thesis.Rnw

% This template for Sweave/knitr document building was  created by 
% Sancar Adali
% This template was originally by R. Jacob Vogelstein
% Updated on March 1, 2010 by Noah J. Cowan

% Your first task should be to remove packages you are not going to need
\documentclass[12pt,oneside,final]{thesis}

%\usepackage[utf8]{inputenc}
\usepackage{cite}
%
\usepackage{amssymb,amsmath,amsthm,amscd}
\usepackage{pgfplots}
%\usetikzlibrary{plotmarks}
\pgfplotsset{compat=newest} 
%\pgfplotsset{plot coordinates/math parser=false}
%\usetikzlibrary{external}
%\tikzexternalize % activate!
%\tikzset{external/system call={pdflatex \tikzexternalcheckshellescape -halt-on-error -interaction=batchmode -jobname "\image" "\texsource"}}
%\tikzset{external/force remake=true} 


\usepackage{graphicx}
\usepackage{subcaption}

\usepackage{ mathrsfs, bm}
\usepackage[pdfa]{hyperref}

\usepackage{algorithm2e}
\usepackage{url}
\renewcommand{\thesubfigure}{}
% justifying
\usepackage{ragged2e}


%include the subdirectories where you store the figures, diagrams,graphs  with relative paths
\graphicspath{{./}{./graphs/}{./figures/}{./../JOFC-GraphMatch/graphs/}{./../JOFC_MatchDetect/graphs/}{./../SeededGraphMatch/graphs/}{./../DataFusion/}{./../DataFusion/graphs/}{./../DataFusion-graphmatch/graphs/}{./../VertexCorrespondence/graphs/}}

\usepackage{fixltx2e}
\usepackage{array}
% wrapfig is fragile: use sparingly
\usepackage{wrapfig} 
\usepackage{cmbright} %clean look
%\usepackage{times}  % Use this for ugly fonts
%\usepackage{ccfonts,eulervm} %Not bad looks nice for serif
%\usepackage[T1]{fontenc}
%\usepackage[urw-garamond]{mathdesign}
%\usepackage{garamondx}
%\usepackage[lf]{venturis} %% lf option gives lining figures as default; 
  		  %% remove option to get oldstyle figures as default
%\usepackage[T1]{fontenc}
%\usepackage[garamond]{mathdesign}
%\usepackage[sfdefault]{quattrocento}
\usepackage[T1]{fontenc}
\usepackage[latin1]{inputenc}




%\usepackage[none]{hyphenat}

\usepackage{verbatim}

\usepackage{multirow}

\usepackage{fancyhdr}    % Use nice looking headers along with the required footer page numbers   
%\usepackage[hypertex]{hyperref}
\usepackage{lscape} 
%Define the header/footer style
\pagestyle{fancy}
\fancyhf{}
\setlength{\headheight}{15pt}
\lhead{\leftmark}
\cfoot{\thepage}
\renewcommand{\headrulewidth}{0pt}
\fancypagestyle{plain}{% Redefine ``plain'' style for chapter boundaries
\fancyhf{} % clear all header and footer fields
\fancyfoot[C]{\thepage} % except the center
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}}

\newtheorem{thm}{Theorem}
\newtheorem{cor}{Corollary}
\newtheorem{lem}{Lemma}
\newtheorem{defn}{Definition}

\usepackage[refpage]{nomencl}
\renewcommand{\nomname}{List of Notations}
\renewcommand*{\pagedeclaration}[1]{\unskip\dotfill\hyperpage{#1}}
%\DeclareTextCommand{\nobreakspace}{T1}{\leavevmode\nobreak\ }

\makenomenclature

\usepackage{makeidx}
\makeindex

%shorthand commands
\input{common.tex}

%The following two commands might not be necessary. 
%They were added during my efforts to create a PDF-1/A compatible pdf file which is required by the JHU library for thesis submissions.
%PDF compliance
\input {glyphtounicode-cmr.tex}
\pdfgentounicode=1

\def\Title{Joint Optimization of Fidelity and Commensurability\\ for Manifold Alignment and Graph Matching}
\def\Author{Sancar Adali}
\def\Subject{Dissertation Submitted for Doctoral Degree}
\def\Keywords{thesis,Multidimensional Scaling,Graph Matching,Fidelity and Commensurability}

%The following sections were added to create a PDF-1/A compatible pdf file including metadata and other features which is required by the JHU library for thesis submissions.
%***************************************************************************
% \convertDate converts D:20080419103507+02'00' to 2008-04-19T10:35:07+02:00
%___________________________________________________________________________

