main.tex

% This template was originally by R. Jacob Vogelstein
% Updated on March 1, 2010 by Noah J. Cowan
% Updated on May 18, 2014 by Brian Weitzner at https://github.com/weitzner/jhu-thesis-template
% Updated on January 29, 2016 by John Muschelli at https://github.com/muschellij2/PhD_Thesis
% Updated on April 13, 2016 by Leonardo Collado Torres and available at https://github.com/lcolladotor/jhu-thesis-template. View (read-only) at Overleaf here https://www.overleaf.com/read/tqdzgmrxgbtg

%% It's your responsability to make sure that your thesis complies with 
%% JHU's formatting rules available at http://guides.library.jhu.edu/etd/formatting

\documentclass[12pt]{report}

%% This was the setup recommended at https://github.com/weitzner/jhu-thesis-template
% \documentclass[12pt,oneside,final]{thesis}

\pdfminorversion=4\relax
\pdfobjcompresslevel=0\relax
%% Followed the information from https://www.overleaf.com/latex/examples/creating-pdf-slash-a-and-pdf-slash-x-files/bbbycnbyqhnm#.Vw6_XBMrLm1 to create a PDF/A file in Overleaf
\usepackage[a-1b]{pdfx} % Need this to create a PDF/A file

\usepackage{pdfpages}

\pagestyle{myheadings}
%\topmargin=0.25in
\topmargin=0.05in
\textheight=8.15in
\textwidth=5.6in
\oddsidemargin=0.7in
\raggedbottom
\newdimen \jot \jot=5mm
\brokenpenalty=10000
 

%\usepackage[utf8]{inputenc} % Seems to cause a conflict with fontenc and lmodern
%\DeclareUnicodeCharacter{00A0}{ }
\usepackage[T1]{fontenc}
\usepackage{lmodern} % load a font with all the characters
%\usepackage{hyperref}
\usepackage{tocbibind} % need this to contents adding for TOC
\usepackage{setspace}
\setstretch{1.05}
\usepackage{RJournal_nogeom} % Changes the colors of links among other things
%\usepackage[all]{hypcap}
\usepackage[hypcap=true]{caption}
\hypersetup{linktocpage}
\usepackage{amsmath,amssymb,array}
\usepackage{booktabs}
\usepackage{subfig}

%% load any required packages here
\usepackage{graphicx}
\usepackage{float}
\usepackage{tikz}
\usepackage{graphics} 
\usetikzlibrary{positioning}
\usetikzlibrary{shapes,arrows}
\usepackage{dcolumn}
% A math shortcut frequently used by John Muschelli
\newcommand{\bbeta}{\mbox{\boldmath $\beta$}}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DOI from Segmentation
% Don't use - needs hyperref
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\makeatletter
%\providecommand{\doi}[1]{%
%  \begingroup
%    \let\bibinfo\@secondoftwo
%    \urlstyle{rm}%
%    \href{http://dx.doi.org/#1}{%
%      doi:\discretionary{}{}{}%
%      \nolinkurl{#1}%
%    }%
%  \endgroup
%}
%\makeatother

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% StartKNITR STUFF -- added by John Muschelli
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{color}
%% maxwidth is the original width if it is less than linewidth
%% otherwise use linewidth (to make sure the graphics do not exceed the margin)
\makeatletter
\def\maxwidth{ %
  \ifdim\Gin@nat@width>\linewidth
    \linewidth
  \else
    \Gin@nat@width
  \fi
}
\makeatother

\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%l
\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%

\usepackage{framed}
\makeatletter
\newenvironment{kframe}{%
 \def\at@end@of@kframe{}%
 \ifinner\ifhmode%
  \def\at@end@of@kframe{\end{minipage}}%
  \begin{minipage}{\columnwidth}%
 \fi\fi%
 \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
 \colorbox{shadecolor}{##1}\hskip-\fboxsep
     % There is no \\@totalrightmargin, so:
     \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
 \MakeFramed {\advance\hsize-\width
   \@totalleftmargin\z@ \linewidth\hsize
   \@setminipage}}%
 {\par\unskip\endMakeFramed%
 \at@end@of@kframe}
\makeatother

\definecolor{shadecolor}{rgb}{.97, .97, .97}
\definecolor{messagecolor}{rgb}{0, 0, 0}
\definecolor{warningcolor}{rgb}{1, 0, 1}
\definecolor{errorcolor}{rgb}{1, 0, 0}
\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
\makeatletter
\newcommand\gobblepars{%
    \@ifnextchar\par%
        {\expandafter\gobblepars\@gobble}%
        {}}
\makeatother
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% End KNITR STUFF
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


