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Commit 39986221 authored by Marc Oudart's avatar Marc Oudart
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Continuité module 2 et création fichier template RMarkdown

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Test templates articles frontiers/Test templates articles frontiers.Rmd 0 → 100644
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---
title: "Article Title"
runtitle: "Short Title"
documentclass: frontiersSCNS # or frontiersHLTH, or frontiersFPHY
author:
- name: First Author
affiliation: '1'
etal: LASTNAME # First author's last name.
- name: Co-Author
affiliation: '2'
- name: Co-Author
affiliation: '1,3'
email: email@uni.edu # Indicates corresponding Author
institution: Laboratory X, Institute X, Department X, Organization X
street: Street X
city: City X
state: State XX # only USA, Australia, Canada
zip: Zip Code X
country: Country X
affiliation:
- id: '1'
department: Department X
institution: Institution X
city: City X
state: State XX # only USA, Australia, Canada
country: Country X
- id: '2'
department: Department X
institution: Institution X
city: City X
state: State XX # only USA, Australia, Canada
country: Country X
- id: '3'
department: Department X
institution: Institution X
city: City X
state: State XX # only USA, Australia, Canada
country: Country X
output: rticles::frontiers_article
csl: frontiers.csl
bibliography: test.bib
---
\begin{abstract}
Abstract length and content varies depending on article type. Refer to
\url{http://www.frontiersin.org/about/AuthorGuidelines} for abstract requirement
and length according to article type.
%All article types: you may provide up to 8 keywords; at least 5 are mandatory.
\tiny
\keyFont{ \section{Keywords:} Text Text Text Text Text Text Text Text }
\end{abstract}
# Introduction {-}
Cite fancy references [@Neuro2013]. As demonstrated in @Gene2012, citations can
also be automatically reference. Multiple references are separated by semicolons
[@Neuro2013; @Neurobot2013].
# Results {-}
<!-- Comments should be HTML-style comments -->
## Subsection 1 {-}
You can use `R` chunks directly to plot graphs.
```{r graph, echo = TRUE, message=FALSE, fig.show = "hide"}
x <- 0:100
set.seed(999)
y <- 2 * (x + rnorm(length(x), sd = 3) + 3)
plot(x, y)
```
## Subsection 2 {-}
Frontiers requires figures to be submitted individually, in the same order as
they are referred to in the manuscript. Figures will then be automatically
embedded at the bottom of the submitted manuscript. Kindly ensure that each
table and figure is mentioned in the text and in numerical order. Permission
must be obtained for use of copyrighted material from other sources (including
the web). Please note that it is compulsory to follow figure instructions.
Figures which are not according to the guidelines will cause substantial delay
during the production process.
# Discussion
# Disclosure/Conflict-of-Interest Statement {-}
<!--
Frontiers follows the recommendations by the International Committee of Medical
Journal Editors (http://www.icmje.org/ethical_4conflicts.html) which require
that all financial, commercial or other relationships that might be perceived by
the academic community as representing a potential conflict of interest must be
disclosed. If no such relationship exists, authors will be asked to declare that
the research was conducted in the absence of any commercial or financial
relationships that could be construed as a potential conflict of interest. When
disclosing the potential conflict of interest, the authors need to address the
following points:
- Did you or your institution at any time receive payment or services from a
third party for any aspect of the submitted work?
- Please declare financial relationships with entities that could be perceived
to influence, or that give the appearance of potentially influencing, what
you wrote in the submitted work.
- Please declare patents and copyrights, whether pending, issued, licensed
and/or receiving royalties relevant to the work.
- Please state other relationships or activities that readers could perceive to
have influenced, or that give the appearance of potentially influencing, what
you wrote in the submitted work.
-->
The authors declare that the research was conducted in the absence of any
commercial or financial relationships that could be construed as a potential
conflict of interest.
# Author Contributions {-}
<!--
When determining authorship the following criteria should be observed:
- Substantial contributions to the conception or design of the work; or the
acquisition, analysis, or interpretation of data for the work; AND
- Drafting the work or revising it critically for important intellectual
content; AND
- Final approval of the version to be published ; AND
- Agreement to be accountable for all aspects of the work in ensuring that
questions related to the accuracy or integrity of any part of the work are
appropriately investigated and resolved.
Contributors who meet fewer than all 4 of the above criteria for authorship
should not be listed as authors, but they should be acknowledged.
(http://www.icmje.org/roles_a.html)
-->
The statement about the authors and contributors can be up to several sentences
long, describing the tasks of individual authors referred to by their initials
and should be included at the end of the manuscript before the References
section.
# Acknowledgments {-}
Funding:
# Supplemental Data
Supplementary Material should be uploaded separately on submission, if there are
Supplementary Figures, please include the caption in the same file as the
figure. LaTeX Supplementary Material templates can be found in the Frontiers
LaTeX folder
# References
A reference list should be automatically created here. However it won't. Pandoc
will place the list of references at the end of the document instead. There are
no convenient solution for now to force Pandoc to do otherwise. The easiest way
to get around this problem is to edit the LaTeX file created by Pandoc before
compiling it again using the traditional LaTeX commands.
# Figures {-}
```{r, Figure-1, ref.label = "graph", results = "hide", echo = FALSE, message = FALSE, fig.height=4, fig.width=4, fig.align='center', fig.cap='Figure caption', out.width = "85mm", out.height = "85mm"}
# You can also refer to code chunks from above to place figures at the bottom.
```
Test templates articles frontiers/Test-templates-articles-frontiers.log 0 → 100644
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Babel <3.15> and hyphenation patterns for 75 language(s) loaded.
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defining Unicode char U+011E (decimal 286)
defining Unicode char U+011F (decimal 287)
defining Unicode char U+0120 (decimal 288)
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defining Unicode char U+0122 (decimal 290)
defining Unicode char U+0123 (decimal 291)
defining Unicode char U+0124 (decimal 292)
defining Unicode char U+0125 (decimal 293)
defining Unicode char U+0128 (decimal 296)
defining Unicode char U+0129 (decimal 297)
defining Unicode char U+012A (decimal 298)
defining Unicode char U+012B (decimal 299)
defining Unicode char U+012C (decimal 300)
defining Unicode char U+012D (decimal 301)
defining Unicode char U+012E (decimal 302)
defining Unicode char U+012F (decimal 303)
defining Unicode char U+0130 (decimal 304)
defining Unicode char U+0131 (decimal 305)
defining Unicode char U+0132 (decimal 306)
defining Unicode char U+0133 (decimal 307)
defining Unicode char U+0134 (decimal 308)
defining Unicode char U+0135 (decimal 309)
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defining Unicode char U+013B (decimal 315)
defining Unicode char U+013C (decimal 316)
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)
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Test templates articles frontiers/Test-templates-articles-frontiers.tex 0 → 100644
View file @ 39986221
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This is just an example/guide for you to refer to when submitting manuscripts to Frontiers, it is not mandatory to use Frontiers .cls files nor frontiers.tex %
% This will only generate the Manuscript, the final article will be typeset by Frontiers after acceptance.
% %
% %
% When submitting your files, remember to upload this *tex file, the pdf generated with it, the *bib file (if bibliography is not within the *tex) and all the figures.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Version 3.4 Generated 2018/06/15 %%%
%%% You will need to have the following packages installed: datetime, fmtcount, etoolbox, fcprefix, which are normally inlcuded in WinEdt. %%%
%%% In http://www.ctan.org/ you can find the packages and how to install them, if necessary. %%%
\documentclass[utf8]{frontiersSCNS}
%\setcitestyle{square} % for Physics and Applied Mathematics and Statistics articles
\usepackage{url,hyperref,lineno,microtype,subcaption}
\usepackage[onehalfspacing]{setspace}
\linenumbers
% BELOW TAKEN FROM rticles plos template
%
% amsmath package, useful for mathematical formulas
\usepackage{amsmath}
% amssymb package, useful for mathematical symbols
\usepackage{amssymb}
% hyperref package, useful for hyperlinks
\usepackage{hyperref}
% graphicx package, useful for including eps and pdf graphics
% include graphics with the command \includegraphics
\usepackage{graphicx}
% Sweave(-like)
\usepackage{fancyvrb}
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
\newenvironment{Schunk}{}{}
\DefineVerbatimEnvironment{Code}{Verbatim}{}
\DefineVerbatimEnvironment{CodeInput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{CodeOutput}{Verbatim}{}
\newenvironment{CodeChunk}{}{}
% cite package, to clean up citations in the main text. Do not remove.
\usepackage{cite}
\usepackage{color}
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
% Below is from frontiers
%
\bibliographystyle{frontiersinSCNS}
% Use doublespacing - comment out for single spacing
%\usepackage{setspace}
%\doublespacing
% Leave a blank line between paragraphs instead of using \\
\def\keyFont{\fontsize{8}{11}\helveticabold }
%% ** EDIT HERE **
%% PLEASE INCLUDE ALL MACROS BELOW
%% END MACROS SECTION
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newenvironment{cslreferences}%
{\setlength{\parindent}{0pt}%
\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces}%
{\par}
\usepackage{color}
\usepackage{fancyvrb}
\newcommand{\VerbBar}{|}
\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\usepackage{framed}
\definecolor{shadecolor}{RGB}{248,248,248}
\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
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\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\def\Authors{
First Author\,\textsuperscript{1},
Co-Author\,\textsuperscript{2},
Co-Author\,\textsuperscript{1,3*}}
\def\Address{
\textsuperscript{1} Department X, Institution X, City X, State
XX, Country X
\textsuperscript{2} Department X, Institution X, City X, State
XX, Country X
\textsuperscript{3} Department X, Institution X, City X, State
XX, Country X
}
\def\firstAuthorLast{LASTNAME {et~al.}}
\def\corrAuthor{Co-Author}\def\corrAddress{Laboratory X, Institute X,
Department X, Organization X\\Street X\\City X, State XX, Zip Code
X Country
X}\def\corrEmail{\href{mailto:email@uni.edu}{\nolinkurl{email@uni.edu}}}
\begin{document}
\onecolumn
\firstpage{1}
\title[Short Title]{Article Title}
\author[\firstAuthorLast]{\Authors}
\address{} %This field will be automatically populated
\correspondance{} %This field will be automatically populated
\extraAuth{}% If there are more than 1 corresponding author, comment this line and uncomment the next one.
%\extraAuth{corresponding Author2 \\ Laboratory X2, Institute X2, Department X2, Organization X2, Street X2, City X2 , State XX2 (only USA, Canada and Australia), Zip Code2, X2 Country X2, email2@uni2.edu}
\maketitle
\begin{abstract}
Abstract length and content varies depending on article type. Refer to
\url{http://www.frontiersin.org/about/AuthorGuidelines} for abstract requirement
and length according to article type.
%All article types: you may provide up to 8 keywords; at least 5 are mandatory.
\tiny
\keyFont{ \section{Keywords:} Text Text Text Text Text Text Text Text }
\end{abstract}
\hypertarget{introduction}{%
\section*{Introduction}\label{introduction}}
\addcontentsline{toc}{section}{Introduction}
Cite fancy references (LastName1 et al., 2013). As demonstrated in
OtherAuthor and Coauthor (2012), citations can also be automatically
reference. Multiple references are separated by semicolons (LastName1 et
al., 2013; Author4 and Author5, 2013).
\hypertarget{results}{%
\section*{Results}\label{results}}
\addcontentsline{toc}{section}{Results}
\hypertarget{subsection-1}{%
\subsection*{Subsection 1}\label{subsection-1}}
\addcontentsline{toc}{subsection}{Subsection 1}
You can use \texttt{R} chunks directly to plot graphs.
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{x \textless{}{-}}\StringTok{ }\DecValTok{0}\OperatorTok{:}\DecValTok{100}
\KeywordTok{set.seed}\NormalTok{(}\DecValTok{999}\NormalTok{)}
\NormalTok{y \textless{}{-}}\StringTok{ }\DecValTok{2} \OperatorTok{*}\StringTok{ }\NormalTok{(x }\OperatorTok{+}\StringTok{ }\KeywordTok{rnorm}\NormalTok{(}\KeywordTok{length}\NormalTok{(x), }\DataTypeTok{sd =} \DecValTok{3}\NormalTok{) }\OperatorTok{+}\StringTok{ }\DecValTok{3}\NormalTok{)}
\KeywordTok{plot}\NormalTok{(x, y)}
\end{Highlighting}
\end{Shaded}
\hypertarget{subsection-2}{%
\subsection*{Subsection 2}\label{subsection-2}}
\addcontentsline{toc}{subsection}{Subsection 2}
Frontiers requires figures to be submitted individually, in the same
order as they are referred to in the manuscript. Figures will then be
automatically embedded at the bottom of the submitted manuscript. Kindly
ensure that each table and figure is mentioned in the text and in
numerical order. Permission must be obtained for use of copyrighted
material from other sources (including the web). Please note that it is
compulsory to follow figure instructions. Figures which are not
according to the guidelines will cause substantial delay during the
production process.
\hypertarget{discussion}{%
\section{Discussion}\label{discussion}}
\hypertarget{disclosureconflict-of-interest-statement}{%
\section*{Disclosure/Conflict-of-Interest
Statement}\label{disclosureconflict-of-interest-statement}}
\addcontentsline{toc}{section}{Disclosure/Conflict-of-Interest
Statement}
The authors declare that the research was conducted in the absence of
any commercial or financial relationships that could be construed as a
potential conflict of interest.
\hypertarget{author-contributions}{%
\section*{Author Contributions}\label{author-contributions}}
\addcontentsline{toc}{section}{Author Contributions}
The statement about the authors and contributors can be up to several
sentences long, describing the tasks of individual authors referred to
by their initials and should be included at the end of the manuscript
before the References section.
\hypertarget{acknowledgments}{%
\section*{Acknowledgments}\label{acknowledgments}}
\addcontentsline{toc}{section}{Acknowledgments}
Funding:
\hypertarget{supplemental-data}{%
\section{Supplemental Data}\label{supplemental-data}}
Supplementary Material should be uploaded separately on submission, if
there are Supplementary Figures, please include the caption in the same
file as the figure. LaTeX Supplementary Material templates can be found
in the Frontiers LaTeX folder
\hypertarget{references}{%
\section{References}\label{references}}
A reference list should be automatically created here. However it won't.
Pandoc will place the list of references at the end of the document
instead. There are no convenient solution for now to force Pandoc to do
otherwise. The easiest way to get around this problem is to edit the
LaTeX file created by Pandoc before compiling it again using the
traditional LaTeX commands.
\hypertarget{figures}{%
\section*{Figures}\label{figures}}
\addcontentsline{toc}{section}{Figures}
\begin{figure}
{\centering \includegraphics[width=85mm,height=85mm]{Test-templates-articles-frontiers_files/figure-latex/Figure-1-1}
}
\caption{Figure caption}\label{fig:Figure-1}
\end{figure}
\hypertarget{refs}{}
\begin{cslreferences}
\leavevmode\hypertarget{ref-Neurobot2013}{}%
Author4, N., and Author5, N. (2013). Title of the article.
\emph{Frontiers in Neurorobotics} 7.
doi:\href{https://doi.org/10.3389/fnbot.2013.56789}{10.3389/fnbot.2013.56789}.
\leavevmode\hypertarget{ref-Neuro2013}{}%
LastName1, A., LastName2, A., and LastName2, A. (2013). Article title.
