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reedthesis.cls
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reedthesis.cls
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%
% This file is copyright (C) 2003 Sam Noble. It may be modified so long
% as my name is not removed and the modifier adds his name to the file.
% Redistribution permitted.
%
% 27 Jan 2004 Sam Noble Removed tocbibind dependency.
% 04 Dec 2001 Sam Noble Class file
% 03 Sep 1995 David Perkinson Title Page
% Acknowledgements Page, David Perkinson & Sam Noble
% May 2005 Patrick Carlisle Table of contents chapter definition
% 2004-2005 Ben Salzberg (BTS) a variety of tweaks here and in the template
% 2015 Chester Ismay (CII) modified to create R Markdown template
%
% Oddities:
%
% We *ASSUME* that any time \cleardoublepage is called
% we actually want a blank back side with NO page number/heading
%
% Minor bug -- seems to be a more general LaTeX thing:
% If you use \frontmatter \mainmatter without any chapters inbetween
% be prepared to have the page numbering messed up. Not a big deal,
% but I'm not sure how to fix it.
%
%
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{reedthesis}[2004/01/27 The Reed College Thesis Class]
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{book}}
\ProcessOptions\relax
\LoadClass{book}
\RequirePackage{fancyhdr}
% Added by CII to produce nice looking code in BeginVerbatimEnvironment
\RequirePackage{fancyvrb}
% Added by CII
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\else % if luatex or xelatex
\ifxetex
\usepackage{mathspec}
\usepackage{xltxtra,xunicode}
\else
\usepackage{fontspec}
\fi
\defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
\newcommand{\euro}{€}
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\usepackage{color}
%\newcommand{\VerbBar}{|}
%\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
\DefineVerbatimEnvironment{verbatim}{Verbatim}{xleftmargin=-1em}
\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{\KeywordTok}[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{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{{#1}}}
% \newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{{#1}}}
% \newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{{#1}}}
% \newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
% \newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{{#1}}}
% \newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
% \newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
% \newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
% \newcommand{\ImportTok}[1]{{#1}}
% \newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{{#1}}}}
% \newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
% \newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
% \newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
% \newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{{#1}}}
% \newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{{#1}}}
% \newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{{#1}}}
% \newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{{#1}}}}
% \newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{{#1}}}}
% \newcommand{\BuiltInTok}[1]{{#1}}
% \newcommand{\ExtensionTok}[1]{{#1}}
% \newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{{#1}}}}
% \newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{{#1}}}
% \newcommand{\RegionMarkerTok}[1]{{#1}}
% \newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
% \newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{{#1}}}}}
% \newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{{#1}}}
% \newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{{#1}}}}
% \newcommand{\NormalTok}[1]{{#1}}
\setlength{\emergencystretch}{3em} % prevent overfull lines
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
% End of CII add
% This gives us rules below the headers
\AtBeginDocument{%
\fancyhf{}
\fancyfoot[LE,RO]{\thepage}
% \fancyhead[RE]{\slshape \leftmark}
% \fancyhead[LO]{\slshape \rightmark}
% The above makes your headers in all caps. If you would like different headers, choose one of the following options (be sure to remove the % symbol from both the right and left headers):
% \fancyhead[RE]{\slshape \nouppercase \leftmark} % This makes the headers on the RIGHT side pages be italic and use lowercase With Capitals When Specified.
% \fancyhead[LO]{\slshape \nouppercase \rightmark} % This does the same thing to the LEFT side pages
% or
\fancyhead[RE]{\itshape \nouppercase \leftmark} % The RIGHT headers will be in small caps.
\fancyhead[LO]{\itshape \nouppercase \rightmark} % And so will the LEFT headers
\pagestyle{fancy}
% Psych majors: You do not need the following six lines, as it conflicts with apacite, so comment them out.
