%% March 2018
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% AGUJournalTemplate.tex: this template file is for articles formatted with LaTeX
%
% This file includes commands and instructions
% given in the order necessary to produce a final output that will
% satisfy AGU requirements, including customized APA reference formatting.
%
% You may copy this file and give it your
% article name, and enter your text.
%
%
% Step 1: Set the \documentclass
%
% There are two options for article format:
%
% PLEASE USE THE DRAFT OPTION TO SUBMIT YOUR PAPERS.
% The draft option produces double spaced output.
%

%% To submit your paper:
\documentclass[$for(classoption)$$classoption$$sep$,$endfor$]{agujournal2018}
\usepackage{apacite}
\usepackage{url} %this package should fix any errors with URLs in refs.
%%%%%%%
% As of 2018 we recommend use of the TrackChanges package to mark revisions.
% The trackchanges package adds five new LaTeX commands:
%
%  \note[editor]{The note}
%  \annote[editor]{Text to annotate}{The note}
%  \add[editor]{Text to add}
%  \remove[editor]{Text to remove}
%  \change[editor]{Text to remove}{Text to add}
%
% complete documentation is here: http://trackchanges.sourceforge.net/
%%%%%%%


%% Enter journal name below.
%% Choose from this list of Journals:
%
% JGR: Atmospheres
% JGR: Biogeosciences
% JGR: Earth Surface
% JGR: Oceans
% JGR: Planets
% JGR: Solid Earth
% JGR: Space Physics
% Global Biogeochemical Cycles
% Geophysical Research Letters
% Paleoceanography and Paleoclimatology
% Radio Science
% Reviews of Geophysics
% Tectonics
% Space Weather
% Water Resources Research
% Geochemistry, Geophysics, Geosystems
% Journal of Advances in Modeling Earth Systems (JAMES)
% Earth's Future
% Earth and Space Science
% Geohealth
%
% ie, \journalname{Water Resources Research}

\journalname{$journal$}

$if(highlighting-macros)$
% Pandoc syntax highlighting
$highlighting-macros$
$endif$

% tightlist command for lists without linebreak
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}

$if(tables)$
% From pandoc table feature
\usepackage{longtable,booktabs,array}
$if(multirow)$
\usepackage{multirow}
$endif$
\usepackage{calc} % for calculating minipage widths
% Correct order of tables after \paragraph or \subparagraph
\usepackage{etoolbox}
\makeatletter
\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
\makeatother
% Allow footnotes in longtable head/foot
\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
\makesavenoteenv{longtable}
$endif$

$if(csl-refs)$
% Pandoc citation processing
$if(pandoc318)$
%From Pandoc 3.1.8
% definitions for citeproc citations
\NewDocumentCommand\citeproctext{}{}
\NewDocumentCommand\citeproc{mm}{%
  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
\makeatletter
 % allow citations to break across lines
 \let\@cite@ofmt\@firstofone
 % avoid brackets around text for \cite:
 \def\@biblabel#1{}
 \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
\makeatother
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
 {\begin{list}{}{%
  \setlength{\itemindent}{0pt}
  \setlength{\leftmargin}{0pt}
  \setlength{\parsep}{0pt}
  % turn on hanging indent if param 1 is 1
  \ifodd #1
   \setlength{\leftmargin}{\cslhangindent}
   \setlength{\itemindent}{-1\cslhangindent}
  \fi
  % set entry spacing
  \setlength{\itemsep}{#2\baselineskip}}}
 {\end{list}}
$else$$if(pandoc317)$
% definitions for citeproc citations
\NewDocumentCommand\citeproctext{}{}
\NewDocumentCommand\citeproc{mm}{%
  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
% avoid brackets around text for \cite:
\makeatletter
 \def\@biblabel#1{}
 \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
\makeatother
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslentryspacing}
\setlength{\cslentryspacing}{0em}
\usepackage{enumitem}
\newlist{CSLReferences}{itemize}{1}
\setlist[CSLReferences]{label={},
  leftmargin=\cslhangindent,
  itemindent=-1\cslhangindent,
  parsep=\parskip,
  itemsep=\cslentryspacing}
$else$
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslentryspacingunit} % times entry-spacing
\setlength{\cslentryspacingunit}{\parskip}
% for Pandoc 2.8 to 2.10.1
\newenvironment{cslreferences}%
  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
  {\par}
% For Pandoc 2.11+
\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
 {% don't indent paragraphs
  \setlength{\parindent}{0pt}
  % turn on hanging indent if param 1 is 1
  \ifodd #1
  \let\oldpar\par
  \def\par{\hangindent=\cslhangindent\oldpar}
  \fi
  % set entry spacing
  \setlength{\parskip}{#2\cslentryspacingunit}
 }%
 {}
$endif$$endif$
\usepackage{calc}
\newcommand{\CSLBlock}[1]{#1\hfill\break}
\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
$endif$