\emph{Frontiers in Neuroscience} 30, 10127--10134.
doi:\href{https://doi.org/10.3389/fnins.2013.12345}{10.3389/fnins.2013.12345}.
\leavevmode\hypertarget{ref-Gene2012}{}%
OtherAuthor, N., and Coauthor, N. S. (2012). Article title.
\emph{Frontiers in Genetics} 30, 16417--16418.
doi:\href{https://doi.org/10.3389/fgene.2012.54321}{10.3389/fgene.2012.54321}.
\end{cslreferences}
\end{document}
Test templates articles frontiers/frontiers.csl 0 → 100644
View file @ 39986221
<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
<info>
<title>Frontiers journals</title>
<id>http://www.zotero.org/styles/frontiers</id>
<link href="http://www.zotero.org/styles/frontiers" rel="self"/>
<link href="http://www.frontiersin.org/about/AuthorGuidelines" rel="documentation"/>
<author>
<name>Sebastian Karcher</name>
</author>
<contributor>
<name>Julian Onions</name>
<email>julian.onions@gmail.com</email>
</contributor>
<category citation-format="author-date"/>
<category field="generic-base"/>
<summary>Style for the Open Access Frontiers in ... Journals</summary>
<updated>2012-09-27T22:06:38+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<macro name="editor">
<names variable="editor" delimiter=", ">
<label form="short" prefix=", "/>
<name and="text" initialize-with=". " delimiter=", " prefix=" "/>
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<macro name="author">
<names variable="author">
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<label form="short" prefix=" "/>
<substitute>
<names variable="editor"/>
<text variable="title"/>
</substitute>
</names>
</macro>
<macro name="author-short">
<names variable="author">
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<substitute>
<names variable="editor"/>
<names variable="translator"/>
<text variable="title"/>
</substitute>
</names>
</macro>
<macro name="access">
<choose>
<if variable="DOI">
<text variable="DOI" prefix="doi:"/>
</if>
<else-if variable="URL">
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<text variable="URL"/>
<group prefix=" [" suffix="]">
<text term="accessed" text-case="capitalize-first" suffix=" "/>
<date variable="accessed">
<date-part name="month" suffix=" "/>
<date-part name="day" suffix=", "/>
<date-part name="year"/>
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</macro>
<macro name="title">
<choose>
<if type="book">
<text variable="title" font-style="italic" suffix="."/>
</if>
<else-if type="chapter">
<text variable="title" quotes="true" suffix=","/>
</else-if>
<else>
<text variable="title" suffix="."/>
</else>
</choose>
</macro>
<macro name="publisher">
<group delimiter=": ">
<text variable="publisher-place"/>
<text variable="publisher"/>
</group>
</macro>
<macro name="year-date">
<date variable="issued">
<date-part name="year"/>
</date>
</macro>
<macro name="edition">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition" suffix="."/>
</else>
</choose>
</macro>
<citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" collapse="year">
<layout prefix="(" suffix=")" delimiter="; ">
<group delimiter=", ">
<text macro="author-short"/>
<text macro="year-date"/>
<text variable="locator"/>
</group>
</layout>
</citation>
<bibliography hanging-indent="true" et-al-min="11" et-al-use-first="10">
<sort>
<key macro="author"/>
<key variable="title"/>
</sort>
<layout suffix=".">
<text macro="author"/>
<date variable="issued" prefix=" (" suffix=").">
<date-part name="year"/>
</date>
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<group delimiter=" " prefix=" ">
<text macro="title"/>
<text macro="edition"/>
<text macro="editor"/>
<text macro="publisher"/>
</group>
</if>
<else-if type="chapter paper-conference" match="any">
<group delimiter=" " prefix=" ">
<text macro="title"/>
<text term="in"/>
<text variable="container-title" font-style="italic"/>
<text variable="collection-title" suffix="."/>
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<text macro="editor"/>
<group suffix=".">
<text macro="publisher" prefix=" (" suffix=")"/>
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<text variable="page"/>
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<group delimiter=" ">
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<text variable="volume"/>
</group>
<text variable="page"/>
</group>
</else>
</choose>
<text prefix=" " macro="access"/>
</layout>
</bibliography>
</style>
Test templates articles frontiers/frontiersFPHY.cls 0 → 100644
View file @ 39986221
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\def\large{\@setfontsize\large{13pt}{14pt}}
\def\Large{\@setfontsize\Large{14pt}{16}}
\def\LARGE{\@setfontsize\LARGE{15pt}{17pt}}
\def\huge{\@setfontsize\huge{22pt}{22pt}}
\def\Huge{\@setfontsize\Huge{30pt}{30pt}}
\DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl}
\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc}
% Line spacing
\setlength\lineskip{1\p@}
\setlength\normallineskip{1\p@}
\renewcommand\baselinestretch{}
% Set inter-para skips
\setlength\smallskipamount{3\p@ \@plus 1\p@ \@minus 1\p@}
\setlength\medskipamount{6\p@ \@plus 2\p@}
\setlength\bigskipamount{12\p@ \@plus 4\p@ \@minus 4\p@}
% Paragraph dimensions and inter-para spacing
\setlength\parindent{3mm}
\setlength{\parskip}{\medskipamount}
% Page break penalties
\@lowpenalty 51
\@medpenalty 151
\@highpenalty 301
% Disallow widows and orphans
\clubpenalty 10000
\widowpenalty 10000
% Disable page breaks before equations, allow pagebreaks after
% equations and discourage widow lines before equations.
\displaywidowpenalty 100
\predisplaypenalty 10000
\postdisplaypenalty 2500
% Allow breaking the page in the middle of a paragraph
\interlinepenalty 0
% Disallow breaking the page after a hyphenated line
\brokenpenalty 10000
% Hyphenation; don't split words into less than three characters
\lefthyphenmin=3
\righthyphenmin=3
%
% Set page layout dimensions
%
\setlength\headheight{16\p@} % height of running head
\setlength\topmargin{1.3pc} % head margin
\addtolength\topmargin{-1in} % subtract out the 1 inch driver margin
\setlength\topskip{10\p@} % height of first line of text
\setlength\headsep{19\p@} % space below running head --
\setlength\footskip{34\p@} % space above footer line
\setlength\maxdepth{1\topskip} % pages can be short or deep by half a line?
\setlength\textwidth{42pc} % text measure excluding margins
\setlength\textheight{56\baselineskip} % 54 lines on a full page,
\addtolength\textheight{\topskip} % including the first
% line on the page
% Set the margins
\setlength\marginparsep{3\p@}
\setlength\marginparpush{3\p@}
\setlength\marginparwidth{35\p@}
\setlength\oddsidemargin{4.5pc}
\addtolength\oddsidemargin{-1in} % subtract out the 1 inch driver margin
\setlength\@tempdima{\paperwidth}
\addtolength\@tempdima{-\textwidth}
\addtolength\@tempdima{-4.5pc}
\setlength\evensidemargin{\@tempdima}
\addtolength\evensidemargin{-1in}
\setlength\columnsep{1.5pc} % space between columns for double-column text
\setlength\columnseprule{0\p@} % width of rule between two columns
% Footnotes
\setlength\footnotesep{9\p@} % space between footnotes
% space between text and footnote
\setlength{\skip\footins}{12\p@ \@plus 6\p@ \@minus 1\p@}
% Float placement parameters
% The total number of floats that can be allowed on a page.
\setcounter{totalnumber}{10}
% The maximum number of floats at the top and bottom of a page.
\setcounter{topnumber}{5}
\setcounter{bottomnumber}{5}
% The maximum part of the top or bottom of a text page that can be
% occupied by floats. This is set so that at least four lines of text
% fit on the page.
\renewcommand\topfraction{.9}
\renewcommand\bottomfraction{.9}
% The minimum amount of a text page that must be occupied by text.
% This should accomodate four lines of text.
\renewcommand\textfraction{.06}
% The minimum amount of a float page that must be occupied by floats.
\renewcommand\floatpagefraction{.94}
% The same parameters repeated for double column output
\renewcommand\dbltopfraction{.9}
\renewcommand\dblfloatpagefraction{.9}
% Space between floats
\setlength\floatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
% Space between floats and text
\setlength\textfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
% Space above and below an inline figure
\setlength\intextsep {18\p@ \@plus 2\p@ \@minus 2\p@}
% For double column floats
\setlength\dblfloatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
\setlength\dbltextfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
% Space left at top, bottom and inbetween floats on a float page.
\setlength\@fptop{0\p@} % no space above float page figures
\setlength\@fpsep{12\p@ \@plus 1fil}
\setlength\@fpbot{0\p@}
% The same for double column
\setlength\@dblfptop{0\p@}
\setlength\@dblfpsep{12\p@ \@plus 1fil}
\setlength\@dblfpbot{0\p@}
% Override settings in mathtime back to TeX defaults
\DeclareMathSizes{5} {5} {5} {5}
\DeclareMathSizes{6} {6} {5} {5}
\DeclareMathSizes{7} {7} {5} {5}
\DeclareMathSizes{8} {8} {6} {5}
\DeclareMathSizes{9} {9} {6.5} {5}
\DeclareMathSizes{10} {10} {7.5} {5}
\DeclareMathSizes{12} {12} {9} {7}
% Page styles
\def\ps@headings
{%
\def\@oddfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
\hbox to \textwidth{\helveticabold\small {Frontiers}\hfill \thepage}%
}}%
\def\@evenfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
\hbox to \textwidth{\helvetica\small {\color{red}This is a provisional file, not the final typeset article}\hfill\helveticabold\color{black}\thepage}%
}}%
\def\@evenhead{\vbox{\hbox to \textwidth{\fontsize{11}{10}\selectfont
\helveticabold{\fontshape{it}\selectfont
\strut\firstAuthorLast}\hfill\strut\rightmark}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
\def\@oddhead{\vbox{\hbox to \textwidth{\fontsize{11}{10}\selectfont
\helveticabold{\fontshape{it}\selectfont
\strut\firstAuthorLast}\hfill\strut\rightmark}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
\def\titlemark##1{\markboth{##1}{##1}}%
\def\authormark##1{\gdef\leftmark{##1}}%
}
\def\ps@opening
{%
\def\@oddfoot{\vbox to 13\p@{\hbox{\rule{\textwidth}{1\p@}}\vss
\hbox to \textwidth{\helvetica
\fontsize{7}{9}\fontshape{n}\selectfont \space %
\hfill\small\helveticabold\thepage}%
}}%
\def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}{1\p@}\vss
\hbox to \textwidth{\helvetica\thepage\hfill
\fontsize{7}{9}\fontshape{n}\selectfont \space }%
}}%
\let\@evenhead\relax
\let\@oddhead\relax}
% Page range
\newif\iflastpagegiven \lastpagegivenfalse
\newcommand\firstpage[1]{%
\gdef\@firstpage{#1}%
\ifnum\@firstpage>\c@page
\setcounter{page}{#1}%
\ClassWarning{BIO}{Increasing pagenumber to \@firstpage}%
\else \ifnum\@firstpage<\c@page
\ClassWarning{BIO}{Firstpage lower than pagenumber}\fi\fi
\xdef\@firstpage{\the\c@page}%
}
\def\@firstpage{1}
\def\pagenumbering#1{%
\global\c@page \@ne
\gdef\thepage{\csname @#1\endcsname \c@page}%
\gdef\thefirstpage{%
\csname @#1\endcsname \@firstpage}%
\gdef\thelastpage{%
\csname @#1\endcsname \@lastpage}%
}
\newcommand\lastpage[1]{\xdef\@lastpage{#1}%
\global\lastpagegiventrue}
\def\@lastpage{0}
\def\setlastpage{\iflastpagegiven\else
\edef\@tempa{@lastpage@}%
\expandafter
\ifx \csname \@tempa \endcsname \relax
\gdef\@lastpage{0}%
\else
\xdef\@lastpage{\@nameuse{@lastpage@}}%
\fi
\fi }
\def\writelastpage{%
\iflastpagegiven \else
\immediate\write\@auxout%
{\string\global\string\@namedef{@lastpage@}{\the\c@page}}%
\fi
}
\def\thepagerange{%
\ifnum\@lastpage =0 {\ \bf ???} \else
\ifnum\@lastpage = \@firstpage \ \thefirstpage\else
\thefirstpage--\thelastpage \fi\fi}
\AtBeginDocument{\setlastpage
\pagenumbering{arabic}%
}
\AtEndDocument{%
\writelastpage
\if@final
\clearemptydoublepage
\else
\clearpage
\fi}
%
% Sectional units
%
% Counters
\newcounter{section}
\newcounter{subsection}[section]
\newcounter{subsubsection}[subsection]
\newcounter{paragraph}[subsubsection]
\newcounter{subparagraph}[paragraph]
\newcounter{figure}
\newcounter{subfigure}
\newcounter{table}
% Form of the numbers
\newcommand\thepage{\arabic{page}}
\renewcommand\thesection{\arabic{section}}
\renewcommand\thesubsection{{\thesection.\arabic{subsection}}}
\renewcommand\thesubsubsection{{\thesubsection.\arabic{subsubsection}}}
\renewcommand\theparagraph{\thesubsubsection.\arabic{paragraph}}
\renewcommand\thesubparagraph{\theparagraph.\arabic{subparagraph}}
\renewcommand\theequation{\arabic{equation}}
% Form of the words
\newcommand\contentsname{Contents}
\newcommand\listfigurename{List of Figures}
\newcommand\listtablename{List of Tables}
\newcommand\partname{Part}
\newcommand\appendixname{Appendix}
\newcommand\abstractname{Abstract}
\newcommand\refname{References}
\newcommand\bibname{References}
\newcommand\indexname{Index}
\newcommand\figurename{Figure}
\newcommand\tablename{Table}
% Clearemptydoublepage should really clear the running heads too
\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}
% Frontmatter, mainmatter and backmatter
\newif\if@mainmatter \@mainmattertrue
\newcommand\frontmatter{%
\clearpage
\@mainmatterfalse
\pagenumbering{roman}}
\newcommand\mainmatter{%
\clearpage
\@mainmattertrue
\pagenumbering{arabic}}
\newcommand\backmatter{%
\clearpage
\@mainmatterfalse}
\newdateformat{mydate}{\THEDAY \ \monthname[ \THEMONTH] \THEYEAR}
\newdateformat{mydate2}{\monthname[\THEMONTH] \THEYEAR}
%********
% TITLE *
%********
\newlength{\dropfromtop}
\setlength{\dropfromtop}{\z@}
% Application Notes
\newif\if@appnotes
\newcommand{\application}{%
% \setlength{\dropfromtop}{-2.25pc}%
\global\@appnotestrue}
% Short Title is for the Title of the Article
% Title is for the Title of the Journal
\long\def\title{\@ifnextchar[{\short@title}{\@@title}}
\def\short@title[#1]{\titlemark{#1}\@@@title}
\def\@@title#1{\authormark{#1}\@@@title{#1}}
\long\def\@@@title#1{\gdef\@title{#1}}
\long\def\author{\@ifnextchar[{\short@uthor}{\@uthor}}
\def\short@uthor[#1]{\authormark{#1}\@@author}
\def\@uthor#1{\authormark{#1}\@@author{#1}}
\long\def\@@author#1{\gdef\@author{#1}}
\def\vol#1{\global\def\@vol{#1}}
\def\issue#1{\global\def\@issue{#1}}
\def\address#1{\global\def\@issue{#1}}
\def\history#1{\global\def\@history{#1}}
\def\correspondance#1{\global\def\@correspondance{#1}}
\def\extraAuth#1{\global\def\@extraAuth{#1}}
\def\address#1{\global\def\@address{#1}}
\def\date#1{\gdef\@date{#1}}
% To define special colors
%***********
% Colors *
%***********
% Other colors
\definecolor{black}{cmyk}{0, 0, 0, 1}
\definecolor{gray}{cmyk}{0, 0, 0, 0.25}
\definecolor{darkgray}{cmyk}{0, 0, 0, 0.5}
\newlength{\extraspace}
\setlength{\extraspace}{\z@}
\newcommand\maketitle{\par
\begingroup
\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
\long\def\@makefntext##1{\parindent 3mm\noindent
% \@textsuperscript{\normalfont\@thefnmark}\raggedright##1}%
\@textsuperscript{\normalfont\@thefnmark}##1}%
\if@twocolumn
\ifnum \col@number=\@ne
\@maketitle
\else
\twocolumn[\@maketitle]%
\fi
\else
\newpage
\global\@topnum\z@ % Prevents figures from going at top of page.
