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Update Copernicus publication template to version 6.2 (#366)
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‎DESCRIPTION‎

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Package: rticles
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Type: Package
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Title: Article Formats for R Markdown
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Version: 0.18.1
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Version: 0.18.2
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Authors@R: c(
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person("JJ", "Allaire", role = "aut", email = "[email protected]"),
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person("Yihui", "Xie", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-0645-5666")),

‎NEWS.md‎

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rticles 0.19
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---------------------------------------------------------------------
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- Update Copernicus Publications template to version 6.2 from 2021-01-15. (thanks, @RLumSK, #366)
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rticles 0.18
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---------------------------------------------------------------------

‎inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_6_1.txt‎ renamed to ‎inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_6_2.txt‎

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File: README_copernicus_package_6_1.txt
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File: README_copernicus_package_6_2.txt
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-------------------------------------------------------------------------
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This is a README file for the Copernicus Publications LaTeX Macro Package
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copernicus_package.zip in the version 6.1, 29 October 2020
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copernicus_package.zip in the version 6.2, 15 January 2021
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-------------------------------------------------------------------------
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It consists of several files, each with its separate copyright.
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This specific archive is collected for journals published by
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Copernicus Publications (Copernicus GmbH).
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Copyright (C) 2020 Copernicus GmbH
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Copyright (C) 2021 Copernicus GmbH
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E-mail: [email protected]
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URL: https://publications.copernicus.org
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Content:
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- copernicus.cls: The LaTeX2e class file designed for Copernicus Publications journals. Current Version 9.21, 20 October 2020
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- copernicus.cfg: The configuration file containing journal-specific information used by the class file. Last update 25 June 2020
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- copernicus.bst: The bibliographic style file for BibTeX. Current Version 1.2, September 2017
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- copernicus.cls: The LaTeX2e class file designed for Copernicus Publications journals. Current Version 9.25, 12 January 2021
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- copernicus.cfg: The configuration file containing journal-specific information used by the class file. Last update 15 January 2021
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- copernicus.bst: The bibliographic style file for BibTeX. Current Version 1.3, January 2021
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- pdfscreencop.sty / pdfscreen.sty
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- template.tex: A LaTeX template in journal style.

‎inst/rmarkdown/templates/copernicus/resources/template.tex‎

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% Natural Hazards and Earth System Sciences (nhess)
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% Nonlinear Processes in Geophysics (npg)
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% Ocean Science (os)
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% Polarforschung - Journal of the German Society for Polar Research (polf)
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% Primate Biology (pb)
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% Proceedings of the International Association of Hydrological Sciences (piahs)
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% Scientific Drilling (sd)

‎inst/rmarkdown/templates/copernicus/skeleton/copernicus.bst‎

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%%
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%% This is file `copernicus.bst', version 1.2 (September 2017),
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%% This is file `copernicus.bst', version 1.3 (January 2021),
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%% generated with the docstrip utility.
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%%
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%% The original source files were:
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}
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FUNCTION {format.note}
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{
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url empty$
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doi empty$
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{ url empty$
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'skip$
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{ "\urlprefix\url{" url * "}" * output }
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if$
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}
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'skip$
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{ "\urlprefix\url{" url * "}" * output }
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if$
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note empty$
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{ "" }

