecological Society of America},
keywords = {allee effects,depensation,gaussian process,maximum annual reproductive rate,recruitment relationship,semiparametric bayesian modeling,slope at the origin,stock},
mendeley-groups = {Review - private},
month = jun,
number = {4},
pages = {699--709},
pmid = {23865223},
title = {{A semiparametric Bayesian approach to estimating maximum reproductive rates at low population sizes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23865223},
volume = {23},
year = {2013}
}

@book{Burnham2002,
author = {Burnham, Kenneth P. and Anderson, David R},
isbn = {9780387953649},
pages = {496},
publisher = {Springer},
title = {{Model Selection and Multi-Model Inference}},
url = {http://www.amazon.com/Selection-Multi-Model-Inference-Kenneth-Burnham/dp/0387953647},
year = {2002}
}

@Article{	  Allen2005,
  author	= {Allen, Deborah and Tanner, Kimberly},
  file		= {:home/cboettig/Documents/Mendeley/Cell biology
		  education/2005/Allen, Tanner - 2005 - Cell biology
		  education.pdf:pdf},
  journal	= {Cell biology education},
  keywords	= {Biology,Biology: education,Curriculum,Educational
		  Technology,Models, Educational,Problem-Based
		  Learning,Problem-Based Learning:
		  methods,Students,Teaching,Teaching: methods,Teaching:
		  standards,active learning,education,large classes},
  mendeley-tags	= {active learning,education,large classes},
  month		= jan,
  number	= {4},
  pages		= {262--8},
  title		= {{Infusing active learning into the large-enrollment
		  biology class: seven strategies, from the simple to
		  complex.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/16344858},
  volume	= {4},
  year		= {2005}
}

@Article{	  Athanassoglou2012,
  author	= {Athanassoglou, Stergios and Xepapadeas, Anastasios},
  doi		= {10.1016/j.jeem.2011.11.001},
  file		= {:home/cboettig/Documents/Mendeley/Journal of Environmental
		  Economics and Management/2012/Athanassoglou, Xepapadeas -
		  2012 - Journal of Environmental Economics and
		  Management.pdf:pdf},
  issn		= {00950696},
  journal	= {Journal of Environmental Economics and Management},
  keywords	= {Pollution control,Precautionary principle,Robust
		  control,Stock dynamics,knightian uncertainty},
  month		= may,
  number	= {3},
  pages		= {304--320},
  publisher	= {Elsevier},
  title		= {{Pollution control with uncertain stock dynamics: When,
		  and how, to be precautious}},
  url		= {http://linkinghub.elsevier.com/retrieve/pii/S0095069611001409}
		  ,
  volume	= {63},
  year		= {2012}
}

@Article{	  Bestelmeyer2012,
  author	= {Bestelmeyer, Brandon T. and Duniway, Michael C. and James,
		  Darren K. and Burkett, Laura M. and Havstad, Kris M.},
  doi		= {10.1111/ele.12045},
  editor	= {Suding, Katharine},
  file		= {:home/cboettig/Documents/Mendeley/Ecology
		  Letters/2012/Bestelmeyer et al. - 2012 - Ecology
		  Letters.pdf:pdf},
  issn		= {1461023X},
  journal	= {Ecology Letters},
  keywords	= {desertification,early warning,grazing,long-term
		  experiment,patch size,regime
		  shift,resilience,state-transi-},
  month		= dec,
  pages		= {n/a--n/a},
  title		= {{A test of critical thresholds and their indicators in a
		  desertification-prone ecosystem: more resilience than we
		  thought}},
  url		= {http://doi.wiley.com/10.1111/ele.12045},
  year		= {2012}
}

@Article{	  Brozovic2011,
  author	= {Brozovi\'{c}, Nicholas and Schlenker, Wolfram},
  doi		= {10.1016/j.ecolecon.2010.10.001},
  file		= {:home/cboettig/Documents/Mendeley/Ecological
		  Economics/2011/Brozovi\'{c}, Schlenker - 2011 - Ecological
		  Economics.pdf:pdf},
  issn		= {09218009},
  journal	= {Ecological Economics},
  keywords	= {Stochastic dynamic programming,Threshold,ecosystem
		  management},
  month		= jan,
  pages		= {1--14},
  publisher	= {Elsevier B.V.},
  title		= {{Optimal management of an ecosystem with an unknown
		  threshold}},
  url		= {http://linkinghub.elsevier.com/retrieve/pii/S0921800910004167}
		  ,
  year		= {2011}
}

@Article{	  Clark1986,
  author	= {Clark, Colin W and Kirkwood, Geoffrey P.},
  doi		= {10.1016/0095-0696(86)90024-0},
  file		= {:home/cboettig/Documents/Mendeley/Journal of Environmental
		  Economics and Management/1986/Clark, Kirkwood - 1986 -
		  Journal of Environmental Economics and Management.pdf:pdf},
  issn		= {00950696},
  journal	= {Journal of Environmental Economics and Management},
  month		= sep,
  number	= {3},
  pages		= {235--244},
  title		= {{On uncertain renewable resource stocks: Optimal harvest
		  policies and the value of stock surveys}},
  url		= {http://linkinghub.elsevier.com/retrieve/pii/0095069686900240}
		  ,
  volume	= {13},
  year		= {1986}
}

@Book{		  Courchamp2008,
  author	= {Courchamp, Franck and Berec, Ludek and Gascoigne, Joanna},
  isbn		= {0198570309},
  pages		= {256},
  publisher	= {Oxford University Press, USA},
  title		= {{Allee Effects in Ecology and Conservation}},
  url		= {http://www.amazon.com/Effects-Ecology-Conservation-Franck-Courchamp/dp/0198570309}
		  ,
  year		= {2008}
}