\@maketitle
\fi
\thispagestyle{opening}\@thanks
\endgroup
\setcounter{footnote}{0}%
\global\let\thanks\relax
\global\let\maketitle\relax
\global\let\@maketitle\relax
\global\let\@address\@empty
\global\let\@history\@empty
\global\let\@extraAuth\@empty
\global\let\@topic\@empty
\global\let\@thanks\@empty
\global\let\@author\@empty
\global\let\@date\@empty
\global\let\@title\@empty
\global\let\@pubyear\@empty
\global\let\address\relax
\global\let\topic\relax
\global\let\extraAuth\relax
\global\let\title\relax
\global\let\author\relax
\global\let\date\relax
\global\let\pubyear\relax
\global\let\@copyrightline\@empty
\global\let\and\relax
\@afterindentfalse\@afterheading
}
\newlength{\aboveskipchk}%for checking oddpage or evenpage top skip
\setlength{\aboveskipchk}{\z@}%
\def\@maketitle{%
\let\footnote\thanks
\clearemptydoublepage
\checkoddpage\ifcpoddpage\setlength{\aboveskipchk}{-7pc}\else\setlength{\aboveskipchk}{-3pc}\fi%for checking oddpage or evenpage top skip%%
\vspace*{\aboveskipchk}%
\vspace{\dropfromtop}%
\hbox to \textwidth{%
\parbox[t]{15pc}{%
\helvetica
\hfil
\flushleft \includegraphics[width=12pc,angle=0]{./logo1.pdf}
}}
\rule{\textwidth}{1\p@}\par%
\helvetica
\hbox to \textwidth{%
\parbox[t]{36.5pc}{%
\vspace*{1sp}
{\helveticabold\fontsize{20}{21}\color{black}\selectfont\raggedright \@title \par}%
\vspace{4.5\p@}
{\helveticabold\fontsize{12}{15}\selectfont\raggedright \@author \par}%
\vspace{4\p@}
{\helvetica\fontsize{12}{12}\selectfont\raggedright\slshape\@address \Address \\ \par}%
\vspace{6\p@}
{\helvetica\fontsize{12}{10}\selectfont\raggedright {Correspondence*:\\ }\@correspondance \corrAuthor \\ \corrEmail \par}
\vspace{4\p@}
{\helvetica\fontsize{12}{12}\selectfont\raggedright\@extraAuth \par}%
\vspace{8\p@}
}%
}
\vspace{14.5\p@}%
}
%***********
% Abstract *
%***********
\newcommand{\absection}[1]{%
\par\noindent{\bfseries #1}\space\ignorespaces}
\newenvironment{abstract}{%
\begingroup
\let\section\absection
\fontfamily{\sfdefault}\fontsize{12}{12}\sffamily\selectfont
{\fontseries{b}\selectfont ABSTRACT}\par}
{\endgroup\smallskip\@afterheading\@afterindentfalse\vskip 12pt plus -2pt minus 2pt}
% Section macros
% Lowest level heading that takes a number by default
\setcounter{secnumdepth}{5}
\renewcommand{\@seccntformat}[1]{\csname the#1\endcsname\quad}
\def\section{%
\@startsection{section}{1}{\z@}
{-10\p@ plus -3\p@}{3\p@}
{\reset@font\raggedright\helveticabold\fontsize{13}{13}\color{black}\selectfont\MakeUppercase}}
\def\subsection{%
\@startsection{subsection}{2}{\z@}
{2\p@ plus -1\p@}{2\p@}
{\reset@font\raggedright\mathversion{bold}\helveticabold\fontsize{11.5}{12}}}
\def\subsubsection{%
\@startsection{subsubsection}{3}{\z@}
{1\p@ plus -1\p@}{1\p@}
{\reset@font\raggedright\mathversion{bold}\helvetica\fontsize{11.5}{12}}}
\def\paragraph{%
\@startsection{paragraph}{4}{\z@}
{1\p@ plus -1\p@}{1\p@}
{\reset@font\itshape\helveticabold\fontsize{11.5}{12}}}
\def\subparagraph{%
\@startsection{subparagraph}{5}{\z@}
{1\p@ plus -1\p@}{1\p@}
{\reset@font\itshape\helvetica\fontsize{11.5}{12}}}
\def\textcolon{\text{\rm :}}
% ********************
% Figures and tables *
% ********************
% Table and array parameters
\setlength\arraycolsep{.5em}
\setlength\tabcolsep{.5em}
\setlength\arrayrulewidth{.5pt}
\setlength\doublerulesep{2.5pt}
\setlength\extrarowheight{\z@}
\renewcommand\arraystretch{1}
%\newlength{\abovecaptionskip}
%\newlength{\belowcaptionskip}
%\setlength{\abovecaptionskip}{13pt}
%\setlength{\belowcaptionskip}{10.5pt}
\long\def\@makecaption#1#2{\vspace{\abovecaptionskip}%
\begingroup
\normalsize
\textbf{#1.}\enskip{#2}\par
\endgroup}
% Table rules
\def\toprule{\noalign{\ifnum0=`}\fi\hrule \@height 0.5pt \hrule \@height 6pt \@width 0pt \futurelet
\@tempa\@xhline}
\def\midrule{\noalign{\ifnum0=`}\fi \hrule \@height 6.75pt \@width 0pt \hrule \@height 0.5pt
\hrule \@height 6pt \@width 0pt \futurelet \@tempa\@xhline}
\def\botrule{\noalign{\ifnum0=`}\fi \hrule \@height 5.75pt \@width 0pt \hrule \@height 0.5pt \futurelet
\@tempa\@xhline}
\def\hrulefill{\leavevmode\leaders\hrule height .5pt\hfill\kern\z@}
\def\thefigure{\@arabic\c@figure}
\def\fps@figure{tbp}
\def\ftype@figure{1}
\def\ext@figure{lof}
\def\fnum@figure{\figurename~\thefigure}
\def\figure{\@float{figure}}
\let\endfigure\end@float
\@namedef{figure*}{\@dblfloat{figure}}
\@namedef{endfigure*}{\end@dblfloat}
\def\thetable{\@arabic\c@table}
\def\fps@table{tbp}
\def\ftype@table{2}
\def\ext@table{lot}
\def\fnum@table{Table~\thetable}
\def\table{\let\source\tablesource\@float{table}}
\def\endtable{\end@float}
\@namedef{table*}{\@dblfloat{table}}
\@namedef{endtable*}{\end@dblfloat}
\newif\if@rotate \@rotatefalse
\newif\if@rotatecenter \@rotatecenterfalse
\def\rotatecenter{\global\@rotatecentertrue}
\def\rotateendcenter{\global\@rotatecenterfalse}
\def\rotate{\global\@rotatetrue}
\def\endrotate{\global\@rotatefalse}
\newdimen\rotdimen
\def\rotstart#1{\special{ps: gsave currentpoint currentpoint translate
#1 neg exch neg exch translate}}
\def\rotfinish{\special{ps: currentpoint grestore moveto}}
\def\rotl#1{\rotdimen=\ht#1\advance\rotdimen by \dp#1
\hbox to \rotdimen{\vbox to\wd#1{\vskip \wd#1
\rotstart{270 rotate}\box #1\vss}\hss}\rotfinish}
\def\rotr#1{\rotdimen=\ht #1\advance\rotdimen by \dp#1
\hbox to \rotdimen{\vbox to \wd#1{\vskip \wd#1
\rotstart{90 rotate}\box #1\vss}\hss}\rotfinish}
\newif\ifsub@@figure \sub@@figuretrue
\def\thesubfigure{\@arabic\c@figure\alph{subfigure}}
\def\fps@subfigure{tbp}
\def\ftype@subfigure{1}
\def\ext@subfigure{lof}
\def\fnum@subfigure{Figure \thesubfigure}
\def\subfigure{\ifsub@@figure\global\sub@@figurefalse\stepcounter{figure}\fi%
\@float{subfigure}}
\let\endsubfigure\end@float
\@namedef{subfigure*}{\ifsub@@figure\global\sub@@figurefalse%
\stepcounter{figure}\fi \@dblfloat{subfigure}}
\@namedef{endsubfigure*}{\end@dblfloat}
\def\endfigure{\global\sub@@figuretrue\end@float}
\@namedef{endfigure*}{\global\sub@@figuretrue\end@dblfloat}
\newdimen\tempdime
\newbox\temptbox
% From ifmtarg.sty
% Copyright Peter Wilson and Donald Arseneau, 2000
\begingroup
\catcode`\Q=3
\long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil}
\long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4}
\long\gdef\@ifnotmtarg#1{\@xifmtarg#1QQ\@firstofone\@gobble\@nil}
\endgroup
\def\tablesize{\@setfontsize\tablesize{10\p@}{10\p@}}
\newenvironment{processtable}[3]{\setbox\temptbox=\hbox{{\tablesize #2}}%
\tempdime\wd\temptbox\@processtable{#1}{#2}{#3}{\tempdime}}
{\relax}
\newcommand{\@processtable}[4]{%
\if@rotate
\setbox4=\vbox to \hsize{\vss\hbox to \textheight{%
\begin{minipage}{#4}%
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
\vskip7\p@\noindent
\parbox{#4}{\fontsize{10}{10}\selectfont #3\par}%
\end{minipage}}\vss}%
\rotr{4}
\else
\hbox to \hsize{\hss\begin{minipage}[t]{#4}%
\vskip2.9pt
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
\vskip6\p@\noindent
\parbox{#4}{\fontsize{8}{9}\selectfont #3\par}%
\end{minipage}\hss}\fi}%
\newcolumntype{P}[1]{>{\raggedright\let\\\@arraycr\hangindent1em}p{#1}}
% ******************************
% List numbering and lettering *
% ******************************
\def\labelenumi{{\rm\arabic{enumi}.}}
\def\theenumi{\arabic{enumi}}
\def\labelenumii{{\rm\alph{enumii}.}}
\def\theenumii{\alph{enumii}}
\def\p@enumii{\theenumi}
\def\labelenumiii{{\rm(\arabic{enumiii})}}
\def\theenumiii{\roman{enumiii}}
\def\p@enumiii{\theenumi(\theenumii)}
\def\labelenumiv{{\rm(\arabic{enumiv})}}
\def\theenumiv{\Alph{enumiv}}
\def\p@enumiv{\p@enumiii\theenumiii}
\def\labelitemi{{\small$\bullet$}}
\def\labelitemii{{\small$\bullet$}}
\def\labelitemiii{{\small$\bullet$}}
\def\labelitemiv{{\small$\bullet$}}
\def\@listI{\leftmargin\leftmargini \topsep\medskipamount}
\let\@listi\@listI
\@listi
\def\@listii{\topsep\z@\leftmargin\leftmarginii}
\def\@listiii{\leftmargin\leftmarginiii \topsep\z@}
\def\@listiv{\leftmargin\leftmarginiv \topsep\z@}
\def\@listv{\leftmargin\leftmarginv \topsep\z@}
\def\@listvi{\leftmargin\leftmarginvi \topsep\z@}
\setlength{\leftmargini}{3mm}
\setlength{\leftmarginii}{\z@}
\setlength{\leftmarginiii}{\z@}
\setlength{\leftmarginiv}{\z@}
% Changes to the list parameters for enumerate
\def\enumargs{%
\partopsep \z@
\itemsep 3\p@
\parsep \z@
\labelsep 0.5em
\listparindent \parindent
\itemindent \z@
\topsep 2\p@
}
\def\enumerate{%
\@ifnextchar[{\@numerate}{\@numerate[0]}}
\def\@numerate[#1]{%
\ifnum \@enumdepth >3 \@toodeep\else
\advance\@enumdepth \@ne
\edef\@enumctr{enum\romannumeral\the\@enumdepth}
\list{\csname label\@enumctr\endcsname}{%
\enumargs
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@enumdepth\endcsname}
\usecounter{\@enumctr}
\settowidth\labelwidth{#1}
\addtolength{\leftmargin}{\labelwidth}
\addtolength{\leftmargin}{\labelsep}
\def\makelabel##1{\hss \llap{##1}}}%
\fi
}
\let\endenumerate\endlist
% Changes to the list parameters for itemize
\def\itemargs{%
\partopsep \z@
\itemsep 3\p@
\parsep \z@
\labelsep 0.5em
\rightmargin \z@
\listparindent \parindent
\itemindent \z@
\topsep 2\p@
}
\def\itemize{%
\@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}}
\def\@itemize[#1]{%
\ifnum \@itemdepth >3 \@toodeep\else
\advance\@itemdepth \@ne
\edef\@itemctr{item\romannumeral\the\@itemdepth}
\list{\csname label\@itemctr\endcsname}{%
\itemargs
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@itemdepth\endcsname}
\settowidth\labelwidth{#1}
\addtolength{\leftmargin}{\labelwidth}
\addtolength{\leftmargin}{\labelsep}
\def\makelabel##1{\hss \llap{##1}}}%
\fi
}
\let\enditemize\endlist
\newenvironment{unlist}{%
\begin{list}{}%
{\setlength{\labelwidth}{\z@}%
\setlength{\labelsep}{\z@}%
\setlength{\topsep}{\medskipamount}%
\setlength{\itemsep}{3\p@}%
\setlength{\leftmargin}{2em}%
\setlength{\itemindent}{-2em}}}
{\end{list}}
% ***********************
% Quotes and Quotations *
% ***********************
\def\quotation{\par\begin{list}{}{
\setlength{\topsep}{\medskipamount}
\setlength{\leftmargin}{2em}%
\setlength{\rightmargin}{\z@}%
\setlength\labelwidth{0pt}%
\setlength\labelsep{0pt}%
\listparindent\parindent}%
\item[]}
\def\endquotation{\end{list}}
\let\quote\quotation
\let\endquote\endquotation
\skip\@mpfootins = \skip\footins
\fboxsep=6\p@
\fboxrule=1\p@
% *******************
% Table of contents *
% *******************
\newcommand\@pnumwidth{4em}