\usepackage[
style = authoryear, 
sorting = none, 
dashed = false,
maxbibnames = 99,
backend = bibtex,
natbib = true
]{biblatex}

% If you want to exclude some portions from the bibliography
\AtEveryBibitem{
\clearfield{note}
\clearfield{month}
}


\usepackage{enumerate}

%\tolerance=10000

%\makeglossary % enable the glossary
\graphicspath{{rnw_chapter/figure/}{rnw_chapter/}} % change it accordingly!


\setcounter{tocdepth}{4}
\setcounter{secnumdepth}{4}
\begin{document}

\newcommand{\bm}[1]{ \mbox{\boldmath $ #1 $} }
\newcommand{\bin}[2]{\left(\begin{array}{@{}c@{}} #1 \\ #2
             \end{array}\right) }
\renewcommand{\contentsname}{Table of Contents}
\baselineskip=24pt
 
% Create cover page of dissertation !
\pagenumbering{roman}
\thispagestyle{empty}
\begin{center}
\vspace*{.25in}
{\bf\LARGE{ JHU Thesis Template title }}\\ % change it accordingly!
\vspace*{.75in}
{\bf by} \\*[18pt]
\vspace*{.2in}
{\bf Your Name}\\ % change it accordingly!
\vspace*{1in}
{\bf A dissertation submitted to The Johns Hopkins University\\
in conformity with the requirements for the degree of\\
Doctor of Philosophy }\\
\vspace*{.75in}
{\bf Baltimore, Maryland} \\
{\bf June, 2016} \\     % change it accordingly!
\vspace*{.5in}
\begin{small}
{\bf \copyright{ }2016 by Your Name} \\ % change the year if needed!
{\bf All rights reserved}
\end{small}
\end{center}
\newpage 

% Add acknowledgements
\pagestyle{plain}
\pagenumbering{roman}
\setcounter{page}{2}
\include{abstract/abstract}
\include{committee/committee}
\include{acknowledgments/acknowledgments}

%\cleardoublepage
%\newpage 
\pagestyle{plain}
\baselineskip=24pt
\tableofcontents
% for the three lines below, change the page numbers if needed!
%\addtocontents{toc}{\contentsline{chapter}{Table of Contents}{iii}}
%\addtocontents{toc}{\protect\contentsline{chapter}{\protect\numberline{}Table of Contents}{iii}}
%\addtocontents{toc}{\protect\contentsline{chapter}{\protect\numberline{}List of Tables}{iv}}
%\addtocontents{toc}{\protect\contentsline{chapter}{\protect\numberline{}List of Figures}{v}}
\listoftables
\listoffigures

\cleardoublepage % Needed because our intro chapter doesn't really have anything
\pagenumbering{arabic}


% add your chapters, best way is to have separate TeX files for each chapter
%\include{chapter0}
%\include{chapter1}

%% The above was the recommended setup by https://github.com/weitzner/jhu-thesis-template but it's no longer needed
%% after Muschelli's changes which stores different chapters in their
%% respective directories. You will still need to add your chapters as
%% TeX files or Rnw files (see rnw_chapter as an example) and please
%% remember to update the makefile accordingly.

\begin{refsection}[intro_chapter/intro_chapter.bib]
\include{intro_chapter/intro_chapter}
\cleardoublepage
\printbibliography[title={References}]
\end{refsection}

%% If using Overleaf, you'll have to upload the resulting tex file & figures
%% since Overleaf does not support Rnw files right now (April 13, 2016)
\begin{refsection}[rnw_chapter/rnw_chapter.bib]
\include{rnw_chapter/rnw_chapter}
\cleardoublepage
\printbibliography[title={References}]
\end{refsection}

\begin{refsection}[conclusion_chapter/conclusion_chapter.bib]
\include{conclusion_chapter/conclusion_chapter}
\cleardoublepage
\printbibliography[title={References}]
\end{refsection}


% CV PDF file downloaded from the moderncv template available at Overleaf
% https://www.overleaf.com/latex/templates/modern-cv-and-cover-letter-2015-version/sttkgjcysttn#.Vw6PFRMrL65
\includepdf[pages={-}, pagecommand={\thispagestyle{plain}}]{moderncv-2015.pdf}


\end{document}