This is an un-official template for Johns Hopkins University theses. This template was originally created by R. Jacob Vogelstein, then updated by Noah J. Cowan, Brian Weitzner, John Muschelli, Leonardo Collado Torres, and Ben Ackerman.
% 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
% Updated on July 17, 2020 by Ben Ackerman and available at https://github.com/benjamin-ackerman/jhu-thesis-template
%% It's your responsability to make sure that your thesis complies with
%% JHU's formatting rules available at https://www.library.jhu.edu/library-services/electronic-theses-dissertations/formatting-requirements/
\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, title must be in ALL CAPS!
\vspace*{.75in}
{\bf by} \\*[18pt]
\vspace*{.2in}
{\bf Your Name}\\ % change it accordingly!
\vspace*{1in}
{\bf A dissertation submitted to Johns Hopkins University\\
in conformity with the requirements for the degree of\\
Doctor of Philosophy }\\
\vspace*{.75in}
{\bf Baltimore, Maryland} \\
{\bf June, 2020} \\ % change it accordingly! Put month of submission, not of thesis defense (if different)
\vspace*{.5in}
\begin{small}
{\bf \copyright{ }2020 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
\addcontentsline{toc}{chapter}{Curriculum Vitae} % CV must be in table of contents
\includepdf[pages={-}, pagecommand={}]{moderncv-2015.pdf} %continue page numbering through CV
\end{document}