\newcommand\@tocrmarg{2.55em plus 1fil}
\newcommand\@dotsep{1000}
\setcounter{tocdepth}{4}
\def\numberline#1{\hbox to \@tempdima{{#1}}}
\def\@authortocline#1#2#3#4#5{%
\vskip 1.5\p@
\ifnum #1>\c@tocdepth \else
{\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip
\parindent #2\relax\@afterindenttrue
\interlinepenalty\@M
\leavevmode
\@tempdima #3\relax
\advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
{\itshape #4}\nobreak
\leaders\hbox{$\m@th
\mkern \@dotsep mu\hbox{.}\mkern \@dotsep
mu$}\hfill
\nobreak
\hb@xt@\@pnumwidth{\hfil}%
\par}%
\fi}
\newcommand*\l@author{\@authortocline{2}{0pt}{30pt}}
\newcommand*\l@section{\@dottedtocline{3}{11pt}{20pt}}
\newcommand*\l@subsection{\@dottedtocline{4}{31pt}{29pt}}
\newcommand*\l@subsubsection[2]{}
% ***********
% Footnotes *
% ***********
\def\footnoterule{\noindent\rule{\columnwidth}{0.5pt}}
\def\@makefnmark{\@textsuperscript{\normalfont\@thefnmark}}%
\newcommand\@makefntext[1]{\noindent{\@makefnmark}\enskip#1}
% ***********
% References *
% ***********
\providecommand{\newblock}{}
\newenvironment{thebibliography}{%
\section{\bibname}%
\begingroup
\small
\begin{list}{}{%
\setlength{\topsep}{\z@}%
\setlength{\labelsep}{\z@}%
\settowidth{\labelwidth}{\z@}%
\setlength{\leftmargin}{4mm}%
\setlength{\itemindent}{-4mm}}\small}
{\end{list}\endgroup}
\usepackage[numbers,square]{natbib}
\renewcommand\@biblabel[1]{\textbf [#1] }
% **********
% Appendix *
% **********
\newif\ifappend
\def\appendix{\par
\setcounter{section}{0}
\setcounter{subsection}{0}
\appendtrue
}
%Math parameters
\setlength{\jot}{5\p@}
\mathchardef\@m=1500 % adapted value
\def\frenchspacing{\sfcode`\.\@m \sfcode`\?\@m \sfcode`\!\@m
\sfcode`\:\@m \sfcode`\;\@m \sfcode`\,\@m}
% Theorems
\def\th@plain{%
%% \let\thm@indent\noindent % no indent
\thm@headfont{\quad\scshape}% heading font is bold
\thm@notefont{\upshape\mdseries}% same as heading font
\thm@headpunct{.}% no period after heading
\thm@headsep 5\p@ plus\p@ minus\p@\relax
\itshape % body font
}
\vbadness=9999
\tolerance=9999
\doublehyphendemerits=10000
\doublehyphendemerits 640000 % corresponds to badness 800
\finalhyphendemerits 1000000 % corresponds to badness 1000
\flushbottom
\frenchspacing
\ps@headings
\twocolumn
% Screen PDF compatability
\newcommand{\medline}[1]{%
\unskip\unskip\ignorespaces}
%%%%for smaller size text
\newenvironment{methods}{%
\begingroup
\def\section{%
\@startsection{section}{1}{\z@}
{-24\p@ plus -3\p@}{4\p@}
{\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
\def\subsection{%
\@startsection{subsection}{2}{\z@}
{-5\p@ plus -2\p@}{4\p@}
{\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
\def\subsubsection{%
\@startsection{subsubsection}{3}{\z@}
{-6\p@ plus -1\p@}{-1em}
{\reset@font\normalfont\normalsize\itshape}}
\footnotesize
\par}
{\par\endgroup\bigskip\@afterheading\@afterindentfalse}
\graphicspath{{g:/artwork/oup/bioinfo/}}
\language=2
\hyphenation{Figure Table Figures Tables}
\newcommand{\href}[2]{#2}
\renewenvironment{proof}[1][\proofname]{\par
\normalfont \topsep6\p@\@plus6\p@\relax
\labelsep 0.5em
\trivlist
\item[\hskip\labelsep\hskip1em\textsc{#1}.]\ignorespaces
}{\endtrivlist\@endpefalse}
%%Different Bonds
\def\sbond{\ensuremath{\raise.25ex\hbox{${-}\!\!\!\!{-}$}}\kern -.9pt}
\def\dbond{\ensuremath{\raise.25ex\hbox{=$\!$=}}}
\def\tbond{\ensuremath{\raise.20ex\hbox{${\equiv}\!\!\!{\equiv}$}}}
\newcommand{\query}[2][0pt]{}%
\renewcommand{\dag}{{\mathversion{normal}$^{\dagger}$}}
\endinput
Test templates articles frontiers/frontiersHLTH.cls 0 → 100644
View file @ 39986221
\newcommand\classname{frontiersHLTH} %this file is based in bioninfo.cls
\newcommand\lastmodifieddate{2016/01/11}
\newcommand\versionnumber{2.6}
% For printing crop marks
\newif\if@cropmarkson \@cropmarksontrue
\NeedsTeXFormat{LaTeX2e}[2013/26/03]
\ProvidesClass{\classname}[\lastmodifieddate\space\versionnumber]
\setlength{\paperheight}{11truein}
\setlength{\paperwidth}{8.5truein}
\newif\if@final
\DeclareOption{draft}{\PassOptionsToPackage{draft}{graphicx}}
\DeclareOption{paper}{\PassOptionsToPackage{paper}{graphicx}}
\DeclareOption{a4paper}{\PassOptionsToPackage{a4}{crop}}
\DeclareOption{centre}{\PassOptionsToPackage{center}{crop}}
\DeclareOption{crop}{\PassOptionsToPackage{cam}{crop}\global\@cropmarksontrue}
\DeclareOption{nocrop}{\PassOptionsToPackage{off}{crop}\global\@cropmarksonfalse}
\DeclareOption{info}{\PassOptionsToPackage{info}{crop}}
\DeclareOption{noinfo}{\PassOptionsToPackage{noinfo}{crop}}
\DeclareOption{final}{\global\@finaltrue}
\DeclareOption{utf8}{\PassOptionsToPackage{utf8}{inputenc}}
\ExecuteOptions{a4paper,nocrop,centre,info,paper}
\ProcessOptions
% Load all necessary packages
\RequirePackage{inputenc,crop,graphicx,amsmath,array,color,amssymb,flushend,stfloats,amsthm,chngpage,times,datetime,parskip}
\def\helvetica{\fontfamily{phv}\selectfont}
\def\helveticaitalic{\fontfamily{phv}\itshape\selectfont}
\def\helveticabold{\fontfamily{phv}\bfseries\selectfont}
\def\helveticabolditalic{\fontfamily{phv}\bfseries\itshape\selectfont}
\usepackage[usenames,dvipsnames]{xcolor}
\usepackage[labelsep=quad,indention=10pt]{caption}
\usepackage[labelfont=bf,list=true]{subcaption}
\newcommand\@ptsize{0}
% Set twoside printing
\@twosidetrue
% Marginal notes are on the outside edge
\@mparswitchfalse
\reversemarginpar
\renewcommand\normalsize{%
\@setfontsize\normalsize{12}{12}%
\abovedisplayskip 10\p@ \@plus2\p@ \@minus5\p@
\abovedisplayshortskip \z@ \@plus3\p@
\belowdisplayshortskip 6\p@ \@plus3\p@ \@minus3\p@
\belowdisplayskip \abovedisplayskip
\let\@listi\@listI}
\normalsize
\let\@bls\baselineskip
\newcommand\small{%
\@setfontsize\small{11}{12}%
\abovedisplayskip 11\p@ minus 3\p@
\belowdisplayskip \abovedisplayskip
\abovedisplayshortskip \z@ plus 2\p@
\belowdisplayshortskip 4\p@ plus 2\p@ minus2\p@
\def\@listi{\topsep 4.5\p@ plus 2\p@ minus 1\p@
\itemsep \parsep
\topsep 4\p@ plus 2\p@ minus 2\p@}}
\newcommand\footnotesize{%
\@setfontsize\footnotesize{8}{10}%
\abovedisplayskip 6\p@ minus 3\p@
\belowdisplayskip\abovedisplayskip
\abovedisplayshortskip \z@ plus 3\p@
\belowdisplayshortskip 6\p@ plus 3\p@ minus 3\p@
\def\@listi{\topsep 3\p@ plus 1\p@ minus 1\p@
\parsep 2\p@ plus 1\p@ minus 1\p@\itemsep \parsep}}
\def\scriptsize{\@setfontsize\scriptsize{11pt}{11pt}}
\def\tiny{\@setfontsize\tiny{10pt}{11pt}}
\def\large{\@setfontsize\large{13pt}{14pt}}
\def\Large{\@setfontsize\Large{14pt}{16}}
\def\LARGE{\@setfontsize\LARGE{15pt}{17pt}}
\def\huge{\@setfontsize\huge{22pt}{22pt}}
\def\Huge{\@setfontsize\Huge{30pt}{30pt}}
\DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl}
\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc}
% Line spacing
\setlength\lineskip{1\p@}
\setlength\normallineskip{1\p@}
\renewcommand\baselinestretch{}
% Set inter-para skips
\setlength\smallskipamount{3\p@ \@plus 1\p@ \@minus 1\p@}
\setlength\medskipamount{6\p@ \@plus 2\p@}
\setlength\bigskipamount{12\p@ \@plus 4\p@ \@minus 4\p@}
% Paragraph dimensions and inter-para spacing
\setlength\parindent{3mm}
\setlength{\parskip}{\medskipamount}
% Page break penalties
\@lowpenalty 51
\@medpenalty 151
\@highpenalty 301
% Disallow widows and orphans
\clubpenalty 10000
\widowpenalty 10000
% Disable page breaks before equations, allow pagebreaks after
% equations and discourage widow lines before equations.
\displaywidowpenalty 100
\predisplaypenalty 10000
\postdisplaypenalty 2500
% Allow breaking the page in the middle of a paragraph
\interlinepenalty 0
% Disallow breaking the page after a hyphenated line
\brokenpenalty 10000
% Hyphenation; don't split words into less than three characters
\lefthyphenmin=3
\righthyphenmin=3
%
% Set page layout dimensions
%
\setlength\headheight{16\p@} % height of running head
\setlength\topmargin{1.3pc} % head margin
\addtolength\topmargin{-1in} % subtract out the 1 inch driver margin
\setlength\topskip{10\p@} % height of first line of text
\setlength\headsep{19\p@} % space below running head --
\setlength\footskip{34\p@} % space above footer line
\setlength\maxdepth{1\topskip} % pages can be short or deep by half a line?
\setlength\textwidth{42pc} % text measure excluding margins
\setlength\textheight{56\baselineskip} % 54 lines on a full page,
\addtolength\textheight{\topskip} % including the first
% line on the page
% Set the margins
\setlength\marginparsep{3\p@}
\setlength\marginparpush{3\p@}
\setlength\marginparwidth{35\p@}
\setlength\oddsidemargin{4.5pc}
\addtolength\oddsidemargin{-1in} % subtract out the 1 inch driver margin
\setlength\@tempdima{\paperwidth}
\addtolength\@tempdima{-\textwidth}
\addtolength\@tempdima{-4.5pc}
\setlength\evensidemargin{\@tempdima}
\addtolength\evensidemargin{-1in}
\setlength\columnsep{1.5pc} % space between columns for double-column text
\setlength\columnseprule{0\p@} % width of rule between two columns
% Footnotes
\setlength\footnotesep{9\p@} % space between footnotes
% space between text and footnote
\setlength{\skip\footins}{12\p@ \@plus 6\p@ \@minus 1\p@}
% Float placement parameters
% The total number of floats that can be allowed on a page.
\setcounter{totalnumber}{10}
% The maximum number of floats at the top and bottom of a page.
\setcounter{topnumber}{5}
\setcounter{bottomnumber}{5}
% The maximum part of the top or bottom of a text page that can be
% occupied by floats. This is set so that at least four lines of text
% fit on the page.
\renewcommand\topfraction{.9}
\renewcommand\bottomfraction{.9}
% The minimum amount of a text page that must be occupied by text.
% This should accomodate four lines of text.
\renewcommand\textfraction{.06}
% The minimum amount of a float page that must be occupied by floats.
\renewcommand\floatpagefraction{.94}
% The same parameters repeated for double column output
\renewcommand\dbltopfraction{.9}
\renewcommand\dblfloatpagefraction{.9}
% Space between floats
\setlength\floatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
% Space between floats and text
\setlength\textfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
% Space above and below an inline figure
\setlength\intextsep {18\p@ \@plus 2\p@ \@minus 2\p@}
% For double column floats
\setlength\dblfloatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
\setlength\dbltextfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
% Space left at top, bottom and inbetween floats on a float page.