$for(header-includes)$
$header-includes$
$endfor$

\begin{document}

$for(include-before)$
$include-before$

$endfor$

%% ------------------------------------------------------------------------ %%
%  Title
%
% (A title should be specific, informative, and brief. Use
% abbreviations only if they are defined in the abstract. Titles that
% start with general keywords then specific terms are optimized in
% searches)
%
%% ------------------------------------------------------------------------ %%

% Example: \title{This is a test title}

\title{$title$}

%% ------------------------------------------------------------------------ %%
%
%  AUTHORS AND AFFILIATIONS
%
%% ------------------------------------------------------------------------ %%

% Authors are individuals who have significantly contributed to the
% research and preparation of the article. Group authors are allowed, if
% each author in the group is separately identified in an appendix.)

% List authors by first name or initial followed by last name and
% separated by commas. Use \affil{} to number affiliations, and
% \thanks{} for author notes.
% Additional author notes should be indicated with \thanks{} (for
% example, for current addresses).

% Example: \authors{A. B. Author\affil{1}\thanks{Current address, Antartica}, B. C. Author\affil{2,3}, and D. E.
% Author\affil{3,4}\thanks{Also funded by Monsanto.}}

\authors{
$for(authors)$
$authors.name$
\affil{$authors.affil$}
$if(authors.thanks)$
\thanks{$authors.thanks$}
$endif$
$endfor$
}


% \affiliation{1}{First Affiliation}
% \affiliation{2}{Second Affiliation}
% \affiliation{3}{Third Affiliation}
% \affiliation{4}{Fourth Affiliation}

$for(affiliations)$
\affiliation{$affiliations.number$}{$affiliations.name$}
$endfor$
%(repeat as many times as is necessary)

%% Corresponding Author:
% Corresponding author mailing address and e-mail address:

% (include name and email addresses of the corresponding author.  More
% than one corresponding author is allowed in this LaTeX file and for
% publication; but only one corresponding author is allowed in our
% editorial system.)

% Example: \correspondingauthor{First and Last Name}{email@address.edu}
$for(corresponding_author)$
\correspondingauthor{$corresponding_author.name$}{$corresponding_author.email$}
$endfor$

%% Keypoints, final entry on title page.

%  List up to three key points (at least one is required)
%  Key Points summarize the main points and conclusions of the article
%  Each must be 100 characters or less with no special characters or punctuation

% Example:
% \begin{keypoints}
% \item	List up to three key points (at least one is required)
% \item	Key Points summarize the main points and conclusions of the article
% \item	Each must be 100 characters or less with no special characters or punctuation
% \end{keypoints}

\begin{keypoints}
$for(keypoints)$
\item $keypoints$
$endfor$
\end{keypoints}

%% ------------------------------------------------------------------------ %%
%
%  ABSTRACT
%
% A good abstract will begin with a short description of the problem
% being addressed, briefly describe the new data or analyses, then
% briefly states the main conclusion(s) and how they are supported and
% uncertainties.
%% ------------------------------------------------------------------------ %%

%% \begin{abstract} starts the second page

\begin{abstract}
$abstract$
\end{abstract}
$if(plain_language_summary)$
\noindent{\bf Plain language summary}\vskip-\parskip

\noindent{$plain_language_summary$}
\vskip18pt
$endif$
$body$

$if(bibliography)$
\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
$endif$

$for(include-after)$
$include-after$

$endfor$

\end{document}