@Article{	  Cressie2009,
  abstract	= {Analyses of ecological data should account for the
		  uncertainty in the process(es) that generated the data.
		  However, accounting for these uncertainties is a difficult
		  task, since ecology is known for its complexity.
		  Measurement and/or process errors are often the only
		  sources of uncertainty modeled when addressing complex
		  ecological problems, yet analyses should also account for
		  uncertainty in sampling design, in model specification, in
		  parameters governing the specified model, and in initial
		  and boundary conditions. Only then can we be confident in
		  the scientific inferences and forecasts made from an
		  analysis. Probability and statistics provide a framework
		  that accounts for multiple sources of uncertainty. Given
		  the complexities of ecological studies, the hierarchical
		  statistical model is an invaluable tool. This approach is
		  not new in ecology, and there are many examples (both
		  Bayesian and non-Bayesian) in the literature illustrating
		  the benefits of this approach. In this article, we provide
		  a baseline for concepts, notation, and methods, from which
		  discussion on hierarchical statistical modeling in ecology
		  can proceed. We have also planted some seeds for discussion
		  and tried to show where the practical difficulties lie. Our
		  thesis is that hierarchical statistical modeling is a
		  powerful way of approaching ecological analysis in the
		  presence of inevitable but quantifiable uncertainties, even
		  if practical issues sometimes require pragmatic
		  compromises.},
  author	= {Cressie, Noel and Calder, Catherine a and Clark, James S
		  and {Ver Hoef}, Jay M and Wikle, Christopher K},
  doi		= {10.1890/07-0744.1},
  file		= {:home/cboettig/Documents/Mendeley/Ecological
		  Applications/2009/Cressie et al. - 2009 - Ecological
		  Applications.pdf:pdf},
  issn		= {1051-0761},
  journal	= {Ecological Applications},
  keywords	= {Animal,Animals,Bayes Theorem,Behavior,Ecology,Ecology:
		  trends,Environment,Markov
		  Chains,Models,Statistical,Uncertainty},
  month		= apr,
  number	= {3},
  pages		= {553--70},
  pmid		= {19425416},
  title		= {{Accounting for uncertainty in ecological analysis: the
		  strengths and limitations of hierarchical statistical
		  modeling.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/19425416},
  volume	= {19},
  year		= {2009}
}

@Article{	  Cuddington2013,
  author	= {Cuddington, Kim M and Fortin, MJ and Gerber, LR},
  doi		= {10.1890/ES12-00178.1},
  file		= {:home/cboettig/Documents/Mendeley/Ecosphere/2013/Cuddington,
		  Fortin, Gerber - 2013 - Ecosphere.pdf:pdf},
  journal	= {Ecosphere},
  keywords	= {accepted 2 january 2013,al,article distributed under
		  the,c,climate
		  change,commons,copyright,corresponding,d,editor,expert
		  opinion,extrapolation,p,peters,published 8 february
		  2013,received 19 june 2012,revised 31 december
		  2012,simulation model,terms of the creative,this is an
		  open-access,\'{o} 2013 cuddington et},
  number	= {February},
  pages		= {1--12},
  title		= {{Process-based models are required to manage ecological
		  systems in a changing world}},
  url		= {http://www.esajournals.org/doi/abs/10.1890/ES12-00178.1},
  volume	= {4},
  year		= {2013}
}

@Article{	  Fischer2009,
  abstract	= {Conservation strategies need to be both effective and
		  efficient to be successful. To this end, two bodies of
		  research should be integrated, namely 'resilience thinking'
		  and 'optimisation for conservation,' both of which are
		  highly policy relevant but to date have evolved largely
		  separately. Resilience thinking provides an integrated
		  perspective for analysis, emphasising the potential of
		  nonlinear changes and the interdependency of social and
		  ecological systems. By contrast, optimisation for
		  conservation is an outcome-oriented tool that recognises
		  resource scarcity and the need to make rational and
		  transparent decisions. Here we propose that actively
		  embedding optimisation analyses within a
		  resilience-thinking framework could draw on the
		  complementary strengths of the two bodies of work, thereby
		  promoting cost-effective and enduring conservation
		  outcomes.},
  author	= {Fischer, Joern and Peterson, Garry D and Gardner, Toby a
		  and Gordon, Line J and Fazey, Ioan and Elmqvist, Thomas and
		  Felton, Adam and Folke, Carl and Dovers, Stephen},
  doi		= {10.1016/j.tree.2009.03.020},
  file		= {:home/cboettig/Documents/Mendeley/Trends in ecology \&
		  evolution/2009/Fischer et al. - 2009 - Trends in ecology \&
		  evolution.pdf:pdf},
  issn		= {0169-5347},
  journal	= {Trends in ecology \& evolution},
  keywords	= {Animals,Conservation of Natural
		  Resources,Humans,Thinking},
  month		= oct,
  number	= {10},
  pages		= {549--54},
  pmid		= {19665820},
  title		= {{Integrating resilience thinking and optimisation for
		  conservation.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/19665820},
  volume	= {24},
  year		= {2009}
}

@Article{	  Geritz2012,
  author	= {Geritz, Stefan A H and Kisdi, Eva},
  doi		= {10.1007/s00285-011-0496-3},
  file		= {:home/cboettig/Documents/Mendeley/Journal of mathematical
		  biology/2012/Geritz, Kisdi - 2012 - Journal of mathematical
		  biology.pdf:pdf},
  issn		= {1432-1416},
  journal	= {Journal of mathematical biology},
  month		= dec,
  number	= {6-7},
  pages		= {1411--5},
  pmid		= {22159789},
  title		= {{Mathematical ecology: why mechanistic models?}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/22159789},
  volume	= {65},
  year		= {2012}
}

