%This is the main thesis file. There will not be much text here. This file should reference the subfiles that contain each of the chapters.

%\documentclass[letterpaper]{report}%use the report format as this handles chapters and larger documents

%draft declaration in this document class line. Use the line above for final document
\documentclass[12pt,letterpaper]{report}%use the report format as this handles chapters and larger documents
%NOTE: the draft tag keeps the images from displaying in the document. Instead it shows a box with file name only.
%\usepackage{draftwatermark}
%\SetWatermarkScale{4}

%thesis must be formatted using 12 point font
\usepackage[top=1.25in,bottom=1.25in,right=1.25in,left=1.75in]{geometry}%required to force LaTex to use letter sized paper.
%margin limits come from general formatting guidelines in thesis packet
%note: bottom margin is from bottom of page to last line of text, not page number. Ensure 0.5'' minimum between bottom of page and page num.

\usepackage{color}%used to make notes to myself during the writing process.
\usepackage{amsmath}
%\usepackage{parallel}
\usepackage{sectsty}

\usepackage[toc,page]{appendix}

\usepackage{comment}
\usepackage{graphicx}
\usepackage{caption}
\usepackage{subcaption}
\usepackage{cleveref}
\crefname{figure}{figure}{figures}
\usepackage{pdflscape}
\usepackage{rotating}
\usepackage{afterpage}
\usepackage{multirow}
\DeclareGraphicsExtensions{.pdf,.png,.jpg}

\chapterfont{\fontsize{14}{14}\selectfont}
\sectionfont{\fontsize{14}{14}\selectfont}%need to play more with the section font size. it must be 14 point font per the thesis package
\subsectionfont{\fontsize{14}{14}\selectfont}
\subsubsectionfont{\fontsize{14}{14}\selectfont}
%http://tex.stackexchange.com/questions/1455/how-to-set-the-font-for-a-section-title-and-chapter-etc

\usepackage{natbib}
%\linespread{1.6}%set line spacing to double space
\usepackage{setspace}
\doublespacing

%will need to do more formatting of the title to match the OU Thesis formatting requirements
%see http://en.wikibooks.org/wiki/LaTeX/Title_Creation for help
\title{Investigation of Cointegration Relationships in Turbulent Flows}
\author{Josh Haines}

\begin{document}

%\maketitle
\input{TitlePage/title.tex}
\pagenumbering{roman}
\setcounter{page}{4}
\input{Sections/FrontMatter.tex}

%article possibly describing how to set font size of heading text
%http://tex.stackexchange.com/questions/59726/change-size-of-section-subsection-subsubsection-paragraph-and-subparagraph-ti

\pagenumbering{arabic}
\setcounter{page}{1}
%abstract will probably go here
%\textcolor{red}{\textbf{LIST OF TO DOS:}}
%
%\begin{enumerate}
%\item Add parenthesis around all equation references: from 4.5 to (4.5)
%\item Fix border around scatter plot in figure 3.1 in section 3.3 spurious regressions
%\item 
%\end{enumerate}

\input{Sections/intro}

%\input{Sections/IntroductionAndOrganization.tex}

%\input{Sections/LiteratureReview}

\input{Sections/TimeSeries}

\input{Sections/Cointegration}

\input{Sections/CointegrationAndTurbulence}

\input{Sections/Conclusion}

%create the bibliography here
%Thesis Packet recommends following the chicago manual of style
%need to figure out what the intext citation style for this is. This may change how I write my sentences with references in them.
\singlespacing %bibliography should be single spaced
\bibliographystyle{plain}
\bibliography{Bibliography/ThesisReferences}
\begin{appendices}
\doublespacing
\input{Sections/AppendixA_InterpolationResults}
\input{Sections/AppendixB}
\input{Sections/AppendixC_FullBuoyancyData}
\end{appendices}



\end{document}