\setlength\@fptop{0\p@} % no space above float page figures
\setlength\@fpsep{12\p@ \@plus 1fil}
\setlength\@fpbot{0\p@}
% The same for double column
\setlength\@dblfptop{0\p@}
\setlength\@dblfpsep{12\p@ \@plus 1fil}
\setlength\@dblfpbot{0\p@}
% Override settings in mathtime back to TeX defaults
\DeclareMathSizes{5} {5} {5} {5}
\DeclareMathSizes{6} {6} {5} {5}
\DeclareMathSizes{7} {7} {5} {5}
\DeclareMathSizes{8} {8} {6} {5}
\DeclareMathSizes{9} {9} {6.5} {5}
\DeclareMathSizes{10} {10} {7.5} {5}
\DeclareMathSizes{12} {12} {9} {7}
% Page styles
\def\ps@headings
{%
\def\@oddfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
\hbox to \textwidth{\helveticabold\small {Frontiers}\hfill \thepage}%
}}%
\def\@evenfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
\hbox to \textwidth{\helvetica\small {\color{red}This is a provisional file, not the final typeset article}\hfill\helveticabold\color{black}\thepage}%
}}%
\def\@evenhead{\vbox{\hbox to \textwidth{\fontsize{11}{10}\selectfont
\helveticabold{\fontshape{it}\selectfont
\strut\firstAuthorLast}\hfill\strut\rightmark}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
\def\@oddhead{\vbox{\hbox to \textwidth{\fontsize{11}{10}\selectfont
\helveticabold{\fontshape{it}\selectfont
\strut\firstAuthorLast}\hfill\strut\rightmark}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
\def\titlemark##1{\markboth{##1}{##1}}%
\def\authormark##1{\gdef\leftmark{##1}}%
}
\def\ps@opening
{%
\def\@oddfoot{\vbox to 13\p@{\hbox{\rule{\textwidth}{1\p@}}\vss
\hbox to \textwidth{\helvetica
\fontsize{7}{9}\fontshape{n}\selectfont \space %
\hfill\small\helveticabold\thepage}%
}}%
\def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}{1\p@}\vss
\hbox to \textwidth{\helvetica\thepage\hfill
\fontsize{7}{9}\fontshape{n}\selectfont \space }%
}}%
\let\@evenhead\relax
\let\@oddhead\relax}
% Page range
\newif\iflastpagegiven \lastpagegivenfalse
\newcommand\firstpage[1]{%
\gdef\@firstpage{#1}%
\ifnum\@firstpage>\c@page
\setcounter{page}{#1}%
\ClassWarning{BIO}{Increasing pagenumber to \@firstpage}%
\else \ifnum\@firstpage<\c@page
\ClassWarning{BIO}{Firstpage lower than pagenumber}\fi\fi
\xdef\@firstpage{\the\c@page}%
}
\def\@firstpage{1}
\def\pagenumbering#1{%
\global\c@page \@ne
\gdef\thepage{\csname @#1\endcsname \c@page}%
\gdef\thefirstpage{%
\csname @#1\endcsname \@firstpage}%
\gdef\thelastpage{%
\csname @#1\endcsname \@lastpage}%
}
\newcommand\lastpage[1]{\xdef\@lastpage{#1}%
\global\lastpagegiventrue}
\def\@lastpage{0}
\def\setlastpage{\iflastpagegiven\else
\edef\@tempa{@lastpage@}%
\expandafter
\ifx \csname \@tempa \endcsname \relax
\gdef\@lastpage{0}%
\else
\xdef\@lastpage{\@nameuse{@lastpage@}}%
\fi
\fi }
\def\writelastpage{%
\iflastpagegiven \else
\immediate\write\@auxout%
{\string\global\string\@namedef{@lastpage@}{\the\c@page}}%
\fi
}
\def\thepagerange{%
\ifnum\@lastpage =0 {\ \bf ???} \else
\ifnum\@lastpage = \@firstpage \ \thefirstpage\else
\thefirstpage--\thelastpage \fi\fi}
\AtBeginDocument{\setlastpage
\pagenumbering{arabic}%
}
\AtEndDocument{%
\writelastpage
\if@final
\clearemptydoublepage
\else
\clearpage
\fi}
%
% Sectional units
%
% Counters
\newcounter{section}
\newcounter{subsection}[section]
\newcounter{subsubsection}[subsection]
\newcounter{paragraph}[subsubsection]
\newcounter{subparagraph}[paragraph]
\newcounter{figure}
\newcounter{subfigure}
\newcounter{table}
% Form of the numbers
\newcommand\thepage{\arabic{page}}
\renewcommand\thesection{\arabic{section}}
\renewcommand\thesubsection{{\thesection.\arabic{subsection}}}
\renewcommand\thesubsubsection{{\thesubsection.\arabic{subsubsection}}}
\renewcommand\theparagraph{\thesubsubsection.\arabic{paragraph}}
\renewcommand\thesubparagraph{\theparagraph.\arabic{subparagraph}}
\renewcommand\theequation{\arabic{equation}}
% Form of the words
\newcommand\contentsname{Contents}
\newcommand\listfigurename{List of Figures}
\newcommand\listtablename{List of Tables}
\newcommand\partname{Part}
\newcommand\appendixname{Appendix}
\newcommand\abstractname{Abstract}
\newcommand\refname{References}
\newcommand\bibname{References}
\newcommand\indexname{Index}
\newcommand\figurename{Figure}
\newcommand\tablename{Table}
% Clearemptydoublepage should really clear the running heads too
\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}
% Frontmatter, mainmatter and backmatter
\newif\if@mainmatter \@mainmattertrue
\newcommand\frontmatter{%
\clearpage
\@mainmatterfalse
\pagenumbering{roman}}
\newcommand\mainmatter{%
\clearpage
\@mainmattertrue
\pagenumbering{arabic}}
\newcommand\backmatter{%
\clearpage
\@mainmatterfalse}
\newdateformat{mydate}{\THEDAY \ \monthname[ \THEMONTH] \THEYEAR}
\newdateformat{mydate2}{\monthname[\THEMONTH] \THEYEAR}
%********
% TITLE *
%********
\newlength{\dropfromtop}
\setlength{\dropfromtop}{\z@}
% Application Notes
\newif\if@appnotes
\newcommand{\application}{%
% \setlength{\dropfromtop}{-2.25pc}%
\global\@appnotestrue}
% Short Title is for the Title of the Article
% Title is for the Title of the Journal
\long\def\title{\@ifnextchar[{\short@title}{\@@title}}
\def\short@title[#1]{\titlemark{#1}\@@@title}
\def\@@title#1{\authormark{#1}\@@@title{#1}}
\long\def\@@@title#1{\gdef\@title{#1}}
\long\def\author{\@ifnextchar[{\short@uthor}{\@uthor}}
\def\short@uthor[#1]{\authormark{#1}\@@author}
\def\@uthor#1{\authormark{#1}\@@author{#1}}
\long\def\@@author#1{\gdef\@author{#1}}
\def\vol#1{\global\def\@vol{#1}}
\def\issue#1{\global\def\@issue{#1}}
\def\address#1{\global\def\@issue{#1}}
\def\history#1{\global\def\@history{#1}}
\def\correspondance#1{\global\def\@correspondance{#1}}
\def\extraAuth#1{\global\def\@extraAuth{#1}}
\def\address#1{\global\def\@address{#1}}
\def\date#1{\gdef\@date{#1}}
%***********
% Colors *
%***********
% Other colors
\definecolor{black}{cmyk}{0, 0, 0, 1}
\definecolor{gray}{cmyk}{0, 0, 0, 0.25}
\definecolor{darkgray}{cmyk}{0, 0, 0, 0.5}
\newlength{\extraspace}
\setlength{\extraspace}{\z@}
\newcommand\maketitle{\par
\begingroup
\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
\long\def\@makefntext##1{\parindent 3mm\noindent
% \@textsuperscript{\normalfont\@thefnmark}\raggedright##1}%
\@textsuperscript{\normalfont\@thefnmark}##1}%
\if@twocolumn
\ifnum \col@number=\@ne
\@maketitle
\else
\twocolumn[\@maketitle]%
\fi
\else
\newpage
\global\@topnum\z@ % Prevents figures from going at top of page.
\@maketitle
\fi
\thispagestyle{opening}\@thanks
\endgroup
\setcounter{footnote}{0}%
\global\let\thanks\relax
\global\let\maketitle\relax
\global\let\@maketitle\relax
\global\let\@address\@empty
\global\let\@history\@empty
\global\let\@extraAuth\@empty
\global\let\@topic\@empty
\global\let\@thanks\@empty
\global\let\@author\@empty
\global\let\@date\@empty
\global\let\@title\@empty
\global\let\@pubyear\@empty
\global\let\address\relax
\global\let\topic\relax
\global\let\extraAuth\relax
\global\let\title\relax
\global\let\author\relax
\global\let\date\relax
\global\let\pubyear\relax
\global\let\@copyrightline\@empty
\global\let\and\relax
\@afterindentfalse\@afterheading
}
\newlength{\aboveskipchk}%for checking oddpage or evenpage top skip
\setlength{\aboveskipchk}{\z@}%
\def\@maketitle{%
\let\footnote\thanks
\clearemptydoublepage
\checkoddpage\ifcpoddpage\setlength{\aboveskipchk}{-7pc}\else\setlength{\aboveskipchk}{-3pc}\fi%for checking oddpage or evenpage top skip%%
\vspace*{\aboveskipchk}%
\vspace{\dropfromtop}%
\hbox to \textwidth{%
\parbox[t]{15pc}{%
\helvetica
\hfil
\flushleft \includegraphics[width=12pc,angle=0]{./logo1.pdf}
}}
\rule{\textwidth}{1\p@}\par%
\helvetica
\hbox to \textwidth{%
\parbox[t]{36.5pc}{%
\vspace*{1sp}
{\helveticabold\fontsize{20}{21}\color{black}\selectfont\raggedright \@title \par}%
\vspace{4.5\p@}
{\helveticabold\fontsize{12}{15}\selectfont\raggedright \@author \par}%
\vspace{4\p@}
{\helvetica\fontsize{12}{12}\selectfont\raggedright\slshape\@address \Address \\ \par}%
\vspace{6\p@}
{\helvetica\fontsize{12}{10}\selectfont\raggedright {Correspondence*:\\ }\@correspondance \corrAuthor \\ \corrEmail \par}
\vspace{4\p@}
{\helvetica\fontsize{12}{12}\selectfont\raggedright\@extraAuth \par}%
\vspace{8\p@}
}%
}
\vspace{14.5\p@}%
}
%***********
% Abstract *
%***********
\newcommand{\absection}[1]{%
\par\noindent{\bfseries #1}\space\ignorespaces}
\newenvironment{abstract}{%
\begingroup
\let\section\absection
\fontfamily{\sfdefault}\fontsize{12}{12}\sffamily\selectfont
{\fontseries{b}\selectfont ABSTRACT}\par}
{\endgroup\smallskip\@afterheading\@afterindentfalse\vskip 12pt plus -2pt minus 2pt}
% Section macros
% Lowest level heading that takes a number by default
\setcounter{secnumdepth}{5}
\renewcommand{\@seccntformat}[1]{\csname the#1\endcsname\quad}
\def\section{%
\@startsection{section}{1}{\z@}
{-10\p@ plus -3\p@}{3\p@}
{\reset@font\raggedright\helveticabold\fontsize{13}{13}\color{black}\selectfont\MakeUppercase}}
\def\section{%
\@startsection{section}{1}{\z@}
{-10\p@ plus -3\p@}{3\p@}
{\reset@font\raggedright\helveticabold\fontsize{13}{13}\color{black}\selectfont\MakeUppercase}}
\def\subsection{%
\@startsection{subsection}{2}{\z@}
{2\p@ plus -1\p@}{2\p@}
{\reset@font\raggedright\mathversion{bold}\helveticabold\fontsize{11.5}{12}}}
\def\subsubsection{%
\@startsection{subsubsection}{3}{\z@}
{1\p@ plus -1\p@}{1\p@}
{\reset@font\raggedright\mathversion{bold}\helvetica\fontsize{11.5}{12}}}
\def\paragraph{%
\@startsection{paragraph}{4}{\z@}
{1\p@ plus -1\p@}{1\p@}
{\reset@font\itshape\helveticabold\fontsize{11.5}{12}}}
\def\subparagraph{%
\@startsection{subparagraph}{5}{\z@}
{1\p@ plus -1\p@}{1\p@}
{\reset@font\itshape\helvetica\fontsize{11.5}{12}}}
\def\textcolon{\text{\rm :}}
% ********************
% Figures and tables *
% ********************
% Table and array parameters
\setlength\arraycolsep{.5em}
\setlength\tabcolsep{.5em}
\setlength\arrayrulewidth{.5pt}
\setlength\doublerulesep{2.5pt}
\setlength\extrarowheight{\z@}
\renewcommand\arraystretch{1}
%\newlength{\abovecaptionskip}
%\newlength{\belowcaptionskip}
%\setlength{\abovecaptionskip}{13pt}
%\setlength{\belowcaptionskip}{10.5pt}
\long\def\@makecaption#1#2{\vspace{\abovecaptionskip}%
\begingroup
\normalsize
\textbf{#1.}\enskip{#2}\par
\endgroup}
% Table rules
\def\toprule{\noalign{\ifnum0=`}\fi\hrule \@height 0.5pt \hrule \@height 6pt \@width 0pt \futurelet
\@tempa\@xhline}
\def\midrule{\noalign{\ifnum0=`}\fi \hrule \@height 6.75pt \@width 0pt \hrule \@height 0.5pt
\hrule \@height 6pt \@width 0pt \futurelet \@tempa\@xhline}
\def\botrule{\noalign{\ifnum0=`}\fi \hrule \@height 5.75pt \@width 0pt \hrule \@height 0.5pt \futurelet
\@tempa\@xhline}
\def\hrulefill{\leavevmode\leaders\hrule height .5pt\hfill\kern\z@}
\def\thefigure{\@arabic\c@figure}
\def\fps@figure{tbp}
\def\ftype@figure{1}
\def\ext@figure{lof}
\def\fnum@figure{\figurename~\thefigure}
\def\figure{\@float{figure}}
\let\endfigure\end@float
\@namedef{figure*}{\@dblfloat{figure}}
\@namedef{endfigure*}{\end@dblfloat}
\def\thetable{\@arabic\c@table}
\def\fps@table{tbp}
\def\ftype@table{2}
\def\ext@table{lot}
\def\fnum@table{Table~\thetable}
\def\table{\let\source\tablesource\@float{table}}
\def\endtable{\end@float}
\@namedef{table*}{\@dblfloat{table}}
\@namedef{endtable*}{\end@dblfloat}
\newif\if@rotate \@rotatefalse
\newif\if@rotatecenter \@rotatecenterfalse
\def\rotatecenter{\global\@rotatecentertrue}
\def\rotateendcenter{\global\@rotatecenterfalse}
\def\rotate{\global\@rotatetrue}
\def\endrotate{\global\@rotatefalse}
\newdimen\rotdimen
\def\rotstart#1{\special{ps: gsave currentpoint currentpoint translate
#1 neg exch neg exch translate}}
\def\rotfinish{\special{ps: currentpoint grestore moveto}}
\def\rotl#1{\rotdimen=\ht#1\advance\rotdimen by \dp#1
\hbox to \rotdimen{\vbox to\wd#1{\vskip \wd#1
\rotstart{270 rotate}\box #1\vss}\hss}\rotfinish}
\def\rotr#1{\rotdimen=\ht #1\advance\rotdimen by \dp#1
\hbox to \rotdimen{\vbox to \wd#1{\vskip \wd#1
\rotstart{90 rotate}\box #1\vss}\hss}\rotfinish}
\newif\ifsub@@figure \sub@@figuretrue
\def\thesubfigure{\@arabic\c@figure\alph{subfigure}}
\def\fps@subfigure{tbp}
\def\ftype@subfigure{1}
\def\ext@subfigure{lof}
\def\fnum@subfigure{Figure \thesubfigure}
\def\subfigure{\ifsub@@figure\global\sub@@figurefalse\stepcounter{figure}\fi%
\@float{subfigure}}
\let\endsubfigure\end@float
\@namedef{subfigure*}{\ifsub@@figure\global\sub@@figurefalse%
\stepcounter{figure}\fi \@dblfloat{subfigure}}
\@namedef{endsubfigure*}{\end@dblfloat}
\def\endfigure{\global\sub@@figuretrue\end@float}
\@namedef{endfigure*}{\global\sub@@figuretrue\end@dblfloat}
\newdimen\tempdime
\newbox\temptbox
% From ifmtarg.sty
% Copyright Peter Wilson and Donald Arseneau, 2000
\begingroup
\catcode`\Q=3
\long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil}
\long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4}
\long\gdef\@ifnotmtarg#1{\@xifmtarg#1QQ\@firstofone\@gobble\@nil}
\endgroup
\def\tablesize{\@setfontsize\tablesize{10\p@}{10\p@}}
\newenvironment{processtable}[3]{\setbox\temptbox=\hbox{{\tablesize #2}}%