\let\oldthebibliography=\thebibliography
\let\endoldthebibliography=\endthebibliography
\renewenvironment{thebibliography}[1]{
\oldthebibliography{#1}
\addcontentsline{toc}{chapter}{\bibname}
}{\endoldthebibliography}
%%%%%% end of things for psych majors to comment out
\let\oldtheindex=\theindex
\let\endoldtheindex=\endtheindex
\renewenvironment{theindex}{
\oldtheindex
\addcontentsline{toc}{chapter}{\indexname}
}{\endoldtheindex}
}
% Stolen from book.cls and modified
\let\RToldchapter\chapter
\renewcommand{\chapter}{\if@openright\RTcleardoublepage
\else\clearpage\fi
\thispagestyle{empty}%
\global\@topnum\z@
\@afterindentfalse
\secdef\@chapter\@schapter}
% Stolen from book.cls PBC 5/12/05
% Using this to actually show "Chapter 1" in TOC instead of "1"
\def\@chapter[#1]#2{\ifnum \c@secnumdepth >\m@ne
\if@mainmatter
\refstepcounter{chapter}%
\typeout{\@chapapp\space\thechapter.}%
\addcontentsline{toc}{chapter}%
{\@chapapp\space\thechapter:\space#1}%
\else
\addcontentsline{toc}{chapter}{#1}%
\fi
\else
\addcontentsline{toc}{chapter}{#1}%
\fi
\chaptermark{#1}%
\addtocontents{lof}{\protect\addvspace{10\p@}}%
\addtocontents{lot}{\protect\addvspace{10\p@}}%
\if@twocolumn
\@topnewpage[\@makechapterhead{#2}]%
\else
\@makechapterhead{#2}%
\@afterheading
\fi}
\newcommand{\RTcleardoublepage}{
\clearpage\if@twoside \ifodd\c@page\else
\thispagestyle{empty}\hbox{}\newpage
\if@twocolumn\hbox{}\newpage\fi\fi\fi}
\let\RToldcleardoublepage\cleardoublepage
\renewcommand{\cleardoublepage}{\RTcleardoublepage}
% adjust margins for binding (changed 2007-04-24 tgp)
\setlength{\oddsidemargin}{.5in}
\setlength{\evensidemargin}{0in}
\setlength{\textwidth}{6.0in}
\setlength{\textheight}{9.0in}
\setlength\topmargin{0in}
\addtolength\topmargin{-\headheight}
\addtolength\topmargin{-\headsep}
%\setlength{\oddsidemargin}{.6in}
%\setlength{\evensidemargin}{0in}
%\setlength{\textwidth}{5.9in}
\addtolength\headheight{2.5pt}
%\addtolength\topmargin{-\headheight}
%\addtolength\topmargin{-\headsep}
%\addtolength\textheight{1in}
%\addtolength\textheight{\headheight}
%\addtolength\textheight{\headsep}
\def\degree#1{\gdef \@degree{#1}}
\def\@degree{\@latex@warning@no@line{No \noexpand\degree given}}
\def\institution#1{\gdef \@institution{#1}}
\def\@institution{\@latex@warning@no@line{No \noexpand\institution given}}
\def\division#1{\gdef \@division{#1}}
\def\@division{\@latex@warning@no@line{No \noexpand\division given}}
\def\department#1{\gdef \@department{#1}}
\def\@department{\@latex@warning@no@line{No \noexpand\department given}}
\def\thedivisionof#1{\gdef \@thedivisionof{#1}}
\def\@thedivisionof{The Division of}
\def\approvedforthe#1{\gdef \@approvedforthe{#1}}
\def\@approvedforthe{Division}
\def\advisor#1{\gdef \@advisor{#1}}
\def\@advisor{\@latex@warning@no@line{No \noexpand\advisor given}}
\def\altadvisor#1{\gdef \@altadvisor{#1} \@altadvisortrue}
\global\let\@altadvisor\@empty
\newif\if@altadvisor
\@altadvisorfalse
\renewcommand\l@chapter[2]{%
\ifnum \c@tocdepth >\m@ne
\addpenalty{-\@highpenalty}%
\vskip 1.0em \@plus\p@
\setlength\@tempdima{1.5em}%
\begingroup
\parindent \z@ \rightskip \@pnumwidth
\parfillskip -\@pnumwidth
\leavevmode \bfseries
\advance\leftskip\@tempdima
\hskip -\leftskip
#1\nobreak\normalfont
\leaders\hbox{$\m@th \mkern \@dotsep mu\hbox{.}\mkern \@dotsep mu$}\hfill
\nobreak\hb@xt@\@pnumwidth{\bfseries \hss #2}\par
\penalty\@highpenalty
\endgroup
\fi}
%%% Added by CII