@Article{	  Gordon1954,
  author	= {Gordon, HS},
  file		= {:home/cboettig/Documents/Mendeley/The Journal of Political
		  Economy/1954/Gordon - 1954 - The Journal of Political
		  Economy.pdf:pdf},
  journal	= {The Journal of Political Economy},
  keywords	= {source:wikipedia},
  mendeley-tags	= {source:wikipedia},
  number	= {2},
  pages		= {124--142},
  title		= {{The economic theory of a common-property resource: the
		  fishery}},
  url		= {http://www.jstor.org/stable/10.2307/1825571},
  volume	= {62},
  year		= {1954}
}

@Article{	  Halpern2013,
  abstract	= {Triple-bottom-line outcomes from resource management and
		  conservation, where conservation goals and equity in social
		  outcomes are maximized while overall costs are minimized,
		  remain a highly sought-after ideal. However, despite
		  widespread recognition of the importance that equitable
		  distribution of benefits or costs across society can play
		  in conservation success, little formal theory exists for
		  how to explicitly incorporate equity into conservation
		  planning and prioritization. Here, we develop that theory
		  and implement it for three very different case studies in
		  California (United States), Raja Ampat (Indonesia), and the
		  wider Coral Triangle region (Southeast Asia). We show that
		  equity tends to trade off nonlinearly with the potential to
		  achieve conservation objectives, such that similar
		  conservation outcomes can be possible with greater equity,
		  to a point. However, these case studies also produce a
		  range of trade-off typologies between equity and
		  conservation, depending on how one defines and measures
		  social equity, including direct (linear) and no trade-off.
		  Important gaps remain in our understanding, most notably
		  how equity influences probability of conservation success,
		  in turn affecting the actual ability to achieve
		  conservation objectives. Results here provide an important
		  foundation for moving the science and practice of
		  conservation planning-and broader spatial planning in
		  general-toward more consistently achieving efficient,
		  equitable, and effective outcomes.},
  author	= {Halpern, Benjamin S and Klein, Carissa J and Brown,
		  Christopher J and Beger, Maria and Grantham, Hedley S and
		  Mangubhai, Sangeeta and Ruckelshaus, Mary and Tulloch,
		  Vivitskaia J and Watts, Matt and White, Crow and
		  Possingham, Hugh P},
  doi		= {10.1073/pnas.1217689110},
  file		= {:home/cboettig/Documents/Mendeley/Proceedings of the
		  National Academy of Sciences of the United States of
		  America/2013/Halpern et al. - 2013 - Proceedings of the
		  National Academy of Sciences of the United States of
		  America.pdf:pdf},
  issn		= {1091-6490},
  journal	= {Proceedings of the National Academy of Sciences of the
		  United States of America},
  keywords	= {Animals,Asia,Biodiversity,California,Conservation of
		  Natural Resources,Conservation of Natural Resources:
		  economics,Conservation of Natural Resources:
		  methods,Ecosystem,Environmental
		  Monitoring,Fisheries,Humans,Indonesia,Southeastern,source:alerts}
		  ,
  mendeley-tags	= {source:alerts},
  month		= apr,
  number	= {15},
  pages		= {6229--34},
  pmid		= {23530207},
  title		= {{Achieving the triple bottom line in the face of inherent
		  trade-offs among social equity, economic return, and
		  conservation.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/23530207
		  http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3625307\&tool=pmcentrez\&rendertype=abstract}
		  ,
  volume	= {110},
  year		= {2013}
}

@Book{		  Hilborn1997,
  annote	= { From Duplicate 2 (

		  The Ecological Detective: Confronting Models with data

		  - Hilborn, Ray; Mangel, Marc )

		  },
  author	= {Hilborn, Ray and Mangel, Marc},
  file		= {:home/cboettig/Documents/Mendeley/Unknown/1997/Hilborn,
		  Mangel - 1997 - Unknown.pdf:pdf},
  isbn		= {0691034974},
  pages		= {330},
  publisher	= {Princeton University Press},
  title		= {{The Ecological Detective: Confronting Models with data}},
  url		= {http://www.amazon.com/The-Ecological-Detective-Confronting-Models/dp/0691034974}
		  ,
  year		= {1997}
}

@Article{	  Hilborn2007,
  author	= {Hilborn, Ray},
  doi		= {10.1007/s10021-007-9100-5},
  file		= {:home/cboettig/Documents/Mendeley/Ecosystems/2007/Hilborn
		  - 2007 - Ecosystems.pdf:pdf},
  issn		= {1432-9840},
  journal	= {Ecosystems},
  keywords	= {fisheries,source:blog},
  mendeley-tags	= {source:blog},
  month		= oct,
  number	= {8},
  pages		= {1362--1369},
  title		= {{Reinterpreting the State of Fisheries and their
		  Management}},
  url		= {http://www.springerlink.com/index/10.1007/s10021-007-9100-5}
		  ,
  volume	= {10},
  year		= {2007}
}