\tempdime\wd\temptbox\@processtable{#1}{#2}{#3}{\tempdime}}
{\relax}
\newcommand{\@processtable}[4]{%
\if@rotate
\setbox4=\vbox to \hsize{\vss\hbox to \textheight{%
\begin{minipage}{#4}%
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
\vskip7\p@\noindent
\parbox{#4}{\fontsize{10}{10}\selectfont #3\par}%
\end{minipage}}\vss}%
\rotr{4}
\else
\hbox to \hsize{\hss\begin{minipage}[t]{#4}%
\vskip2.9pt
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
\vskip6\p@\noindent
\parbox{#4}{\fontsize{8}{9}\selectfont #3\par}%
\end{minipage}\hss}\fi}%
\newcolumntype{P}[1]{>{\raggedright\let\\\@arraycr\hangindent1em}p{#1}}
% ******************************
% List numbering and lettering *
% ******************************
\def\labelenumi{{\rm\arabic{enumi}.}}
\def\theenumi{\arabic{enumi}}
\def\labelenumii{{\rm\alph{enumii}.}}
\def\theenumii{\alph{enumii}}
\def\p@enumii{\theenumi}
\def\labelenumiii{{\rm(\arabic{enumiii})}}
\def\theenumiii{\roman{enumiii}}
\def\p@enumiii{\theenumi(\theenumii)}
\def\labelenumiv{{\rm(\arabic{enumiv})}}
\def\theenumiv{\Alph{enumiv}}
\def\p@enumiv{\p@enumiii\theenumiii}
\def\labelitemi{{\small$\bullet$}}
\def\labelitemii{{\small$\bullet$}}
\def\labelitemiii{{\small$\bullet$}}
\def\labelitemiv{{\small$\bullet$}}
\def\@listI{\leftmargin\leftmargini \topsep\medskipamount}
\let\@listi\@listI
\@listi
\def\@listii{\topsep\z@\leftmargin\leftmarginii}
\def\@listiii{\leftmargin\leftmarginiii \topsep\z@}
\def\@listiv{\leftmargin\leftmarginiv \topsep\z@}
\def\@listv{\leftmargin\leftmarginv \topsep\z@}
\def\@listvi{\leftmargin\leftmarginvi \topsep\z@}
\setlength{\leftmargini}{3mm}
\setlength{\leftmarginii}{\z@}
\setlength{\leftmarginiii}{\z@}
\setlength{\leftmarginiv}{\z@}
% Changes to the list parameters for enumerate
\def\enumargs{%
\partopsep \z@
\itemsep 3\p@
\parsep \z@
\labelsep 0.5em
\listparindent \parindent
\itemindent \z@
\topsep 2\p@
}
\def\enumerate{%
\@ifnextchar[{\@numerate}{\@numerate[0]}}
\def\@numerate[#1]{%
\ifnum \@enumdepth >3 \@toodeep\else
\advance\@enumdepth \@ne
\edef\@enumctr{enum\romannumeral\the\@enumdepth}
\list{\csname label\@enumctr\endcsname}{%
\enumargs
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@enumdepth\endcsname}
\usecounter{\@enumctr}
\settowidth\labelwidth{#1}
\addtolength{\leftmargin}{\labelwidth}
\addtolength{\leftmargin}{\labelsep}
\def\makelabel##1{\hss \llap{##1}}}%
\fi
}
\let\endenumerate\endlist
% Changes to the list parameters for itemize
\def\itemargs{%
\partopsep \z@
\itemsep 3\p@
\parsep \z@
\labelsep 0.5em
\rightmargin \z@
\listparindent \parindent
\itemindent \z@
\topsep 2\p@
}
\def\itemize{%
\@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}}
\def\@itemize[#1]{%
\ifnum \@itemdepth >3 \@toodeep\else
\advance\@itemdepth \@ne
\edef\@itemctr{item\romannumeral\the\@itemdepth}
\list{\csname label\@itemctr\endcsname}{%
\itemargs
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@itemdepth\endcsname}
\settowidth\labelwidth{#1}
\addtolength{\leftmargin}{\labelwidth}
\addtolength{\leftmargin}{\labelsep}
\def\makelabel##1{\hss \llap{##1}}}%
\fi
}
\let\enditemize\endlist
\newenvironment{unlist}{%
\begin{list}{}%
{\setlength{\labelwidth}{\z@}%
\setlength{\labelsep}{\z@}%
\setlength{\topsep}{\medskipamount}%
\setlength{\itemsep}{3\p@}%
\setlength{\leftmargin}{2em}%
\setlength{\itemindent}{-2em}}}
{\end{list}}
% ***********************
% Quotes and Quotations *
% ***********************
\def\quotation{\par\begin{list}{}{
\setlength{\topsep}{\medskipamount}
\setlength{\leftmargin}{2em}%
\setlength{\rightmargin}{\z@}%
\setlength\labelwidth{0pt}%
\setlength\labelsep{0pt}%
\listparindent\parindent}%
\item[]}
\def\endquotation{\end{list}}
\let\quote\quotation
\let\endquote\endquotation
\skip\@mpfootins = \skip\footins
\fboxsep=6\p@
\fboxrule=1\p@
% *******************
% Table of contents *
% *******************
\newcommand\@pnumwidth{4em}
\newcommand\@tocrmarg{2.55em plus 1fil}
\newcommand\@dotsep{1000}
\setcounter{tocdepth}{4}
\def\numberline#1{\hbox to \@tempdima{{#1}}}
\def\@authortocline#1#2#3#4#5{%
\vskip 1.5\p@
\ifnum #1>\c@tocdepth \else
{\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip
\parindent #2\relax\@afterindenttrue
\interlinepenalty\@M
\leavevmode
\@tempdima #3\relax
\advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
{\itshape #4}\nobreak
\leaders\hbox{$\m@th
\mkern \@dotsep mu\hbox{.}\mkern \@dotsep
mu$}\hfill
\nobreak
\hb@xt@\@pnumwidth{\hfil}%
\par}%
\fi}
\newcommand*\l@author{\@authortocline{2}{0pt}{30pt}}
\newcommand*\l@section{\@dottedtocline{3}{11pt}{20pt}}
\newcommand*\l@subsection{\@dottedtocline{4}{31pt}{29pt}}
\newcommand*\l@subsubsection[2]{}
% ***********
% Footnotes *
% ***********
\def\footnoterule{\noindent\rule{\columnwidth}{0.5pt}}
\def\@makefnmark{\@textsuperscript{\normalfont\@thefnmark}}%
\newcommand\@makefntext[1]{\noindent{\@makefnmark}\enskip#1}
% ***********
% References *
% ***********
\providecommand{\newblock}{}
\newenvironment{thebibliography}{%
\section{\bibname}%
\begingroup
\small
\begin{list}{}{%
\setlength{\topsep}{\z@}%
\setlength{\labelsep}{\z@}%
\settowidth{\labelwidth}{\z@}%
\setlength{\leftmargin}{4mm}%
\setlength{\itemindent}{-4mm}}\small}
{\end{list}\endgroup}
\usepackage[numbers,round]{natbib}
\renewcommand\@biblabel[1]{\textbf #1 .}
% **********
% Appendix *
% **********
\newif\ifappend % Are we in the Appendix?
\def\appendix{\par
\setcounter{section}{0}
\setcounter{subsection}{0}
\appendtrue
}
%Math parameters
\setlength{\jot}{5\p@}
\mathchardef\@m=1500 % adapted value
\def\frenchspacing{\sfcode`\.\@m \sfcode`\?\@m \sfcode`\!\@m
\sfcode`\:\@m \sfcode`\;\@m \sfcode`\,\@m}
% Theorems
\def\th@plain{%
%% \let\thm@indent\noindent % no indent
\thm@headfont{\quad\scshape}% heading font is bold
\thm@notefont{\upshape\mdseries}% same as heading font
\thm@headpunct{.}% no period after heading
\thm@headsep 5\p@ plus\p@ minus\p@\relax
\itshape % body font
}
\vbadness=9999
\tolerance=9999
\doublehyphendemerits=10000
\doublehyphendemerits 640000 % corresponds to badness 800
\finalhyphendemerits 1000000 % corresponds to badness 1000
\flushbottom
\frenchspacing
\ps@headings
\twocolumn
% Screen PDF compatability
\newcommand{\medline}[1]{%
\unskip\unskip\ignorespaces}
%%%%for smaller size text
\newenvironment{methods}{%
\begingroup
\def\section{%
\@startsection{section}{1}{\z@}
{-24\p@ plus -3\p@}{4\p@}
{\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
\def\subsection{%
\@startsection{subsection}{2}{\z@}
{-5\p@ plus -2\p@}{4\p@}
{\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
\def\subsubsection{%
\@startsection{subsubsection}{3}{\z@}
{-6\p@ plus -1\p@}{-1em}
{\reset@font\normalfont\normalsize\itshape}}
\footnotesize
\par}
{\par\endgroup\bigskip\@afterheading\@afterindentfalse}
\graphicspath{{g:/artwork/oup/bioinfo/}}
\language=2
\hyphenation{Figure Table Figures Tables}
\newcommand{\href}[2]{#2}
\renewenvironment{proof}[1][\proofname]{\par
\normalfont \topsep6\p@\@plus6\p@\relax
\labelsep 0.5em
\trivlist
\item[\hskip\labelsep\hskip1em\textsc{#1}.]\ignorespaces
}{\endtrivlist\@endpefalse}
%%Different Bonds
\def\sbond{\ensuremath{\raise.25ex\hbox{${-}\!\!\!\!{-}$}}\kern -.9pt}
\def\dbond{\ensuremath{\raise.25ex\hbox{=$\!$=}}}
\def\tbond{\ensuremath{\raise.20ex\hbox{${\equiv}\!\!\!{\equiv}$}}}
\newcommand{\query}[2][0pt]{}%
\renewcommand{\dag}{{\mathversion{normal}$^{\dagger}$}}
\endinput
Test templates articles frontiers/frontiersSCNS.cls 0 → 100644
View file @ 39986221
\newcommand\classname{frontiersSCNS} %this file is based in bioninfo.cls
\newcommand\lastmodifieddate{2016/11/10}
\newcommand\versionnumber{2.6}
% For printing crop marks
\newif\if@cropmarkson \@cropmarksontrue
\NeedsTeXFormat{LaTeX2e}[2013/26/03]
\ProvidesClass{\classname}[\lastmodifieddate\space\versionnumber]
\setlength{\paperheight}{11truein}
\setlength{\paperwidth}{8.5truein}
\newif\if@final
\DeclareOption{draft}{\PassOptionsToPackage{draft}{graphicx}}
\DeclareOption{paper}{\PassOptionsToPackage{paper}{graphicx}}
\DeclareOption{a4paper}{\PassOptionsToPackage{a4}{crop}}
\DeclareOption{centre}{\PassOptionsToPackage{center}{crop}}
\DeclareOption{crop}{\PassOptionsToPackage{cam}{crop}\global\@cropmarksontrue}
\DeclareOption{nocrop}{\PassOptionsToPackage{off}{crop}\global\@cropmarksonfalse}
\DeclareOption{info}{\PassOptionsToPackage{info}{crop}}
\DeclareOption{noinfo}{\PassOptionsToPackage{noinfo}{crop}}
\DeclareOption{final}{\global\@finaltrue}
\DeclareOption{utf8}{\PassOptionsToPackage{utf8}{inputenc}}
\ExecuteOptions{a4paper,nocrop,centre,info,paper}
\ProcessOptions
% Load all necessary packages
\RequirePackage{inputenc,crop,graphicx,amsmath,array,color,amssymb,flushend,stfloats,amsthm,chngpage,times,datetime,parskip}
\def\helvetica{\fontfamily{phv}\selectfont}
\def\helveticaitalic{\fontfamily{phv}\itshape\selectfont}
\def\helveticabold{\fontfamily{phv}\bfseries\selectfont}
\def\helveticabolditalic{\fontfamily{phv}\bfseries\itshape\selectfont}
\usepackage[usenames,dvipsnames]{xcolor}
\usepackage[labelsep=quad,indention=10pt]{caption}
\usepackage[labelfont=bf,list=true]{subcaption}
\newcommand\@ptsize{0}
% Set twoside printing
\@twosidetrue
% Marginal notes are on the outside edge
\@mparswitchfalse
\reversemarginpar
\renewcommand\normalsize{%
\@setfontsize\normalsize{12}{12}%
\abovedisplayskip 10\p@ \@plus2\p@ \@minus5\p@
\abovedisplayshortskip \z@ \@plus3\p@
\belowdisplayshortskip 6\p@ \@plus3\p@ \@minus3\p@
\belowdisplayskip \abovedisplayskip
\let\@listi\@listI}
\normalsize
\let\@bls\baselineskip
\newcommand\small{%
\@setfontsize\small{11}{12}%
\abovedisplayskip 11\p@ minus 3\p@
\belowdisplayskip \abovedisplayskip
\abovedisplayshortskip \z@ plus 2\p@
\belowdisplayshortskip 4\p@ plus 2\p@ minus2\p@
\def\@listi{\topsep 4.5\p@ plus 2\p@ minus 1\p@
\itemsep \parsep
\topsep 4\p@ plus 2\p@ minus 2\p@}}
\newcommand\footnotesize{%
\@setfontsize\footnotesize{8}{10}%
\abovedisplayskip 6\p@ minus 3\p@
\belowdisplayskip\abovedisplayskip
\abovedisplayshortskip \z@ plus 3\p@
\belowdisplayshortskip 6\p@ plus 3\p@ minus 3\p@
\def\@listi{\topsep 3\p@ plus 1\p@ minus 1\p@
\parsep 2\p@ plus 1\p@ minus 1\p@\itemsep \parsep}}
\def\scriptsize{\@setfontsize\scriptsize{11pt}{11pt}}
\def\tiny{\@setfontsize\tiny{10pt}{11pt}}
\def\large{\@setfontsize\large{13pt}{14pt}}
\def\Large{\@setfontsize\Large{14pt}{16}}
\def\LARGE{\@setfontsize\LARGE{15pt}{17pt}}
\def\huge{\@setfontsize\huge{22pt}{22pt}}
\def\Huge{\@setfontsize\Huge{30pt}{30pt}}
\DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl}
\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc}
% Line spacing
\setlength\lineskip{1\p@}
\setlength\normallineskip{1\p@}
\renewcommand\baselinestretch{}
% Set inter-para skips
\setlength\smallskipamount{3\p@ \@plus 1\p@ \@minus 1\p@}
\setlength\medskipamount{6\p@ \@plus 2\p@}
\setlength\bigskipamount{12\p@ \@plus 4\p@ \@minus 4\p@}
% Paragraph dimensions and inter-para spacing
\setlength\parindent{3mm}
\setlength{\parskip}{\medskipamount}
% Page break penalties
\@lowpenalty 51
\@medpenalty 151
\@highpenalty 301
% Disallow widows and orphans
\clubpenalty 10000
\widowpenalty 10000
% Disable page breaks before equations, allow pagebreaks after
% equations and discourage widow lines before equations.
\displaywidowpenalty 100
\predisplaypenalty 10000
\postdisplaypenalty 2500
% Allow breaking the page in the middle of a paragraph
\interlinepenalty 0
% Disallow breaking the page after a hyphenated line
\brokenpenalty 10000
% Hyphenation; don't split words into less than three characters
\lefthyphenmin=3
\righthyphenmin=3
%
% Set page layout dimensions
%
\setlength\headheight{16\p@} % height of running head
\setlength\topmargin{1.3pc} % head margin
\addtolength\topmargin{-1in} % subtract out the 1 inch driver margin
\setlength\topskip{10\p@} % height of first line of text
\setlength\headsep{19\p@} % space below running head --
\setlength\footskip{34\p@} % space above footer line
\setlength\maxdepth{1\topskip} % pages can be short or deep by half a line?
\setlength\textwidth{42pc} % text measure excluding margins
\setlength\textheight{56\baselineskip} % 54 lines on a full page,
\addtolength\textheight{\topskip} % including the first
% line on the page
% Set the margins
\setlength\marginparsep{3\p@}
\setlength\marginparpush{3\p@}
\setlength\marginparwidth{35\p@}
\setlength\oddsidemargin{4.5pc}
\addtolength\oddsidemargin{-1in} % subtract out the 1 inch driver margin
\setlength\@tempdima{\paperwidth}
\addtolength\@tempdima{-\textwidth}
\addtolength\@tempdima{-4.5pc}
\setlength\evensidemargin{\@tempdima}
\addtolength\evensidemargin{-1in}
\setlength\columnsep{1.5pc} % space between columns for double-column text
\setlength\columnseprule{0\p@} % width of rule between two columns
% Footnotes
\setlength\footnotesep{9\p@} % space between footnotes
% space between text and footnote
\setlength{\skip\footins}{12\p@ \@plus 6\p@ \@minus 1\p@}
% Float placement parameters
% The total number of floats that can be allowed on a page.
