% For defining the report class and structure for the thesis
\documentclass[12pt]{report}
%\usepackage[utf8]{inputenc} % Seems to cause a conflict with fontenc and lmodern
\usepackage[T1]{fontenc}
\usepackage{lmodern}
\usepackage{tocbibind} %need this to contents adding for TOC
\usepackage{booktabs}
\usepackage{subfig}
\usepackage{graphicx}
\graphicspath{ {images/} }

%% This was the setup recommended at https:/ /github.com/weitzner/jhu-thesis-template
\pdfminorversion=4\relax
\pdfobjcompresslevel=0\relax

\usepackage[a-1b]{pdfx} % Need this to create a PDF/A file

\usepackage{pdfpages}

% For creating correct margins for JHU requirements
\pagestyle{myheadings}
%\topmargin=0.25in
\topmargin=0.05in
\textheight=8.15in
\textwidth=5.6in
\oddsidemargin=0.7in
\raggedbottom
\newdimen \jot \jot=5mm
\brokenpenalty=10000

% For using captions and subcaptions for figures and subfigures, respectively
\usepackage[hypcap=true]{caption}
\hypersetup{linktocpage}

% For creating reference list and in-paper citations
\usepackage{natbib}
\bibpunct{(}{)}{;}{a}{,}{,}

% For mathematical notations
\usepackage{amsmath}
\usepackage{mathrsfs}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{bbm}
\usepackage{amsthm}

% For line spacing
\usepackage{setspace}
\setstretch{1.05}

% For using numbered lists and commenting
\usepackage{enumerate}
\usepackage{comment}

% For creating the figures for the models
\usepackage{tikz}
\usetikzlibrary{shapes,arrows,positioning}

% Shortcuts I created for useful commands
\newcommand{\beqa}{\begin{eqnarray*}}
\newcommand{\eeqa}{\end{eqnarray*}}
\newcommand{\beqn}{\begin{eqnarray}}
\newcommand{\eeqn}{\end{eqnarray}}
\newcommand{\be}{\begin{enumerate}}
\newcommand{\ee}{\end{enumerate}}
\newcommand{\bi}{\begin{itemize}}
\newcommand{\ei}{\end{itemize}}
\newcommand{\beq}{\begin{equation}}
\newcommand{\eeq}{\end{equation}}
\newtheorem{mydef}{Theorem}

% For creating an index and using index commands
\usepackage{imakeidx}
\makeindex

\tikzstyle{decision} = [diamond, draw,text width=4.5em, text badly centered, node distance=3cm, inner sep=0pt]
\tikzstyle{block} = [rectangle, draw, text width=5em, text centered, rounded corners, minimum height=4em]
\tikzstyle{line} = [draw, -latex']
\tikzstyle{cloud} = [draw, ellipse, node distance=3cm, minimum height=2em]

\tikzstyle{var} = [rectangle]
\tikzstyle{obsvar} = [rectangle, draw=black]
\tikzstyle{latvar} = [circle, draw=black]
\tikzstyle{line} = [draw, -stealth']

\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{ Likelihood-Based Methods of Mediation Analysis in the Context of Health Disparities }}\\ % change it accordingly!
\vspace*{.75in}
{\bf by} \\*[18pt]
\vspace*{.2in}
{\bf Therri Usher}\\ % 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 July, 2016} \\     % change it accordingly!
\vspace*{.5in}
\begin{small}
{\bf \copyright{ }2016 by Therri Usher} \\ % change the year if needed!
{\bf All rights reserved}
\end{small}
\end{center}
\newpage

\pagestyle{plain}
\baselineskip=24pt

\include{abstract}

\include{acknowledgements}

\include{dedication}

%\cleardoublepage
%\newpage 
\tableofcontents
\listoffigures
\listoftables

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

\chapter{Introduction}
\input{chapters/introduction}

\chapter{Health Disparities Background}
\input{chapters/chapter02}

\chapter{Existing Techniques of Mediation Analysis}
\input{chapters/chapter03}

\chapter{New Methods of Assessing Mediation}
\input{chapters/chapter04}

\chapter{Example: Race, Diet, and Hypertension in NHANES}
\input{chapters/chapter05}

\chapter{Conclusion}
\input{chapters/conclusion}

\bibliographystyle{apalike}
\bibliography{references}

\includepdf[pages={-}, pagecommand={}]{CV.pdf}

\end{document}