\newenvironment{acknowledgements}{%
\if@twocolumn
\@restonecoltrue\onecolumn
\else
\@restonecolfalse
\fi
\chapter*{Remerciements}
\fontsize{12}{14}\selectfont
}{\clearpage \if@restonecol\twocolumn\fi}%
\newenvironment{preface}{%
\if@twocolumn
\@restonecoltrue\onecolumn
\else
\@restonecolfalse
\fi
\chapter*{}
\fontsize{12}{14}\selectfont
}{\clearpage \if@restonecol\twocolumn\fi
\begin{center}
\includegraphics[scale=0.32]{P10200612.JPG}
\end{center}
}%
% End of CII add
\newenvironment{abstract}{%
\if@twocolumn
\@restonecoltrue\onecolumn
\else
\@restonecolfalse
\fi
\chapter*{Résumé de la thèse / Abstract}
\fontsize{12}{14}\selectfont
}{\clearpage \if@restonecol\twocolumn\fi}%
\newenvironment{dedication}{%
\if@twocolumn
\@restonecoltrue\onecolumn
\else
\@restonecolfalse
\fi
\chapter*{Liste des abréviations}
\fontsize{12}{14}\selectfont
}{\clearpage \if@restonecol\twocolumn\fi}%
\ifx\@pdfoutput\@undefined
\newcommand{\RTpercent}{\@percentchar\space}
\AtBeginDvi{\special{!\RTpercent Reed College LaTeX Thesis Class 2001/12/04 SN}}
\AtBeginDvi{\special{rawpostscript \RTpercent Reed College LaTeX Thesis Class 2001/12/04 SN}}
\else
\AtEndDocument{\pdfinfo{/Creator (Reed College LaTeX Thesis Class 2001/12/04 SN)}}
\fi
% I hacked the title page to all be the same font size
% as requested by the library, BTS 2005
\renewcommand{\maketitle}{
{\pagestyle{fancy}
\begin{titlepage}
\newpage
\begin{titlepage}
\newgeometry{left=2.5cm, bottom=3cm, top=2cm, right=2.5cm}
\tikz[remember picture,overlay] \node[opacity=1,inner sep=0pt, outer sep=0pt] at (72.2mm, -114.25mm){\includegraphics{PhD_Couverture_Fond.pdf}};
\fontfamily{phv}\fontseries{mc}\selectfont
%*****************************************************
%******************** TITRE **************************
%*****************************************************
\centering
\color{Valentia}
\fontsize{18}{13}\selectfont
\textbf{THÈSE POUR OBTENIR LE GRADE DE DOCTEUR\\ DE L’UNIVERSITÉ DE MONTPELLIER}
\normalsize
\color{black}
\bigskip
\textbf{En Écologie et Biodiversité}
\bigskip
\textbf{École doctorale GAIA}
\bigskip
\textbf{Unité de recherche MIVEGEC (UMR 224)}
\color{Titleblue}
\fontsize{17}{20.4}\selectfont
\vspace{2cm}
\textbf{Fouille de données spatio-temporelles pour l’étude du risque de transmission résiduelle du paludisme à échelle paysagère en milieu rural ouest-africain}
%*****************************************************
\vspace{2cm}
\fontsize{15}{18}\selectfont
\color{black}
\textbf{Présentée par Paul TACONET\\
le 2 juin 2022}
\bigskip
\fontsize{13}{15.6}\selectfont
\textbf{Sous la direction de Nicolas MOIROUX\\}
%et [Prénom NOM du co-Directeur de thèse le cas échéant]}
\vspace{1.5cm}
\normalsize
\textbf{Devant le jury composé de}\\
\bigskip
\fontsize{10}{12}\selectfont
\vspace{1.5mm}
\begin{tabular}{p{12cm}l}
\textbf{Catherine LINARD, Professeure, Université de Namur} & \textbf{Rapportrice} \\
\textbf{Ibrahima DIA, Directeur de recherche, Institut Pasteur de Dakar} & \textbf{Rapporteur} \\
\textbf{Florence FOURNET, Directrice de recherche, IRD (UMR 224)} & \textbf{Examinatrice, Présidente} \\
\textbf{Jean GAUDART, Professeur, Aix Marseille Université (UMR 1252)} & \textbf{Examinateur} \\
\textbf{Emmanuel ROUX, Chargé de recherche, IRD (UMR 228)} & \textbf{Examinateur} \\
\textbf{Nicolas MOIROUX, Chargé de recherche, IRD (UMR 224)} & \textbf{Directeur de thèse} \\
\textbf{Annelise TRAN, Chargée de recherche, CIRAD (UMR 1470)} & \textbf{Invitée} \\