\setcounter{totalnumber}{10}
% The maximum number of floats at the top and bottom of a page.
\setcounter{topnumber}{5}
\setcounter{bottomnumber}{5}
% The maximum part of the top or bottom of a text page that can be
% occupied by floats. This is set so that at least four lines of text
% fit on the page.
\renewcommand\topfraction{.9}
\renewcommand\bottomfraction{.9}
% The minimum amount of a text page that must be occupied by text.
% This should accomodate four lines of text.
\renewcommand\textfraction{.06}
% The minimum amount of a float page that must be occupied by floats.
\renewcommand\floatpagefraction{.94}
% The same parameters repeated for double column output
\renewcommand\dbltopfraction{.9}
\renewcommand\dblfloatpagefraction{.9}
% Space between floats
\setlength\floatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
% Space between floats and text
\setlength\textfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
% Space above and below an inline figure
\setlength\intextsep {18\p@ \@plus 2\p@ \@minus 2\p@}
% For double column floats
\setlength\dblfloatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
\setlength\dbltextfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
% Space left at top, bottom and inbetween floats on a float page.
\setlength\@fptop{0\p@} % no space above float page figures
\setlength\@fpsep{12\p@ \@plus 1fil}
\setlength\@fpbot{0\p@}
% The same for double column
\setlength\@dblfptop{0\p@}
\setlength\@dblfpsep{12\p@ \@plus 1fil}
\setlength\@dblfpbot{0\p@}
% Override settings in mathtime back to TeX defaults
\DeclareMathSizes{5} {5} {5} {5}
\DeclareMathSizes{6} {6} {5} {5}
\DeclareMathSizes{7} {7} {5} {5}
\DeclareMathSizes{8} {8} {6} {5}
\DeclareMathSizes{9} {9} {6.5} {5}
\DeclareMathSizes{10} {10} {7.5} {5}
\DeclareMathSizes{12} {12} {9} {7}
% Page styles
\def\ps@headings
{%
\def\@oddfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
\hbox to \textwidth{\helveticabold\small {Frontiers}\hfill \thepage}%
}}%
\def\@evenfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
\hbox to \textwidth{\helvetica\small {\color{red}This is a provisional file, not the final typeset article}\hfill\helveticabold\color{black}\thepage}%
}}%
\def\@evenhead{\vbox{\hbox to \textwidth{\fontsize{11}{10}\selectfont
\helveticabold{\fontshape{it}\selectfont
\strut\firstAuthorLast}\hfill\strut\rightmark}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
\def\@oddhead{\vbox{\hbox to \textwidth{\fontsize{11}{10}\selectfont
\helveticabold{\fontshape{it}\selectfont
\strut\firstAuthorLast}\hfill\strut\rightmark}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
\def\titlemark##1{\markboth{##1}{##1}}%
\def\authormark##1{\gdef\leftmark{##1}}%
}
\def\ps@opening
{%
\def\@oddfoot{\vbox to 13\p@{\hbox{\rule{\textwidth}{1\p@}}\vss
\hbox to \textwidth{\helvetica
\fontsize{7}{9}\fontshape{n}\selectfont \space %
\hfill\small\helveticabold\thepage}%
}}%
\def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}{1\p@}\vss
\hbox to \textwidth{\helvetica\thepage\hfill
\fontsize{7}{9}\fontshape{n}\selectfont \space }%
}}%
\let\@evenhead\relax
\let\@oddhead\relax}
% Page range
\newif\iflastpagegiven \lastpagegivenfalse
\newcommand\firstpage[1]{%
\gdef\@firstpage{#1}%
\ifnum\@firstpage>\c@page
\setcounter{page}{#1}%
\ClassWarning{BIO}{Increasing pagenumber to \@firstpage}%
\else \ifnum\@firstpage<\c@page
\ClassWarning{BIO}{Firstpage lower than pagenumber}\fi\fi
\xdef\@firstpage{\the\c@page}%
}
\def\@firstpage{1}
\def\pagenumbering#1{%
\global\c@page \@ne
\gdef\thepage{\csname @#1\endcsname \c@page}%
\gdef\thefirstpage{%
\csname @#1\endcsname \@firstpage}%
\gdef\thelastpage{%
\csname @#1\endcsname \@lastpage}%
}
\newcommand\lastpage[1]{\xdef\@lastpage{#1}%
\global\lastpagegiventrue}
\def\@lastpage{0}
\def\setlastpage{\iflastpagegiven\else
\edef\@tempa{@lastpage@}%
\expandafter
\ifx \csname \@tempa \endcsname \relax
\gdef\@lastpage{0}%
\else
\xdef\@lastpage{\@nameuse{@lastpage@}}%
\fi
\fi }
\def\writelastpage{%
\iflastpagegiven \else
\immediate\write\@auxout%
{\string\global\string\@namedef{@lastpage@}{\the\c@page}}%
\fi
}
\def\thepagerange{%
\ifnum\@lastpage =0 {\ \bf ???} \else
\ifnum\@lastpage = \@firstpage \ \thefirstpage\else
\thefirstpage--\thelastpage \fi\fi}
\AtBeginDocument{\setlastpage
\pagenumbering{arabic}%
}
\AtEndDocument{%
\writelastpage
\if@final
\clearemptydoublepage
\else
\clearpage
\fi}
%
% Sectional units
%
% Counters
\newcounter{section}
\newcounter{subsection}[section]
\newcounter{subsubsection}[subsection]
\newcounter{paragraph}[subsubsection]
\newcounter{subparagraph}[paragraph]
\newcounter{figure}
\newcounter{subfigure}
\newcounter{table}
% Form of the numbers
\newcommand\thepage{\arabic{page}}
\renewcommand\thesection{\arabic{section}}
\renewcommand\thesubsection{{\thesection.\arabic{subsection}}}
\renewcommand\thesubsubsection{{\thesubsection.\arabic{subsubsection}}}
\renewcommand\theparagraph{\thesubsubsection.\arabic{paragraph}}
\renewcommand\thesubparagraph{\theparagraph.\arabic{subparagraph}}
\renewcommand\theequation{\arabic{equation}}
% Form of the words
\newcommand\contentsname{Contents}
\newcommand\listfigurename{List of Figures}
\newcommand\listtablename{List of Tables}
\newcommand\partname{Part}
\newcommand\appendixname{Appendix}
\newcommand\abstractname{Abstract}
\newcommand\refname{References}
\newcommand\bibname{References}
\newcommand\indexname{Index}
\newcommand\figurename{Figure}
\newcommand\tablename{Table}
% Clearemptydoublepage should really clear the running heads too
\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}
% Frontmatter, mainmatter and backmatter
\newif\if@mainmatter \@mainmattertrue
\newcommand\frontmatter{%
\clearpage
\@mainmatterfalse
\pagenumbering{roman}}
\newcommand\mainmatter{%
\clearpage
\@mainmattertrue
\pagenumbering{arabic}}
\newcommand\backmatter{%
\clearpage
\@mainmatterfalse}
\newdateformat{mydate}{\THEDAY \ \monthname[\THEMONTH] \THEYEAR}
\newdateformat{mydate2}{\monthname[\THEMONTH] \THEYEAR}
%********
% TITLE *
%********
\newlength{\dropfromtop}
\setlength{\dropfromtop}{\z@}
% Application Notes
\newif\if@appnotes
\newcommand{\application}{%
% \setlength{\dropfromtop}{-2.25pc}%
\global\@appnotestrue}
% Short Title is for the Title of the Article
% Title is for the Title of the Journal
\long\def\title{\@ifnextchar[{\short@title}{\@@title}}
\def\short@title[#1]{\titlemark{#1}\@@@title}
\def\@@title#1{\authormark{#1}\@@@title{#1}}
\long\def\@@@title#1{\gdef\@title{#1}}
\long\def\author{\@ifnextchar[{\short@uthor}{\@uthor}}
\def\short@uthor[#1]{\authormark{#1}\@@author}
\def\@uthor#1{\authormark{#1}\@@author{#1}}
\long\def\@@author#1{\gdef\@author{#1}}
\def\vol#1{\global\def\@vol{#1}}
\def\issue#1{\global\def\@issue{#1}}
\def\address#1{\global\def\@issue{#1}}
\def\history#1{\global\def\@history{#1}}
\def\correspondance#1{\global\def\@correspondance{#1}}
\def\extraAuth#1{\global\def\@extraAuth{#1}}
\def\address#1{\global\def\@address{#1}}
\def\date#1{\gdef\@date{#1}}
%***********
% Colors *
%***********
% Other colors
\definecolor{black}{cmyk}{0, 0, 0, 1}
\definecolor{gray}{cmyk}{0, 0, 0, 0.25}
\definecolor{darkgray}{cmyk}{0, 0, 0, 0.5}
\newlength{\extraspace}
\setlength{\extraspace}{\z@}
\newcommand\maketitle{\par
\begingroup
\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
\long\def\@makefntext##1{\parindent 3mm\noindent
% \@textsuperscript{\normalfont\@thefnmark}\raggedright##1}%
\@textsuperscript{\normalfont\@thefnmark}##1}%
\if@twocolumn
\ifnum \col@number=\@ne
\@maketitle
\else
\twocolumn[\@maketitle]%
\fi
\else
\newpage
\global\@topnum\z@ % Prevents figures from going at top of page.
\@maketitle
\fi
\thispagestyle{opening}\@thanks
\endgroup
\setcounter{footnote}{0}%
\global\let\thanks\relax
\global\let\maketitle\relax
\global\let\@maketitle\relax
\global\let\@address\@empty
\global\let\@history\@empty
\global\let\@extraAuth\@empty
\global\let\@topic\@empty
\global\let\@thanks\@empty
\global\let\@author\@empty
\global\let\@date\@empty
\global\let\@title\@empty
\global\let\@pubyear\@empty
\global\let\address\relax
\global\let\topic\relax
\global\let\extraAuth\relax
\global\let\title\relax
\global\let\author\relax
\global\let\date\relax
\global\let\pubyear\relax
\global\let\@copyrightline\@empty
\global\let\and\relax
\@afterindentfalse\@afterheading
}
\newlength{\aboveskipchk}%for checking oddpage or evenpage top skip
\setlength{\aboveskipchk}{\z@}%
\def\@maketitle{%
\let\footnote\thanks
\clearemptydoublepage
\checkoddpage\ifcpoddpage\setlength{\aboveskipchk}{-7pc}\else\setlength{\aboveskipchk}{-3pc}\fi%for checking oddpage or evenpage top skip%%
\vspace*{\aboveskipchk}%
\vspace{\dropfromtop}%
\hbox to \textwidth{%
\parbox[t]{15pc}{%
\helvetica
\hfil
\flushleft \includegraphics[width=12pc,angle=0]{./logo1.pdf}
}}
\rule{\textwidth}{1\p@}\par%
\helvetica
\hbox to \textwidth{%
\parbox[t]{36.5pc}{%
\vspace*{1sp}
{\helveticabold\fontsize{20}{21}\color{black}\selectfont\raggedright \@title \par}%
\vspace{4.5\p@}
{\helveticabold\fontsize{12}{15}\selectfont\raggedright \@author \par}%
\vspace{4\p@}
{\helvetica\fontsize{12}{12}\selectfont\raggedright\slshape\@address \Address \\ \par}%
\vspace{6\p@}
{\helvetica\fontsize{12}{10}\selectfont\raggedright {Correspondence*:\\ }\@correspondance \corrAuthor \\ \corrEmail \par}
\vspace{4\p@}
{\helvetica\fontsize{12}{12}\selectfont\raggedright\@extraAuth \par}%
\vspace{8\p@}
}%
}
\vspace{14.5\p@}%
}
%***********
% Abstract *
%***********
\newcommand{\absection}[1]{%
\par\noindent{\bfseries #1}\space\ignorespaces}
\newenvironment{abstract}{%
\begingroup
\let\section\absection
\fontfamily{\sfdefault}\fontsize{12}{12}\sffamily\selectfont
{\fontseries{b}\selectfont ABSTRACT}\par}
{\endgroup\smallskip\@afterheading\@afterindentfalse\vskip 12pt plus -2pt minus 2pt}
% Section macros
% Lowest level heading that takes a number by default
\setcounter{secnumdepth}{5}
\renewcommand{\@seccntformat}[1]{\csname the#1\endcsname\quad}
\def\section{%
\@startsection{section}{1}{\z@}
{-10\p@ plus -3\p@}{3\p@}
{\reset@font\raggedright\helveticabold\fontsize{13}{13}\color{black}\selectfont\MakeUppercase}}
\def\subsection{%
\@startsection{subsection}{2}{\z@}
{2\p@ plus -1\p@}{2\p@}
{\reset@font\raggedright\mathversion{bold}\helveticabold\fontsize{11.5}{12}}}
\def\subsubsection{%
\@startsection{subsubsection}{3}{\z@}
{1\p@ plus -1\p@}{1\p@}
{\reset@font\raggedright\mathversion{bold}\helvetica\fontsize{11.5}{12}}}
\def\paragraph{%
\@startsection{paragraph}{4}{\z@}
{1\p@ plus -1\p@}{1\p@}
{\reset@font\itshape\helveticabold\fontsize{11.5}{12}}}
\def\subparagraph{%
\@startsection{subparagraph}{5}{\z@}
{1\p@ plus -1\p@}{1\p@}
{\reset@font\itshape\helvetica\fontsize{11.5}{12}}}
\def\textcolon{\text{\rm :}}
% ********************
% Figures and tables *
% ********************
% Table and array parameters
\setlength\arraycolsep{.5em}
\setlength\tabcolsep{.5em}
\setlength\arrayrulewidth{.5pt}
\setlength\doublerulesep{2.5pt}
\setlength\extrarowheight{\z@}
\renewcommand\arraystretch{1}
%\newlength{\abovecaptionskip}
%\newlength{\belowcaptionskip}
%\setlength{\abovecaptionskip}{13pt}
%\setlength{\belowcaptionskip}{10.5pt}
\long\def\@makecaption#1#2{\vspace{\abovecaptionskip}%
\begingroup
\normalsize
\textbf{#1.}\enskip{#2}\par
\endgroup}
% Table rules
\def\toprule{\noalign{\ifnum0=`}\fi\hrule \@height 0.5pt \hrule \@height 6pt \@width 0pt \futurelet
\@tempa\@xhline}
\def\midrule{\noalign{\ifnum0=`}\fi \hrule \@height 6.75pt \@width 0pt \hrule \@height 0.5pt
\hrule \@height 6pt \@width 0pt \futurelet \@tempa\@xhline}
\def\botrule{\noalign{\ifnum0=`}\fi \hrule \@height 5.75pt \@width 0pt \hrule \@height 0.5pt \futurelet
\@tempa\@xhline}
\def\hrulefill{\leavevmode\leaders\hrule height .5pt\hfill\kern\z@}
\def\thefigure{\@arabic\c@figure}
\def\fps@figure{tbp}
\def\ftype@figure{1}
\def\ext@figure{lof}
\def\fnum@figure{\figurename~\thefigure}
\def\figure{\@float{figure}}