 
%\def\pdfcreationdate{2013-03-21T10:35:07+05:00}

%*********
% XMP data
%_________

\usepackage{hyperxmp}


% ----------------------------------------------
% Add metadata

\hypersetup{% 
       pdftitle={\Title},
       pdfauthor={\Author},
       pdfauthortitle={},
       pdfcopyright={Copyright (C) 2014, Sancar Adali},
       pdfsubject={\Subject},
       pdfkeywords={\Keywords},
       pdflicenseurl={},
       pdfcaptionwriter={},
       pdfcontactaddress={Johns Hopkins University},
       pdfcontactcity={Baltimore},
       pdfcontactpostcode={21218},
       pdfcontactcountry={USA},
       pdfcontactemail={sadali1@jhu.edu},
       pdfcontacturl={http://www.ams.jhu.edu/~adali},
       pdflang={en},
       bookmarksopen=true,
       bookmarksopenlevel=3,
       hypertexnames=false,
       linktocpage=true,
       plainpages=false,
       breaklinks
     }






%\usepackage[T1]{fontenc}
%SA: This package is not necessary unless you want to create a slideshow-like  plot window like I did.
\usepackage{animate}
%\tolerance=10000

%\makeglossary % enable the glossary
% SA: The following package makes subtle corrections to the rendering of the document. See http://www.khirevich.com/latex/microtype/
%\usepackage[protrusion=true,final,tracking=true,kerning=true,spacing=true,factor=1100,stretch=10,shrink=10]{microtype}

\begin{document}
%\SweaveOpts{concordance=TRUE}

<<include=FALSE>>=
opts_chunk$set(concordance=TRUE,eval=FALSE)
@


\title{Joint Optimization of Fidelity and Commensurability\\ for Manifold Alignment and Graph Matching}
\author{Sancar Adali}
\degreemonth{March}
\degreeyear{2014} 
\dissertation
\doctorphilosophy
\copyrightnotice



% add your chapters, best way is to have separate TeX files for each chapter
%SA: Each chapter has its own Sweave/knitr file, these children documents can be removed by changing "eval" to FALSE


<<'child-chapter0.Rnw', child='chapter0.Rnw',eval=TRUE>>=
@


<<'child-chapter1.Rnw', child='chapter1.Rnw',eval=TRUE>>=
@


<<'child-chapter2_related_work.Rnw', child='chapter2_related_work.Rnw',eval=TRUE>>=
@


<<'child-chapter3_MDS.Rnw',child='chapter3_MDS.Rnw',eval=TRUE>>=
@


<<'child-chapter9_Match_test.Rnw', child='chapter9_Match_test.Rnw',eval=TRUE>>=
@


<<'child-chapter4_FidComm.Rnw', child='chapter4_FidComm.Rnw',eval=TRUE>>=
@

<<'child-chapter14_datamodels.Rnw', child='chapter14_datamodels.Rnw',eval=TRUE>>=
@


<<'child-chapter5_PCA_Procrustes.Rnw', child='chapter5_PCA_Procrustes.Rnw',eval=TRUE>>=
@


<<'child-chapter6_CCA.Rnw', child='chapter6_CCA.Rnw',eval=TRUE>>=
@


<<'child-chapter8_MDS_multmin.Rnw', child='chapter8_MDS_multmin.Rnw',eval=TRUE>>=
@


<<'child-chapter7_Sim_Exp_MatchTest.Rnw', child='chapter7_Sim_Exp_MatchTest.Rnw',eval=TRUE>>=
@


<<'child-chapter10_Graph_Match.Rnw', child='chapter10_Graph_Match.Rnw',eval=FALSE>>=
@

<<'child-chapter11_Graph_Match.Rnw', child='chapter11-Graph_Match_JOFC_Exp.Rnw',eval=TRUE>>=
@

<<'child-chapter15_conclusion.Rnw', child='chapter15_conclusion.Rnw',eval=TRUE>>=
@


\include{appendix}

%% REFERENCES

% if you use BIBTEX
\bibliographystyle{IEEEtran}
\bibliography{priebe-thesis-JOFC}
% 
 \begin{vita}
% 
 \begin{wrapfigure}{l}{0pt}
 \includegraphics[width=2in,height=2.5in,clip,keepaspectratio]{sancarheadshot}
 \end{wrapfigure}

%Include your brief biography here

 
 \end{vita}
\end{document}