\textbf{Morgan MANGEAS, Directeur de Recherche, IRD (UMR 250)} & \textbf{Invité} \\
\end{tabular}
%************************************
%** LOGO UNIVERSITÉ
%*****************************************************
\vspace{\fill}
\begin{center}
\includegraphics[scale=1]{logo_um.png}
\end{center}
\vspace{-27mm}
\endgroup
\end{titlepage}
}
}
%
%
% \newcommand{\bgimg}[1]{
% \AddToShipoutPicture
% {
% \put(\LenToUnit{0 cm},\LenToUnit{0 cm})
% {
% \includegraphics[width=\paperwidth,height=\paperheight]{#1}
% }
% }
% }
%
%
%
%
% \renewcommand{\maketitle}{
% {\pagestyle{fancy}
% \begin{titlepage}
% \newpage
% \renewcommand{\headrulewidth}{0pt}
%
% % \fancyfoot[C]{\includegraphics{logo_um.png}}
% % \bgimg{image_um.jpg}
%
% \center
%
% {\fontfamily{phv}\fontseries{ux}\selectfont
% \textcolor{mypink3}{\textbf{\large{THESE POUR OBTENIR LE GRADE DE DOCTEUR \newline DE L'UNIVERSITE DE MONTPELLIER}}} \\[1cm]
% \color{black}
% \textbf{En \@division}\\[0.5cm]
% \textbf{Ecole doctorale \@institution}\\[0.5cm]
% \textbf{Unité de recherche \@department}\\[2 cm]
%
% \color{gray}\textbf{\large{\@title}} \\[3cm]
% \color{black}
% \textbf{Présentée par \@author}\\
% \textbf{Le \@date}\\[1 cm]
%
% \textbf{Sous la direction de \@advisor}\\[2cm]
% %et [Prénom NOM du co-Directeur de thèse le cas échéant]}\\[2cm]
%
% \textbf{Devant le jury composé de}\\
%
%
% \begin{itemize}[label=]
% \item {\footnotesize Prénom NOM, titre, établissement; Statut jury}
% \item {\footnotesize Prénom NOM, titre, établissement; Statut jury}
% \item {\footnotesize Prénom NOM, titre, établissement; Statut jury}
% \item {\footnotesize Prénom NOM, titre, établissement; Statut jury}
% \item {\footnotesize Prénom NOM, titre, établissement; Statut jury}
% \end{itemize}}
% \end{titlepage}
% }
%
% }
%%% solution en intégrant un pdf tout fait :
% \renewcommand{\maketitle}{
% \begin{titlepage}
% \includepdf{page_garde.pdf}
% \end{titlepage}
% }
%
%
% \renewcommand{\maketitle}{%
% {\pagestyle{empty}
% \fontsize{12}{14}\selectfont
% \begin{titlepage}
% \newpage
% \let\footnotesize\small
% \let\footnoterule\relax
% \let \footnote \thanks
%
% \baselineskip = 1.4\baselineskip
% \setbox0=\hbox{of the Requirements for the Degree}
%
% \begin{center}
% \setcounter{page}{1}
% \null\vfil
% {\fontsize{12}{14}\selectfont \@title}
% \vfil
% \centerline{\hbox to \wd0 {\hbox{}\hrulefill\hbox{}}}
% \vfil
% A Thesis \\
% Presented to \\
% \@thedivisionof \ \@division \\
% \@institution
% \vfil
% \centerline{\hbox to \wd0 {\hbox{}\hrulefill\hbox{}}}
% \vfil
% In Partial Fulfillment \\
% of the Requirements for the Degree \\
% \@degree
% \vfil
% \centerline{\hbox to \wd0 {\hbox{}\hrulefill\hbox{}}}
% \bigskip
% \centerline{}
% \bigskip
% {\fontsize{12}{14}\selectfont \lineskip .75em
% \begin{tabular}[t]{c}%
% \@author
% \end{tabular}\par}
% \vskip 1.5em
% {\fontsize{12}{14}\selectfont \@date \par}
% \end{center}\par
% \end{titlepage}
% }
% }
%
%
% From JSS
% Added by CII
\renewcommand{\title}[1]{\def\@title{#1}}
%\newcommand{\Shorttitle}[1]{\def\@Shorttitle{#1}}
\newcommand{\Plainauthor}[1]{\def\@Plainauthor{#1}}
\newcommand{\Abstract}[1]{\def\@Abstract{#1}}
%\newcommand{\Keywords}[1]{\def\@Keywords{#1}}
%\newcommand{\Plainkeywords}[1]{\def\@Plainkeywords{#1}}
\newcommand{\Acknowledgements}[1]{\def\@Acknowledgements{#1}}
\newcommand{\Dedication}[1]{\def\@Dedication{#1}}
\newcommand{\Preface}[1]{\def\@Preface{#1}}
% End of CII add