@Article{	  Hughes2013,
  abstract	= {Regime shifts from one ecological state to another are
		  often portrayed as sudden, dramatic, and difficult to
		  reverse. Yet many regime shifts unfold slowly and
		  imperceptibly after a tipping point has been exceeded,
		  especially at regional and global scales. These long,
		  smooth transitions between equilibrium states are easy to
		  miss, ignore, or deny, confounding management and
		  governance. However, slow responses by ecosystems after
		  transgressing a dangerous threshold also affords borrowed
		  time - a window of opportunity to return to safer
		  conditions before the new state eventually locks in and
		  equilibrates. In this context, the most important challenge
		  is a social one: convincing enough people to confront
		  business-as-usual before time runs out to reverse unwanted
		  regime shifts even after they have already begun.},
  author	= {Hughes, Terry P and Linares, Cristina and Dakos, Vasilis
		  and van de Leemput, Ingrid a and van Nes, Egbert H},
  doi		= {10.1016/j.tree.2012.08.022},
  file		= {:home/cboettig/Documents/Mendeley/Trends in ecology \&
		  evolution/2013/Hughes et al. - 2013 - Trends in ecology \&
		  evolution.pdf:pdf},
  issn		= {0169-5347},
  journal	= {Trends in ecology \& evolution},
  keywords	= {alternate stable states,and that take even,borrowed
		  time,climate change,dynamics,flips,longer to
		  reverse,or,regime shift,resilience,slow
		  responses,surprises,that,thresholds,transient,transitions
		  represent more typical,unfold in slow motion},
  month		= mar,
  number	= {3},
  pages		= {149--55},
  pmid		= {22995893},
  title		= {{Living dangerously on borrowed time during slow,
		  unrecognized regime shifts.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/22995893},
  volume	= {28},
  year		= {2013}
}

@Manual{	  knitr,
  annote	= {R package version 0.4.2},
  author	= {Xie, Yihui},
  title		= {{knitr: A general-purpose package for dynamic report
		  generation in R}},
  url		= {http://yihui.name/knitr/},
  year		= {2012}
}

@Book{Xie_2013,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2013},
  note = {ISBN 978-1482203530},
  url = {http://yihui.name/knitr/},
}

@Article{	  Kocijan2005,
  author	= {Kocijan, Ju\v{s} and Girard, Agathe and Banko, Bla\v{z}
		  and Murray-Smith, Roderick},
  doi		= {10.1080/13873950500068567},
  file		= {:home/cboettig/Documents/Mendeley/Mathematical and
		  Computer Modelling of Dynamical Systems/2005/Kocijan et al.
		  - 2005 - Mathematical and Computer Modelling of Dynamical
		  Systems.pdf:pdf},
  issn		= {1387-3954},
  journal	= {Mathematical and Computer Modelling of Dynamical Systems},
  number	= {4},
  pages		= {411--424},
  title		= {{Dynamic systems identification with Gaussian processes}},
  url		= {http://www.tandfonline.com/doi/abs/10.1080/13873950500068567}
		  ,
  volume	= {11},
  year		= {2005}
}

@Article{	  Ludwig1982,
  author	= {Ludwig, Donald and Walters, Carl J},
  doi		= {10.1016/0304-3800(82)90023-0},
  file		= {:home/cboettig/Documents/Mendeley/Ecological
		  Modelling/1982/Ludwig, Walters - 1982 - Ecological
		  Modelling.pdf:pdf},
  issn		= {03043800},
  journal	= {Ecological Modelling},
  keywords	= {parameter uncertainty},
  mendeley-tags	= {parameter uncertainty},
  month		= jan,
  number	= {3-4},
  pages		= {273--292},
  title		= {{Optimal harvesting with imprecise parameter estimates}},
  url		= {http://linkinghub.elsevier.com/retrieve/pii/0304380082900230}
		  ,
  volume	= {14},
  year		= {1982}
}

@Book{		  Mangel1988,
  address	= {Princeton},
  author	= {Mangel, Marc and Clark, Colin W},
  editor	= {Krebs, John and Clutton-Brock, Tim},
  file		= {:home/cboettig/Documents/Mendeley/Unknown/1988/Mangel,
		  Clark - 1988 - Unknown.pdf:pdf},
  isbn		= {9780691085067},
  publisher	= {Princeton University Press},
  title		= {{Dynamic Modeling in Behavioral Ecology}},
  year		= {1988}
}

@Article{	  Marescot2013,
  author	= {Marescot, Lucile and Chapron, Guillaume and Chad\`{e}s,
		  Iadine and Fackler, Paul L. and Duchamp, Christophe and
		  Marboutin, Eric and Gimenez, Olivier},
  doi		= {10.1111/2041-210X.12082},
  file		= {:home/cboettig/Documents/Mendeley/Methods in Ecology and
		  Evolution/2013/Marescot et al. - 2013 - Methods in Ecology
		  and Evolution.pdf:pdf},
  issn		= {2041210X},
  journal	= {Methods in Ecology and Evolution},
  month		= jun,
  pages		= {n/a--n/a},
  title		= {{Complex decisions made simple: a primer on stochastic
		  dynamic programming}},
  url		= {http://doi.wiley.com/10.1111/2041-210X.12082},
  year		= {2013}
}

@Article{	  May1979,
  abstract	= {With the overexploitation of many conventional fish
		  stcocks, and growing interest in harvesting new kinds of
		  food from the sea, there is increasing need for managers of
		  fisheries to take account of interactions among species. In
		  particular, as Antarctic krill-fishing industries grow,
		  there is a need to agree upon sound principles for managing
		  the Southern Ocean ecosystem. Using simple models, we
		  discuss the way multispecies food webs respond to the
		  harvesting of species at differrent trophic levels. These
		  biological and economic insights are applied to a
		  discussion of fisheries in the Southern Otean and the North
		  Sea and to enunciate some for harvesting in multispecies
		  systems.},
  author	= {May, Robert M and Beddington, John R and Clark, Colin W
		  and Holt, Sidney J and Laws, R M},
  doi		= {10.1126/science.205.4403.267},
  file		= {:home/cboettig/Documents/Mendeley/Science (New York,
		  N.Y.)/1979/May et al. - 1979 - Science (New York,
		  N.Y.).pdf:pdf},
  issn		= {0036-8075},
  journal	= {Science (New York, N.Y.)},
  keywords	= {forage fish},
  mendeley-tags	= {forage fish},
  month		= jul,
  number	= {4403},
  pages		= {267--77},
  pmid		= {17747032},
  title		= {{Management of multispecies fisheries.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/17747032},
  volume	= {205},
  year		= {1979}
}