‎inst/rmarkdown/templates/copernicus/skeleton/copernicus.cfg‎

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\newif\ifprp \DeclareOption{prp} {\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue \@bartrue \prptrue}
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\newif\ifgtes \DeclareOption{gtes} {\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue \@bartrue \gtestrue}
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\newif\ifcopyediting \DeclareOption{copyediting}{\copyeditingtrue\@noreftrue}
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\newif\ifpolf \DeclareOption{polf}{\@sansseriffacetrue\@sansserifheadertrue\polftrue}
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\newif\ifjbji \DeclareOption{jbji}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\jbjitrue}
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\newif\ifmr \DeclareOption{mr}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\@twostagejnltrue\mrtrue}
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\DeclareOption{mrd}{\@sansseriffacetrue\@sansserifheadertrue\@abstractcenteredtrue\@bartrue\@stage@finalfalse\mrtrue}
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\def\@journalnameshort{JBJI}
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\def\@journalnameshortlower{jbji}
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\def\@journalstartyear{2016}
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\def\@sentence{Published by Copernicus Publications on behalf of the European Bone and Joint Infection Society.}
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\def\@sentence{Published by Copernicus Publications on behalf of of EBJIS and MSIS.}
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\def\@journalurl{https://jbji.copernicus.org/}
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\def\@journallogo{\includegraphics{JBJI_Logo.pdf}}
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\definecolor{textcol}{rgb}{0.161,0.337,0.361}
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\definecolor{bgcol}{rgb}{1,1,1}
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\definecolor{barcol}{rgb}{1.0,1.0,1.0}
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\definecolor{rulecol}{rgb}{0.161,0.337,0.361}
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\fi
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\ifpolf%classical
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\def\@journalname{Polarforschung - Journal of the German Society for Polar Research}
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\def\@journalnameabbreviation{Polarforschung}
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\def\@journalnameshort{POLF}
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\def\@journalnameshortlower{polf}
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\def\@journalstartyear{2021}
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\def\@sentence{Published by Copernicus Publications on behalf of the Deutsche Gesellschaft für Polarforschung e.V.}
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\def\@journalurl{https://polf.copernicus.org}
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\def\@journallogo{\includegraphics{POLF_Logo.pdf}}
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\definecolor{textcol}{rgb}{0.306,0.525,0.682}
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\definecolor{bgcol}{rgb}{1,1,1}
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\definecolor{rulecol}{rgb}{1.0,1.0,1.0}
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\fi
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}

