diff --git a/Test templates articles frontiers/Test templates articles frontiers.Rmd b/Test templates articles frontiers/Test templates articles frontiers.Rmd new file mode 100644 index 0000000000000000000000000000000000000000..c69f996c9a2de1242d1bd930954febeb1ae0a3e8 --- /dev/null +++ b/Test templates articles frontiers/Test templates articles frontiers.Rmd @@ -0,0 +1,170 @@ +--- +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 {-} + + + +## 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 {-} + + + +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 {-} + + + +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. +``` + diff --git a/Test templates articles frontiers/Test-templates-articles-frontiers.log b/Test templates articles frontiers/Test-templates-articles-frontiers.log new file mode 100644 index 0000000000000000000000000000000000000000..46a5fd8610a9ce9d87ac27b024cecdda1182be27 --- /dev/null +++ b/Test templates articles frontiers/Test-templates-articles-frontiers.log @@ -0,0 +1,1004 @@ +This is pdfTeX, Version 3.14159265-2.6-1.40.18 (MiKTeX 2.9.6500 64-bit) (preloaded format=pdflatex 2018.1.29) 6 APR 2020 13:04 +entering extended mode 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% +% % +% 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}} +\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}} +\newcommand{\BuiltInTok}[1]{#1} +\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}} +\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}} +\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}} +\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}} +\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}} +\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}} +\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}} +\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}} +\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}} +\newcommand{\ExtensionTok}[1]{#1} +\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}} +\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}} +\newcommand{\ImportTok}[1]{#1} +\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}} +\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}} +\newcommand{\NormalTok}[1]{#1} +\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}} +\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}} +\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}} +\newcommand{\RegionMarkerTok}[1]{#1} +\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}} +\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}} +\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}} +\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}} +\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}} +\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} diff --git a/Test templates articles frontiers/Test-templates-articles-frontiers_files/figure-latex/Figure-1-1.pdf b/Test templates articles frontiers/Test-templates-articles-frontiers_files/figure-latex/Figure-1-1.pdf new file mode 100644 index 0000000000000000000000000000000000000000..04bc61e8a5f9580f200c42308cf5f09fb84c1885 Binary files /dev/null and b/Test templates articles frontiers/Test-templates-articles-frontiers_files/figure-latex/Figure-1-1.pdf differ diff --git a/Test templates articles frontiers/Test-templates-articles-frontiers_files/figure-latex/graph-1.pdf b/Test templates articles frontiers/Test-templates-articles-frontiers_files/figure-latex/graph-1.pdf new file mode 100644 index 0000000000000000000000000000000000000000..5098cf2eaaeb1d1534d08b96481d3ecaa38c2f68 Binary files /dev/null and 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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 diff --git a/Test templates articles frontiers/frontiersHLTH.cls b/Test templates articles frontiers/frontiersHLTH.cls new file mode 100644 index 0000000000000000000000000000000000000000..dfafa0b738803e87a6f5a2790ecf95235ca54e1a --- /dev/null +++ b/Test templates articles frontiers/frontiersHLTH.cls @@ -0,0 +1,956 @@ +\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 diff --git a/Test templates articles frontiers/frontiersSCNS.cls b/Test templates articles frontiers/frontiersSCNS.cls new file mode 100644 index 0000000000000000000000000000000000000000..a9abea40b7d9d9c8f02b0fe9e2fb64c8ef020e84 --- /dev/null +++ b/Test templates articles frontiers/frontiersSCNS.cls @@ -0,0 +1,955 @@ +\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 diff --git a/Test templates articles frontiers/logo1.pdf b/Test templates articles frontiers/logo1.pdf new file mode 100644 index 0000000000000000000000000000000000000000..dc6c6a33291a60866db89c97a1a363928b974b0a Binary files /dev/null and b/Test templates articles frontiers/logo1.pdf differ diff --git a/Test templates articles frontiers/test.bib b/Test templates articles frontiers/test.bib new file mode 100644 index 0000000000000000000000000000000000000000..cbe76bbfc614bc44ab3d06f896f6a9a3d7962cb9 --- /dev/null +++ b/Test templates articles frontiers/test.bib @@ -0,0 +1,34 @@ +@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" +} diff --git a/journal/Journal-de-bord_MOOC-RR_Marc-Oudart_2.Rmd b/journal/Journal-de-bord_MOOC-RR_Marc-Oudart_2.Rmd index 9e2606a9a94f9086e7d1e1b2ca6caa6946d17d13..3355a6ded7fe35784132b0099d3dc5272054106c 100644 --- a/journal/Journal-de-bord_MOOC-RR_Marc-Oudart_2.Rmd +++ b/journal/Journal-de-bord_MOOC-RR_Marc-Oudart_2.Rmd @@ -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_ + +