@Article{	  McAllister1998,
  author	= {McAllister, MK},
  doi		= {10.1006/jmsc.1998.0425},
  file		= {:home/cboettig/Documents/Mendeley/ICES Journal of Marine
		  Science/1998/McAllister - 1998 - ICES Journal of Marine
		  Science.pdf:pdf},
  issn		= {10543139},
  journal	= {ICES Journal of Marine Science},
  keywords	= {accepted 3 june 1998,bayesian,centre,decision
		  analysis,distribution,fishery
		  management,k,kirkwood,m,mcallister and g,p,policy
		  evaluation,posterior,prior distribution,received 19
		  february 1997,renewable resources assessment group,stock
		  assessment,uncertainty},
  month		= dec,
  number	= {6},
  pages		= {1031--1060},
  title		= {{Bayesian stock assessment: a review and example
		  application using the logistic model}},
  url		= {http://icesjms.oxfordjournals.org/content/55/6/1031.short
		  http://icesjms.oxfordjournals.org/cgi/doi/10.1006/jmsc.1998.0425}
		  ,
  volume	= {55},
  year		= {1998}
}

@Article{	  Munch2005,
  author	= {Munch, Stephan B and Snover, Melissa L. and Watters,
		  George M. and Mangel, Marc},
  doi		= {10.1111/j.1461-0248.2005.00766.x},
  file		= {:home/cboettig/Documents/Mendeley/Ecology
		  Letters/2005/Munch et al. - 2005 - Ecology
		  Letters.pdf:pdf},
  issn		= {1461023X},
  journal	= {Ecology Letters},
  keywords	= {1 melissa
		  l,2005,691,695,8,behaviour,bottom-up,competition,ecology
		  letters,forage
		  fish,munch,predation,recruitment,reproduction,stephan
		  b,top-down,trophic cascade},
  mendeley-tags	= {forage fish,trophic cascade},
  month		= may,
  number	= {7},
  pages		= {691--695},
  title		= {{A unified treatment of top-down and bottom-up control of
		  reproduction in populations}},
  url		= {http://doi.wiley.com/10.1111/j.1461-0248.2005.00766.x},
  volume	= {8},
  year		= {2005}
}

@Article{	  Munch2005a,
  author	= {Munch, Stephan B and Kottas, Athanasios and Mangel, Marc},
  doi		= {10.1139/f05-073},
  file		= {:home/cboettig/Documents/Mendeley/Canadian Journal of
		  Fisheries and Aquatic Sciences/2005/Munch, Kottas, Mangel -
		  2005 - Canadian Journal of Fisheries and Aquatic
		  Sciences.pdf:pdf},
  issn		= {0706-652X},
  journal	= {Canadian Journal of Fisheries and Aquatic Sciences},
  month		= aug,
  number	= {8},
  pages		= {1808--1821},
  title		= {{Bayesian nonparametric analysis of stock-recruitment
		  relationships}},
  url		= {http://www.nrcresearchpress.com/doi/abs/10.1139/f05-073},
  volume	= {62},
  year		= {2005}
}

@Article{	  Myers1995,
  abstract	= {Models of population dynamics in which per capita
		  reproductive success declines at low population levels
		  (variously known as depensation, the Allee effect, and
		  inverse density-dependence) predict that populations can
		  have multiple equilibria and may suddenly shift from one
		  equilibrium to another. If such depensatory dynamics exist,
		  reduced mortality may be insufficient to allow recovery of
		  a population after abundance has been severely reduced by
		  harvesting. Estimates of spawner abundance and number of
		  surviving progeny for 128 fish stocks indicated only 3
		  stocks with significant depensation. Estimates of the
		  statistical power of the tests strengthen the conclusion
		  that depensatory dynamics are not apparent for fish
		  populations at the levels studied.},
  author	= {Myers, R A and Barrowman, N J and Hutchings, J A and
		  Rosenberg, Andrew a},
  doi		= {10.1126/science.269.5227.1106},
  file		= {:home/cboettig/Documents/Mendeley/Science (New York,
		  N.Y.)/1995/Myers et al. - 1995 - Science (New York,
		  N.Y.).pdf:pdf},
  issn		= {0036-8075},
  journal	= {Science (New York, N.Y.)},
  month		= aug,
  number	= {5227},
  pages		= {1106--8},
  pmid		= {17755535},
  title		= {{Population dynamics of exploited fish stocks at low
		  population levels.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/17755535},
  volume	= {269},
  year		= {1995}
}

@Article{	  Polasky2011,
  abstract	= {Global change issues are complex and the consequences of
		  decisions are often highly uncertain. The large spatial and
		  temporal scales and stakes involved make it important to
		  take account of present and potential consequences in
		  decision-making. Standard approaches to decision-making
		  under uncertainty require information about the likelihood
		  of alternative states, how states and actions combine to
		  form outcomes and the net benefits of different outcomes.
		  For global change issues, however, the set of potential
		  states is often unknown, much less the probabilities,
		  effect of actions or their net benefits. Decision theory,
		  thresholds, scenarios and resilience thinking can expand
		  awareness of the potential states and outcomes, as well as
		  of the probabilities and consequences of outcomes under
		  alternative decisions.},
  author	= {Polasky, Stephen and Carpenter, Stephen R and Folke, Carl
		  and Keeler, Bonnie},
  doi		= {10.1016/j.tree.2011.04.007},
  file		= {:home/cboettig/Documents/Mendeley/Trends in ecology \&
		  evolution/2011/Polasky et al. - 2011 - Trends in ecology \&
		  evolution.pdf:pdf},
  issn		= {0169-5347},
  journal	= {Trends in ecology \& evolution},
  month		= may,
  pages		= {1--7},
  pmid		= {21616553},
  publisher	= {Elsevier Ltd},
  title		= {{Decision-making under great uncertainty: environmental
		  management in an era of global change.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/21616553},
  year		= {2011}
}