‎inst/rmarkdown/templates/copernicus/skeleton/copernicus.cls‎

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%% -----------------------------------------------------------------
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\NeedsTeXFormat{LaTeX2e}[1995/12/01]
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\ProvidesClass{copernicus}
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[2020/10/29 9.21 Copernicus papers]
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[2021/01/12 9.25 Copernicus papers]
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\frenchspacing
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\clubpenalty10000
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\widowpenalty10000
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\ifdim\wd\z@>100mm\strut\newline\strut\fi
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\fi
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\fi
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\ifx\@published\@undefined\else \hbox{Published:\nobreakspace\@published}\fi
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\ifx\@published\@undefined\else \strut\hbox{Published:\nobreakspace\@published}\fi
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\strut\par\egroup
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\ifx\@howtocite\@empty\else\item[{How to cite:}]\@howtocite\fi
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\ifx\abstractexists\@undefined
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\fi
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\def\@tempa{%
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\def\introductionname{Introduction}%
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\def\authorcontributionname{Author contributions}%
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\def\secabstractname{Kurzfassung}%
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\def\conclusionname{Conclusions}%
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\def\copyrightstatementname{Copyright statement}%
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\def\codeavailabilityname{Code availability}%
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\def\dataavailabilityname{Data availability}%
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\def\ercavailabilityname{Executable research compendium (ERC)}%
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\def\codedataavailabilityname{Code and data availability}%
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\def\sampleavailabilityname{Sample availability}%
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\def\authorcontributionname{Author contributions}%
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\def\competinginterestsname{Competing interests}%
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\def\videosupplementname{Video supplement}%
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\def\dosupplementname{Supplement}%
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\def\copyrightstatementname{Urheberrechtserklärung}%
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\def\codeavailabilityname{Codeverfügbarkeit}%
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\def\dataavailabilityname{Datenverfügbarkeit}%
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\def\ercavailabilityname{Executable research compendium (ERC)}%
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\def\codedataavailabilityname{Code- und Datenverfügbarkeit}%
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\def\sampleavailabilityname{Probenverfügbarkeit}%
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\def\authorcontributionname{Autorenmitwirkung}%
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\def\copyrightstatementname{Affirmation du droit d'auteur}%
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\def\codeavailabilityname{Disponibilité du code}%
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\def\dataavailabilityname{Disponibilité des données}%
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\def\ercavailabilityname{Executable research compendium (ERC)}%
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\def\sampleavailabilityname{Disponibilité des examples}%
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\def\codedataavailabilityname{Disponibilité du code et des données}%
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\def\authorcontributionname{Collaborateurs}%
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\setcounter{reaction}{0}%
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\def\theequation{\thesection\@arabic\c@equation}%
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\def\thereaction{\thesection R\@arabic\c@reaction}%
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\let\c@org@lst\c@listings%
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\let\c@org@eq\c@equation%
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\let\org@theeq\theequation%
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\if@stage@final
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\@addtoreset{table}{section}%
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\setcounter{table}{0}%
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\def\thetable{\thesection\@arabic\c@table}%
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\@addtoreset{listings}{section}%
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\setcounter{listings}{0}%
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\def\thelistings{\thesection\@arabic\c@listings}%
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\fi
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\global\let\old@sect\@sect
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\def\@sect##1##2##3##4##5##6[##7]##8{%
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\ifx\old@sect\@undefined\else\global\let\@sect\old@sect\fi
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\ifx\old@ssect\@undefined\else\global\let\@ssect\old@ssect\fi
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\def\thefigure{\@arabic\c@figure}%
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\def\thelistings{\@arabic\c@listings}%
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\def\thetable{\@arabic\c@table}}
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\IfFileExists{url.sty}
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{\RequirePackage{url}\urlstyle{same}}%
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\g@addto@macro\subfiguresend{\global\let\theHfigure\thefigure@original}
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\g@addto@macro\subtablesend{\global\let\theHtable\thetable@original}}
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{\CopernicusWarningNoLine{Cannot find subfloat.sty; proceeding without it}}
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\RequirePackage[authoryear,round]{natbib}
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\def\NAT@sort{0}\def\NAT@cmprs{0}
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\bibstyle{copernicus}
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\setlength\bibsep\z@
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\let\bibfont\small
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\renewcommand\bibitem{\@ifnextchar[{\@lbibitem}{\@lbibitem[??(????)]}}%]
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\ifx\xmltexversion\@undefined\else
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\NAT@set@cites
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\let\NAT@set@cites\relax
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\fi
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\AtBeginDocument{\let\@citex\NAT@citex}
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\newcommand\urlprefix{}
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\renewenvironment{thebibliography}[1]
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{\bibsection
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\if@secline\leavevmode\vspace*{-\baselineskip}\nobreak\fi
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\parindent\z@
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\bibpreamble
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\bibfont
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\list{\@biblabel{\arabic{NAT@ctr}}}{\@bibsetup{#1}%