\let\endfigure\end@float
\@namedef{figure*}{\@dblfloat{figure}}
\@namedef{endfigure*}{\end@dblfloat}
\def\thetable{\@arabic\c@table}
\def\fps@table{tbp}
\def\ftype@table{2}
\def\ext@table{lot}
\def\fnum@table{Table~\thetable}
\def\table{\let\source\tablesource\@float{table}}
\def\endtable{\end@float}
\@namedef{table*}{\@dblfloat{table}}
\@namedef{endtable*}{\end@dblfloat}
\newif\if@rotate \@rotatefalse
\newif\if@rotatecenter \@rotatecenterfalse
\def\rotatecenter{\global\@rotatecentertrue}
\def\rotateendcenter{\global\@rotatecenterfalse}
\def\rotate{\global\@rotatetrue}
\def\endrotate{\global\@rotatefalse}
\newdimen\rotdimen
\def\rotstart#1{\special{ps: gsave currentpoint currentpoint translate
#1 neg exch neg exch translate}}
\def\rotfinish{\special{ps: currentpoint grestore moveto}}
\def\rotl#1{\rotdimen=\ht#1\advance\rotdimen by \dp#1
\hbox to \rotdimen{\vbox to\wd#1{\vskip \wd#1
\rotstart{270 rotate}\box #1\vss}\hss}\rotfinish}
\def\rotr#1{\rotdimen=\ht #1\advance\rotdimen by \dp#1
\hbox to \rotdimen{\vbox to \wd#1{\vskip \wd#1
\rotstart{90 rotate}\box #1\vss}\hss}\rotfinish}
\newif\ifsub@@figure \sub@@figuretrue
\def\thesubfigure{\@arabic\c@figure\alph{subfigure}}
\def\fps@subfigure{tbp}
\def\ftype@subfigure{1}
\def\ext@subfigure{lof}
\def\fnum@subfigure{Figure \thesubfigure}
\def\subfigure{\ifsub@@figure\global\sub@@figurefalse\stepcounter{figure}\fi%
\@float{subfigure}}
\let\endsubfigure\end@float
\@namedef{subfigure*}{\ifsub@@figure\global\sub@@figurefalse%
\stepcounter{figure}\fi \@dblfloat{subfigure}}
\@namedef{endsubfigure*}{\end@dblfloat}
\def\endfigure{\global\sub@@figuretrue\end@float}
\@namedef{endfigure*}{\global\sub@@figuretrue\end@dblfloat}
\newdimen\tempdime
\newbox\temptbox
% From ifmtarg.sty
% Copyright Peter Wilson and Donald Arseneau, 2000
\begingroup
\catcode`\Q=3
\long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil}
\long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4}
\long\gdef\@ifnotmtarg#1{\@xifmtarg#1QQ\@firstofone\@gobble\@nil}
\endgroup
\def\tablesize{\@setfontsize\tablesize{10\p@}{10\p@}}
\newenvironment{processtable}[3]{\setbox\temptbox=\hbox{{\tablesize #2}}%
\tempdime\wd\temptbox\@processtable{#1}{#2}{#3}{\tempdime}}
{\relax}
\newcommand{\@processtable}[4]{%
\if@rotate
\setbox4=\vbox to \hsize{\vss\hbox to \textheight{%
\begin{minipage}{#4}%
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
\vskip7\p@\noindent
\parbox{#4}{\fontsize{10}{10}\selectfont #3\par}%
\end{minipage}}\vss}%
\rotr{4}
\else
\hbox to \hsize{\hss\begin{minipage}[t]{#4}%
\vskip2.9pt
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
\vskip6\p@\noindent
\parbox{#4}{\fontsize{8}{9}\selectfont #3\par}%
\end{minipage}\hss}\fi}%
\newcolumntype{P}[1]{>{\raggedright\let\\\@arraycr\hangindent1em}p{#1}}
% ******************************
% List numbering and lettering *
% ******************************
\def\labelenumi{{\rm\arabic{enumi}.}}
\def\theenumi{\arabic{enumi}}
\def\labelenumii{{\rm\alph{enumii}.}}
\def\theenumii{\alph{enumii}}
\def\p@enumii{\theenumi}
\def\labelenumiii{{\rm(\arabic{enumiii})}}
\def\theenumiii{\roman{enumiii}}
\def\p@enumiii{\theenumi(\theenumii)}
\def\labelenumiv{{\rm(\arabic{enumiv})}}
\def\theenumiv{\Alph{enumiv}}
\def\p@enumiv{\p@enumiii\theenumiii}
\def\labelitemi{{\small$\bullet$}}
\def\labelitemii{{\small$\bullet$}}
\def\labelitemiii{{\small$\bullet$}}
\def\labelitemiv{{\small$\bullet$}}
\def\@listI{\leftmargin\leftmargini \topsep\medskipamount}
\let\@listi\@listI
\@listi
\def\@listii{\topsep\z@\leftmargin\leftmarginii}
\def\@listiii{\leftmargin\leftmarginiii \topsep\z@}
\def\@listiv{\leftmargin\leftmarginiv \topsep\z@}
\def\@listv{\leftmargin\leftmarginv \topsep\z@}
\def\@listvi{\leftmargin\leftmarginvi \topsep\z@}
\setlength{\leftmargini}{3mm}
\setlength{\leftmarginii}{\z@}
\setlength{\leftmarginiii}{\z@}
\setlength{\leftmarginiv}{\z@}
% Changes to the list parameters for enumerate
\def\enumargs{%
\partopsep \z@
\itemsep 3\p@
\parsep \z@
\labelsep 0.5em
\listparindent \parindent
\itemindent \z@
\topsep 2\p@
}
\def\enumerate{%
\@ifnextchar[{\@numerate}{\@numerate[0]}}
\def\@numerate[#1]{%
\ifnum \@enumdepth >3 \@toodeep\else
\advance\@enumdepth \@ne
\edef\@enumctr{enum\romannumeral\the\@enumdepth}
\list{\csname label\@enumctr\endcsname}{%
\enumargs
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@enumdepth\endcsname}
\usecounter{\@enumctr}
\settowidth\labelwidth{#1}
\addtolength{\leftmargin}{\labelwidth}
\addtolength{\leftmargin}{\labelsep}
\def\makelabel##1{\hss \llap{##1}}}%
\fi
}
\let\endenumerate\endlist
% Changes to the list parameters for itemize
\def\itemargs{%
\partopsep \z@
\itemsep 3\p@
\parsep \z@
\labelsep 0.5em
\rightmargin \z@
\listparindent \parindent
\itemindent \z@
\topsep 2\p@
}
\def\itemize{%
\@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}}
\def\@itemize[#1]{%
\ifnum \@itemdepth >3 \@toodeep\else
\advance\@itemdepth \@ne
\edef\@itemctr{item\romannumeral\the\@itemdepth}
\list{\csname label\@itemctr\endcsname}{%
\itemargs
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@itemdepth\endcsname}
\settowidth\labelwidth{#1}
\addtolength{\leftmargin}{\labelwidth}
\addtolength{\leftmargin}{\labelsep}
\def\makelabel##1{\hss \llap{##1}}}%
\fi
}
\let\enditemize\endlist
\newenvironment{unlist}{%
\begin{list}{}%
{\setlength{\labelwidth}{\z@}%
\setlength{\labelsep}{\z@}%
\setlength{\topsep}{\medskipamount}%
\setlength{\itemsep}{3\p@}%
\setlength{\leftmargin}{2em}%
\setlength{\itemindent}{-2em}}}
{\end{list}}
% ***********************
% Quotes and Quotations *
% ***********************
\def\quotation{\par\begin{list}{}{
\setlength{\topsep}{\medskipamount}
\setlength{\leftmargin}{2em}%
\setlength{\rightmargin}{\z@}%
\setlength\labelwidth{0pt}%
\setlength\labelsep{0pt}%
\listparindent\parindent}%
\item[]}
\def\endquotation{\end{list}}
\let\quote\quotation
\let\endquote\endquotation
\skip\@mpfootins = \skip\footins
\fboxsep=6\p@
\fboxrule=1\p@
% *******************
% Table of contents *
% *******************
\newcommand\@pnumwidth{4em}
\newcommand\@tocrmarg{2.55em plus 1fil}
\newcommand\@dotsep{1000}
\setcounter{tocdepth}{4}
\def\numberline#1{\hbox to \@tempdima{{#1}}}
\def\@authortocline#1#2#3#4#5{%
\vskip 1.5\p@
\ifnum #1>\c@tocdepth \else
{\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip
\parindent #2\relax\@afterindenttrue
\interlinepenalty\@M
\leavevmode
\@tempdima #3\relax
\advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
{\itshape #4}\nobreak
\leaders\hbox{$\m@th
\mkern \@dotsep mu\hbox{.}\mkern \@dotsep
mu$}\hfill
\nobreak
\hb@xt@\@pnumwidth{\hfil}%
\par}%
\fi}
\newcommand*\l@author{\@authortocline{2}{0pt}{30pt}}
\newcommand*\l@section{\@dottedtocline{3}{11pt}{20pt}}
\newcommand*\l@subsection{\@dottedtocline{4}{31pt}{29pt}}
\newcommand*\l@subsubsection[2]{}
% ***********
% Footnotes *
% ***********
\def\footnoterule{\noindent\rule{\columnwidth}{0.5pt}}
\def\@makefnmark{\@textsuperscript{\normalfont\@thefnmark}}%
\newcommand\@makefntext[1]{\noindent{\@makefnmark}\enskip#1}
% ***********
% References *
% ***********
\providecommand{\newblock}{}
\newenvironment{thebibliography}{%
\section{\bibname}%
\begingroup
\small
\begin{list}{}{%
\setlength{\topsep}{\z@}%
\setlength{\labelsep}{\z@}%
\settowidth{\labelwidth}{\z@}%
\setlength{\leftmargin}{4mm}%
\setlength{\itemindent}{-4mm}}\small}
{\end{list}\endgroup}
\RequirePackage{natbib}
% **********
% Appendix *
% **********
\newif\ifappend
\def\appendix{\par
\setcounter{section}{0}
\setcounter{subsection}{0}
\appendtrue
}
%Math parameters
\setlength{\jot}{5\p@}
\mathchardef\@m=1500 % adapted value
\def\frenchspacing{\sfcode`\.\@m \sfcode`\?\@m \sfcode`\!\@m
\sfcode`\:\@m \sfcode`\;\@m \sfcode`\,\@m}
% Theorems
\def\th@plain{%
%% \let\thm@indent\noindent % no indent
\thm@headfont{\quad\scshape}% heading font is bold
\thm@notefont{\upshape\mdseries}% same as heading font
\thm@headpunct{.}% no period after heading
\thm@headsep 5\p@ plus\p@ minus\p@\relax
\itshape % body font
}
\vbadness=9999
\tolerance=9999
\doublehyphendemerits=10000
\doublehyphendemerits 640000 % corresponds to badness 800
\finalhyphendemerits 1000000 % corresponds to badness 1000
\flushbottom
\frenchspacing
\ps@headings
\twocolumn
% Screen PDF compatability
\newcommand{\medline}[1]{%
\unskip\unskip\ignorespaces}
%%%%for smaller size text
\newenvironment{methods}{%
\begingroup
\def\section{%
\@startsection{section}{1}{\z@}
{-24\p@ plus -3\p@}{4\p@}
{\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
\def\subsection{%
\@startsection{subsection}{2}{\z@}
{-5\p@ plus -2\p@}{4\p@}
{\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
\def\subsubsection{%
\@startsection{subsubsection}{3}{\z@}
{-6\p@ plus -1\p@}{-1em}
{\reset@font\normalfont\normalsize\itshape}}
\footnotesize
\par}
{\par\endgroup\bigskip\@afterheading\@afterindentfalse}
\graphicspath{{g:/artwork/oup/bioinfo/}}
\language=2
\hyphenation{Figure Table Figures Tables}
\newcommand{\href}[2]{#2}
\renewenvironment{proof}[1][\proofname]{\par
\normalfont \topsep6\p@\@plus6\p@\relax
\labelsep 0.5em
\trivlist
\item[\hskip\labelsep\hskip1em\textsc{#1}.]\ignorespaces
}{\endtrivlist\@endpefalse}
%%Different Bonds
\def\sbond{\ensuremath{\raise.25ex\hbox{${-}\!\!\!\!{-}$}}\kern -.9pt}
\def\dbond{\ensuremath{\raise.25ex\hbox{=$\!$=}}}
\def\tbond{\ensuremath{\raise.20ex\hbox{${\equiv}\!\!\!{\equiv}$}}}
\newcommand{\query}[2][0pt]{}%
\renewcommand{\dag}{{\mathversion{normal}$^{\dagger}$}}
\endinput
Test templates articles frontiers/test.bib 0 → 100644
View file @ 39986221
@Article{ Neuro2013,
author = "Author1 LastName1 and Author2 LastName2 and Author3 LastName2",
title = "Article Title",
volume = "30",
number = "30",
pages = "10127--10134",
year = "2013",
doi = "10.3389/fnins.2013.12345",
URL = "http://www.frontiersin.org/Neuroscience/10.3389/fnins.2013.12345/abstract",
journal = "Frontiers in Neuroscience"
}
@Article{ Gene2012,
author = "Name OtherAuthor and Name S. Coauthor",
title = "Article Title",
volume = "30",
number = "49",
pages = "16417--16418",
year = "2012",
doi = "10.3389/fgene.2012.54321",
URL = "http://www.frontiersin.org/Genetics/10.3389/fgene.2012.54321/abstract",
journal = "Frontiers in Genetics"
}
@Article{ Neurobot2013,
author = "Name4 Author4 and Name5 Author5",
title = "Title of the Article",
volume = "7",
number = "25",
year = "2013",
doi = "10.3389/fnbot.2013.56789",
URL = "http://www.frontiersin.org/Neurorobotics/10.3389/fnbot.2013.56789/abstract",
journal = "Frontiers in Neurorobotics"
}
journal/Journal-de-bord_MOOC-RR_Marc-Oudart_2.Rmd
View file @ 39986221
......@@ -162,6 +162,36 @@ Egalement pour un cahier de laboratoire avec classement par thèmes et étiquett
Enfin, pour un article reproductible.
- RStudio : possibilité de faire article et facile d'accès. Navigation limitée.
## Rendre compte de son activité
1. Le reporting
Compte rendu d'activité pour décrire à peu près tout ce qu'on fait pour que le tuteur puisse suivre et aider, pour faire un rapport ou article, pour que les travaux continus, pour la science ouverte.
2. Logistique
Avoir un dépot en ligne (Github/Gitlab).
Rendu public.
Faire les reporting tant que les infos sont fraiches.
3. Organisation du CRA
Structure :
- Résultats : ref biblio mais PAS ToDo list.
- Développement :
- Journal : Reporting.
- Travail effectué
- Points bloquants et questions. C'est cette partie auquelle le référant peut apporter sa contribution.
- Travaux prévus
- Conclusion : A la fin du stage. Quoi faire ensuite ? Comment j'ai tenu ce journal ? Comment continuer mon travail ?
Comme un cahier de labo, il ne faut pas éditer ce qu'on a déjà écrit ou alors il faut le préciser avec une petite marque __edit__.
### Templates RMarkdown pour articles scientifiques
```{r}
install.packages("rticles")
```
Ensuite _File_ --> _New file_ --> _RMarkdown_ --> _From template_
<!-- ## R Markdown
......
Markdown is supported
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