@Manual{	  R2jags,
  annote	= {R package version 0.03-11},
  author	= {Su, Yu-Sung and {Masanao Yajima}},
  title		= {{R2jags: A Package for Running jags from R}},
  url		= {http://cran.r-project.org/package=R2jags},
  year		= {2013}
}

@Book{		  Rasmussen2006,
  address	= {Boston},
  author	= {Rasmussen, Carl Edward and Williams, C K I},
  editor	= {{Thomas Dietterich}},
  file		= {:home/cboettig/Documents/Mendeley/Unknown/2006/Rasmussen,
		  Williams - 2006 - Unknown.pdf:pdf},
  keywords	= {Bayesian,Gaussian processes,inference,machine learning},
  publisher	= {MIT Press,},
  title		= {{Gaussian Processes for Machine Learning}},
  url		= {www.GaussianProcess.org/gpml},
  year		= {2006}
}

@Article{	  Reed1979,
  author	= {Reed, William J},
  doi		= {10.1016/0095-0696(79)90014-7},
  file		= {:home/cboettig/Documents/Mendeley/Journal of Environmental
		  Economics and Management/1979/Reed - 1979 - Journal of
		  Environmental Economics and Management.pdf:pdf},
  issn		= {00950696},
  journal	= {Journal of Environmental Economics and Management},
  keywords	= {fisheries,optimal control},
  mendeley-tags	= {fisheries,optimal control},
  month		= dec,
  number	= {4},
  pages		= {350--363},
  publisher	= {Elsevier},
  title		= {{Optimal escapement levels in stochastic and deterministic
		  harvesting models}},
  url		= {http://www.sciencedirect.com/science/article/pii/0095069679900147
		  http://linkinghub.elsevier.com/retrieve/pii/0095069679900147}
		  ,
  volume	= {6},
  year		= {1979}
}

@Article{	  Roughgarden1996,
  author	= {Roughgarden, Joan E and Smith, F.},
  file		= {:home/cboettig/Documents/Mendeley/Proceedings of the
		  National Academy of Sciences of the United States of
		  America/1996/Roughgarden, Smith - 1996 - Proceedings of the
		  National Academy of Sciences of the United States of
		  America.pdf:pdf},
  issn		= {0132-8867},
  journal	= {Proceedings of the National Academy of Sciences of the
		  United States of America},
  number	= {10},
  pages		= {5078},
  publisher	= {National Acad Sciences},
  title		= {{Why fisheries collapse and what to do about it}},
  url		= {http://www.pnas.org/content/93/10/5078.short},
  volume	= {93},
  year		= {1996}
}

@Manual{	  RTeam,
  address	= {Vienna, Austria},
  author	= {{R Core Team}},
  organization	= {R Foundation for Statistical Computing},
  title		= {{R: A Language and Environment for Statistical
		  Computing}},
  url		= {http://www.r-project.org/},
  year		= {2013}
}

@Article{	  Schapaugh2013,
  author	= {Schapaugh, Adam W and Tyre, Andrew J.},
  doi		= {10.1016/j.ecolmodel.2013.01.003},
  file		= {:home/cboettig/Documents/Mendeley/Ecological
		  Modelling/2013/Schapaugh, Tyre - 2013 - Ecological
		  Modelling.pdf:pdf},
  issn		= {03043800},
  journal	= {Ecological Modelling},
  keywords	= {source:human},
  mendeley-tags	= {source:human},
  month		= apr,
  pages		= {15--21},
  title		= {{Accounting for parametric uncertainty in Markov decision
		  processes}},
  url		= {http://linkinghub.elsevier.com/retrieve/pii/S0304380013000306}
		  ,
  volume	= {254},
  year		= {2013}
}

@Article{	  Scheffer2001,
  abstract	= {All ecosystems are exposed to gradual changes in climate,
		  nutrient loading, habitat fragmentation or biotic
		  exploitation. Nature is usually assumed to respond to
		  gradual change in a smooth way. However, studies on lakes,
		  coral reefs, oceans, forests and arid lands have shown that
		  smooth change can be interrupted by sudden drastic switches
		  to a contrasting state. Although diverse events can trigger
		  such shifts, recent studies show that a loss of resilience
		  usually paves the way for a switch to an alternative state.
		  This suggests that strategies for sustainable management of
		  such ecosystems should focus on maintaining resilience.},
  author	= {Scheffer, Marten and Carpenter, Stephen R and Foley, J A
		  and Folke, C and Walker, B},
  doi		= {10.1038/35098000},
  file		= {:home/cboettig/Documents/Mendeley/Nature/2001/Scheffer et
		  al. - 2001 - Nature.pdf:pdf},
  issn		= {0028-0836},
  journal	= {Nature},
  keywords	= {Animals,Biological,Cnidaria,Conservation of Natural
		  Resources,Desert Climate,Ecosystem,Fresh
		  Water,Models,Oceans and Seas,Stochastic Processes,Trees},
  month		= oct,
  number	= {6856},
  pages		= {591--6},
  pmid		= {11595939},
  publisher	= {Nature Publishing Group},
  title		= {{Catastrophic shifts in ecosystems.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/11595939},
  volume	= {413},
  year		= {2001}
}