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\setcounter{NAT@ctr}{0}}%
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\ifNAT@openbib
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\renewcommand\newblock{\par}
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\else
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\renewcommand\newblock{\hskip .11em \@plus.33em \@minus.07em}%
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\fi
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\sloppy
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%\clubpenalty4000\widowpenalty4000
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\sfcode`\.=1000\relax
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\let\citeN\cite \let\shortcite\cite
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\let\citeasnoun\cite}
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{\def\@noitemerr{%
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\PackageWarning{natbib}{Empty `thebibliography' environment}}%
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\endlist\vskip-\lastskip}
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\def\bibsection{%
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\if@stage@final
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\if@manuscript\newpage\fi
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\pdfbookmark[1]{\refname}{biblio}%
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\fi
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\noappendix\section*{\refname\if@cop@home\ifonline\hypertarget{references}{}\fi\fi}}
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\newif\ifNAT@openbib
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\IfFileExists{natbib.sty}
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{\RequirePackage[authoryear,round]{natbib}
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\bibpunct{(}{)}{;}{a}{,}{,~}
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\def\NAT@sort{0}\def\NAT@cmprs{0}
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\setlength\bibsep\z@
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\let\bibfont\small
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\renewcommand\bibitem{\@ifnextchar[{\@lbibitem}{\@lbibitem[??(????)]}}%]
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\ifx\xmltexversion\@undefined\else
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\NAT@set@cites
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\let\NAT@set@cites\relax
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\fi
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\AtBeginDocument{\let\@citex\NAT@citex}
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\newcommand\urlprefix{}
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\renewenvironment{thebibliography}[1]
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{\bibsection
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\if@secline\leavevmode\vspace*{-\baselineskip}\nobreak\fi
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\parindent\z@
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\bibpreamble
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\bibfont
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\list{\@biblabel{\arabic{NAT@ctr}}}{\@bibsetup{##1}%
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\setcounter{NAT@ctr}{0}}%
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\ifNAT@openbib
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\renewcommand\newblock{\par}
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\else
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\renewcommand\newblock{\hskip .11em \@plus.33em \@minus.07em}%
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\fi
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\sloppy
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% \clubpenalty4000\widowpenalty4000
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\sfcode`\.=1000\relax
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\let\citeN\cite \let\shortcite\cite
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\let\citeasnoun\cite}
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{\def\@noitemerr{%
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\PackageWarning{natbib}{Empty `thebibliography' environment}}%
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\endlist\vskip-\lastskip}
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\def\bibsection{%
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\if@stage@final
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\if@manuscript\newpage\fi
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\pdfbookmark[1]{\refname}{biblio}%
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\fi
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\noappendix\section*{\refname\if@cop@home\ifonline\hypertarget{references}{}\fi\fi}}
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}{\CopernicusWarningNoLine{Cannot find natbib.sty; proceeding without it}}
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\RequirePackage{rotating}
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\def\@rotxdblfloat#1[#2]{%
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\@float{#1}[#2]%
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\long\def\codeavailability#1{\ifx\thesection\theolds\else\noappendix\fi\section{\codeavailabilityname}#1}
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\long\def\dataavailability#1{\ifx\thesection\theolds\else\noappendix\fi\section{\dataavailabilityname}#1}
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\long\def\codedataavailability#1{\ifx\thesection\theolds\else\noappendix\fi\section{\codedataavailabilityname}#1}
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\long\def\ercavailability#1{\ifx\thesection\theolds\else\noappendix\fi\section{\ercavailabilityname}#1}
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\else
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\generateCommand{codeavailability} {\endlist\egroup}
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\generateCommand{dataavailability} {\endlist\egroup}
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\generateCommand{codedataavailability}{\endlist\egroup}
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\generateCommand{ercavailability}{\endlist\egroup}
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\fi
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\generateCommand{authorcontribution}{\endlist\egroup}
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\generateCommand{sampleavailability}{\endlist\egroup}
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\generateCommand{disclaimer} {\endlist\egroup}
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\generateCommand{sistatement} {\endlist\egroup}
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\generateCommand{dosupplement} {\endlist\egroup}
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\generateCommand{financialsupport} {\endlist\egroup}
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\generateCommand{financialsupport} {\endlist\egroup}
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\generateCommand{reviewstatement} {\endlist\egroup}
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\long\def\specialsection#1#2{%
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\expandafter\def\csname specialsection-#1name\endcsname{#1}%
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\expandafter\ifx\csname specialsection-#1name\endcsname\@empty
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\PackageError{copernicus.cls}{\string\specialsection\space needs a heading.}{Make sure that \string\specialsection{}{}\space has two arguments and that the first argument contains a heading.}%
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\else
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\generateCommand{specialsection-#1} {\endlist\egroup}%
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\csname specialsection-#1\endcsname{#2}%
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\fi}
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\generateCommand{acknowledgement} {} \def\endacknowledgement{\endlist\egroup}
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\generateCommand{acknowledgements} {} \def\endacknowledgements{\endlist\egroup}

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