@Article{	  Sethi2005,
  author	= {Sethi, Gautam and Costello, Christopher and Fisher,
		  Anthony and Hanemann, Michael and Karp, Larry},
  doi		= {10.1016/j.jeem.2004.11.005},
  file		= {:home/cboettig/Documents/Mendeley/Journal of Environmental
		  Economics and Management/2005/Sethi et al. - 2005 - Journal
		  of Environmental Economics and Management.pdf:pdf},
  issn		= {00950696},
  journal	= {Journal of Environmental Economics and Management},
  keywords	= {dynamic optimization,fisheries management,incomplete
		  information,markovian,risk,uncertainty},
  month		= sep,
  number	= {2},
  pages		= {300--318},
  title		= {{Fishery management under multiple uncertainty}},
  url		= {http://linkinghub.elsevier.com/retrieve/pii/S0095069605000057}
		  ,
  volume	= {50},
  year		= {2005}
}

@Article{	  Weitzman2013,
  author	= {Weitzman, Martin L},
  doi		= {10.1007/s10640-013-9646-y},
  file		= {:home/cboettig/Documents/Mendeley/Environmental and
		  Resource Economics/2013/Weitzman - 2013 - Environmental and
		  Resource Economics.pdf:pdf},
  issn		= {0924-6460},
  journal	= {Environmental and Resource Economics},
  keywords	= {1 introduction via climate,a striking feature
		  of,catastrophe,change,change is that worst-case,climate
		  change,fat tail,scenarios are both,the economics of
		  climate,uncertainty},
  month		= mar,
  number	= {2},
  pages		= {159--173},
  title		= {{A Precautionary Tale of Uncertain Tail Fattening}},
  url		= {http://link.springer.com/10.1007/s10640-013-9646-y},
  volume	= {55},
  year		= {2013}
}

@Article{	  Williams2001,
  author	= {Williams, Byron K.},
  doi		= {10.1023/A:1011395725123},
  file		= {:home/cboettig/Documents/Mendeley/Environmental and
		  Ecological Statistics/2001/Williams - 2001 - Environmental
		  and Ecological Statistics.pdf:pdf},
  journal	= {Environmental and Ecological Statistics},
  keywords	= {adaptive resource management,bayes,dynamic model,optimal
		  control,theorem,wildlife populations},
  pages		= {269 -- 288},
  title		= {{Uncertainty , learning , and the optimal management of
		  wildlife}},
  volume	= {8},
  year		= {2001}
}

@Article{	  Worm2006,
  abstract	= {Human-dominated marine ecosystems are experiencing
		  accelerating loss of populations and species, with largely
		  unknown consequences. We analyzed local experiments,
		  long-term regional time series, and global fisheries data
		  to test how biodiversity loss affects marine ecosystem
		  services across temporal and spatial scales. Overall, rates
		  of resource collapse increased and recovery potential,
		  stability, and water quality decreased exponentially with
		  declining diversity. Restoration of biodiversity, in
		  contrast, increased productivity fourfold and decreased
		  variability by 21\%, on average. We conclude that marine
		  biodiversity loss is increasingly impairing the ocean's
		  capacity to provide food, maintain water quality, and
		  recover from perturbations. Yet available data suggest that
		  at this point, these trends are still reversible.},
  author	= {Worm, Boris and Barbier, Edward B and Beaumont, Nicola and
		  Duffy, J Emmett and Folke, Carl and Halpern, Benjamin S and
		  Jackson, Jeremy B C and Lotze, Heike K and Micheli,
		  Fiorenza and Palumbi, Stephen R and Sala, Enric and Selkoe,
		  Kimberley a and Stachowicz, John J and Watson, Reg},
  doi		= {10.1126/science.1132294},
  file		= {:home/cboettig/Documents/Mendeley/Science (New York,
		  N.Y.)/2006/Worm et al. - 2006 - Science (New York,
		  N.Y.).pdf:pdf},
  issn		= {1095-9203},
  journal	= {Science (New York, N.Y.)},
  keywords	= {Animals,Biodiversity,Conservation of Natural
		  Resources,Databases,
		  Factual,Ecosystem,Eukaryota,Fisheries,Fishes,Forecasting,Invertebrates,Oceans
		  and Seas,Plants,PopBioCore,Population
		  Dynamics,Seafood,Seawater,Stachowicz,Water
		  Pollution,Winter2008},
  mendeley-tags	= {PopBioCore,Stachowicz,Winter2008},
  month		= nov,
  number	= {5800},
  pages		= {787--90},
  pmid		= {17082450},
  title		= {{Impacts of biodiversity loss on ocean ecosystem
		  services.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/17082450},
  volume	= {314},
  year		= {2006}
}

@Article{	  Worm2009,
  abstract	= {After a long history of overexploitation, increasing
		  efforts to restore marine ecosystems and rebuild fisheries
		  are under way. Here, we analyze current trends from a
		  fisheries and conservation perspective. In 5 of 10
		  well-studied ecosystems, the average exploitation rate has
		  recently declined and is now at or below the rate predicted
		  to achieve maximum sustainable yield for seven systems. Yet
		  63\% of assessed fish stocks worldwide still require
		  rebuilding, and even lower exploitation rates are needed to
		  reverse the collapse of vulnerable species. Combined
		  fisheries and conservation objectives can be achieved by
		  merging diverse management actions, including catch
		  restrictions, gear modification, and closed areas,
		  depending on local context. Impacts of international fleets
		  and the lack of alternatives to fishing complicate
		  prospects for rebuilding fisheries in many poorer regions,
		  highlighting the need for a global perspective on
		  rebuilding marine resources.},
  author	= {Worm, Boris and Hilborn, Ray and Baum, Julia K and Branch,
		  Trevor A and Collie, Jeremy S and Costello, Christopher and
		  Fogarty, Michael J and Fulton, Elizabeth a and Hutchings,
		  Jeffrey a and Jennings, Simon and Jensen, Olaf P and Lotze,
		  Heike K and Mace, Pamela M and McClanahan, Tim R and Minto,
		  C\'{o}il\'{\i}n and Palumbi, Stephen R and Parma, Ana M and
		  Ricard, Daniel and Rosenberg, Andrew a and Watson, Reg and
		  Zeller, Dirk},
  doi		= {10.1126/science.1173146},
  file		= {:home/cboettig/Documents/Mendeley/Science (New York,
		  N.Y.)/2009/Worm et al. - 2009 - Science (New York,
		  N.Y.).pdf:pdf;:home/cboettig/Documents/Mendeley/Science
		  (New York, N.Y.)/2009/Worm et al. - 2009 - Science (New
		  York, N.Y.)(2).pdf:pdf},
  issn		= {1095-9203},
  journal	= {Science (New York, N.Y.)},
  keywords	= {Animals,Biodiversity,Biological,Biomass,Conservation of
		  Natural Resources,Ecosystem,Fisheries,Fisheries:
		  methods,Fishes,Fishes: anatomy \&
		  histology,Internationality,Marine Biology,Models,Oceans and
		  Seas,Population Dynamics,fisheries},
  mendeley-tags	= {fisheries},
  month		= jul,
  number	= {5940},
  pages		= {578--85},
  pmid		= {19644114},
  title		= {{Rebuilding global fisheries.}},
  url		= {http://www.ncbi.nlm.nih.gov/pubmed/19644114},
  volume	= {325},
  year		= {2009}
}

repo_name: cboettig/nonparametric-bayes

repo_language: TeX

mime_type: text/plain


text:
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text:
sensitivity_trends <- function(allee, sigma, seed){
  sigma_g <- sigma
  p <- c(r = p[[1]], K = p[[2]], C = allee)

  # seed indicates replicate training data, generated from f with parameters p
  yields <- sapply(seed,
                   function(seed_i){
                     set.seed(seed_i)

                     x <- numeric(Tobs)
                     x[1] <- Xo
                     nz <- 1
                     for(t in 1:(Tobs-1))
                       x[t+1] = z_g() * f(x[t], h=0, p=p)

                     X = c(rep(0,nz), pmax(rep(0,Tobs-1), x[1:(Tobs-1)]))
                     Y = c(rep(0,nz), x[2:Tobs])

                     ## @knitr gp-priors
                     s2.p <- c(5,5)
                     d.p = c(10, 1/0.1)

                     ## @knitr gp
                     gp <- gp_mcmc(X, y=Y, n=1e5, s2.p = s2.p, d.p = d.p)
                     gp_dat <- gp_predict(gp, x_grid, burnin=1e4, thin=300)

                     matrices_gp <- gp_transition_matrix(gp_dat$Ef_posterior, gp_dat$Vf_posterior, x_grid, h_grid)
                     opt_gp <- value_iteration(matrices_gp, x_grid, h_grid, MaxT, xT, profit, delta, reward)

                     ## @knitr mle-opt
                     matrices_true <- f_transition_matrix(f, p, x_grid, h_grid, sigma_g)
                     opt_true <- value_iteration(matrices_true, x_grid, h_grid, OptTime=MaxT, xT, profit, delta=delta)

                     OPT = data.frame(GP = opt_gp$D, True = opt_true$D)
                     policies <- melt(data.frame(stock=x_grid, sapply(OPT, function(x) x_grid[x])), id="stock")
                     names(policies) <- c("stock", "method", "value")

                     sims <- lapply(OPT, function(D){
                       set.seed(1)
                       lapply(1:100, function(i)
                         ForwardSimulate(f, p, x_grid, h_grid, x0, D, z_g, profit=profit, OptTime=OptTime)
                              )
                       })

                     dat <- melt(sims, id=names(sims[[1]][[1]]))
                     sims_data <- data.table(dat)
                     setnames(sims_data, c("L1", "L2"), c("method", "reps"))
                     # Legend in original ordering please, not alphabetical:
                     sims_data$method = factor(sims_data$method, ordered=TRUE, levels=names(OPT))

                     Profit <- sims_data[, sum(profit), by=c("reps", "method")]
                     tmp <- dcast(Profit, reps ~ method)
                     tmp <- tmp / tmp[,"True"]
                     tmp <- melt(tmp[2:dim(tmp)[2]])
                     tmp$value[tmp$variable == "GP"]
                     })

  yields_dat <- melt(yields)
  names(yields_dat) <- c("replicate", "simulation", "value")

  # Make ids factors, not integers
  yields_dat$replicate <- as.factor(yields_dat$replicate)
  yields_dat$simulation <- as.factor(yields_dat$simulation)

  # definitions of id codes.  In this case the id number is it's own definition.
  rep_ids <-  levels(yields_dat$replicate)
  names(rep_ids) <- rep_ids
  sim_ids <-  levels(yields_dat$simulation)
  names(sim_ids) <- sim_ids

  dat <- data.frame(allee = p[[3]],
                    replicate = yields_dat$replicate,
                    sim = yields_dat$simulation,
                    value = yields_dat$value,
                    noise = sigma_g)
}


text:
library(testthat)
library(nonparametricbayes)

test_check("nonparametricbayes")


text:
library("knitr")
#knit(system.file("examples", "gaussian-process-basics.Rmd", package="nonparametricbayes"))
#knit(system.file("examples", "gp_mcmc_example.Rmd", package="nonparametricbayes"))
## No "Error" should appear
#expect_equal(length(grep("Error", readLines("gp_mcmc_example.md"))), 0)
#expect_equal(length(grep("Error", readLines("gaussian-process-basics.md"))), 0)