Johnson-thesis.tex

\documentclass[11pt,          % font size: 11pt or 12pt
               phd,           % degree:    ms or phd
               onehalfspacing % spacing: onehalfspacing or doublespacing
               ]{ncsuthesis}

%%----------------------------------------------------------------------------%%
%%------------------------------ Import Packages -----------------------------%%
%%----------------------------------------------------------------------------%%

\usepackage{booktabs}  % professionally typeset tables
\usepackage{amsmath}%,amssymb,amsfonts}
\usepackage{textcomp}  % better copyright sign, among other things
%\usepackage{xcolor}
\usepackage{lipsum}    % filler text
\usepackage{subfig}    % composite figures
\usepackage{listings}

\usepackage[T1]{fontenc}
\usepackage[latin1]{inputenc}
\usepackage[table, svgnames]{xcolor} 
\usepackage{color} 
\usepackage{url}
\usepackage{graphicx, array, blindtext}
\usepackage[tight,footnotesize]{subfigure}
\usepackage{mdframed}
\usepackage{latexsym}
\usepackage{boxedminipage}
\usepackage{ amssymb }
\usepackage[normalem]{ulem}
\usepackage{flushend}

\usepackage{ocgx}
\usepackage{tikz}
\usetikzlibrary{ocgx}

\usepackage{setspace} 

%http://tex.stackexchange.com/questions/106285/boxed-equation-but-framed-only-some-sides
\newcommand{\professional}[1]{\hspace{-1mm}\setlength\arraycolsep{1pt}
	$\begin{array}{|l|}\hline\textnormal{#1}\\\hline\end{array}$\xspace
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\newcommand*{\mybox}[1]{\framebox{#1}}

%%ORTIZ PACKAGES


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% Old bibliography commands
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
%\usepackage[super,sort&compress,comma,square,authoryear]{natbib} %\cite command %Added by Ortiz

%use the following line with plainnat
%\usepackage[super,sort&compress,comma,square,numbers]{natbib} %\cite command %Added by Ortiz
%\usepackage{natbib}

%\usepackage[style=alphabetic,natbib=true,backend=bibtex
%sorting=nyt,firstinits=true,isbn=false,doi=false,url=false]{biblatex} %couldn't get backend=biber to work

%\usepackage{filecontents}

%\bibliography{Ortiz-thesis2}
%\bibliographystyle{plain}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% Hack for alphanumeric bibliography
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
\RequirePackage[
			style=alphabetic,%numeric-comp,%authoryear-comp,%
			sorting=nyt,%ynt					
			hyperref=true, %	
			firstinits=true,%
			backend=bibtex,
			natbib=true,
			url=false,
			isbn=false,
			maxnames=2, %for et al to be used
			maxalphanames=1, %to avoid printing a + for every et al in the abbreviation
			doi=false]{biblatex}		
			

%needed to do et al after two names
%http://tex.stackexchange.com/questions/44048/use-et-al-in-biblatex-custom-style
\renewcommand*{\finalnamedelim}{\addspace\&\space}

%Simplify abbreviation (the default uses either one or two authors and it indicates et al with a +)
%The following five lines make it so that only the first author is used in the abbreviation
%http://tex.stackexchange.com/questions/27956/label-only-from-first-author
\renewcommand*{\labelalphaothers}{}
    \renewcommand*{\intitlepunct}{}
    \DefineBibliographyStrings{german}{in={}}
    \DefineBibliographyStrings{english}{in={}}
    \DeclareNameAlias{sortname}{last-first}
    \DeclareNameAlias{default}{last-first}
	
%\AtEveryCitekey{\ifciteseen{}{\defcounter{maxnames}{99}}} %authoryear			
\DeclareFieldFormat[article,periodical]{volume}{\mkbibbold{#1}}
\makeatletter

\newrobustcmd*{\parentexttrack}[1]{%
  \begingroup
  \blx@blxinit
  \blx@setsfcodes
  \blx@bibopenparen#1\blx@bibcloseparen
  \endgroup}

\AtEveryCite{%
  \let\parentext=\parentexttrack%
  \let\bibopenparen=\bibopenbracket%
  \let\bibcloseparen=\bibclosebracket}

\makeatother
\renewcommand{\cite}[1]{\parencite{#1}}


\renewbibmacro{in:}{%
  \ifentrytype{article}{}{%
  \printtext{\bibstring{in}\intitlepunct}}}
  
\AtEveryBibitem{\clearfield{month}}

\AtEveryBibitem{\clearfield{language}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%\addbibresource{Ortiz-thesis2.bib}
%\addbibresource{Ortiz-thesisURL.bib}
\addbibresource{Johnson-thesis.bib}

 \defbibheading{myheading}[BIBLIOGRAPHY]{
 \chapter*{#1}
 %\centerline{\bf{#1}}
 \markboth{#1}{#1}}

%\usepackage{amsmath,amssymb,amsfonts} %amssymb and amsfonts cannot be used in conjunction with mdput
%\usepackage{graphicx,subfig}% Include figure files
\usepackage{dcolumn}% Align table columns on decimal point
\usepackage{bm}% bold math
%\usepackage{hyperref}% add hypertext capabilities
%\usepackage{hypernat}% make hyperref and natbib work together
\usepackage{cancel}
\usepackage{verbatim}% multiline commenting
\usepackage{ifthen}
\usepackage{url}
\usepackage{sectsty}
\usepackage{balance} 
%\usepackage{caption}
\usepackage{graphicx} %eps figures can be used instead
\usepackage{lastpage}
\usepackage{pdfpages}
\usepackage[format=plain,justification=RaggedRight,singlelinecheck=false,font=small,labelfont=bf,labelsep=space]{caption} 
\usepackage{fancyhdr}
\pagestyle{fancy}

%http://tex.stackexchange.com/questions/100817/error-when-using-bc-from-abbrevs-in-caption
%Getting BC
\usepackage{abbrevs}
\usepackage{etoolbox}
\robustify{\DateMark} % after having loaded abbrevs

\usepackage{units} %Needed to solve bug from citation Hydrodynamics in 21/2 dimensions
%see http://www.latex-community.org/viewtopic.php?f=5&t=989

\usepackage[sharp]{easylist} %used for brainstorming purposes 
%\usepackage{mathabx} % used for \Asterisk for convolution %conflicts with \widering

%compile on single pass
%\usepackage[backend=biber,...]{biblatex}


%%%%%%%%%%%%
%%% Hack to make chapters start on odd pages
% http://tex.stackexchange.com/questions/73591/how-to-have-a-blank-even-page-before-every-chapter
%%%%%%%%%%%%
%\newcommand{\ensureoddstart}{\checkoddpage\ifoddpage\else\newpage\mbox{}\fi}
%\newcommand{\ensureoddstart}{}


%%%Fancy tables
%http://tex.stackexchange.com/questions/94032/fancy-tables-in-latex
\usepackage[table]{xcolor}
\usepackage{array,booktabs}
% \usepackage{colortbl}
\newcolumntype{L}{@{}>{\kern\tabcolsep}l<{\kern\tabcolsep}}



%%%%%%%%%%
%%%%% Hack to allow more levels in outline
%%%%%%%%%%
%\setcounter{secnumdepth}{5}
%\setcounter{tocdepth}{5} %may violate ETD
%Usage http://pleasemakeanote.blogspot.com/2010/06/how-to-activate-subsubsubsection-in.html
%\section{} % level 1
%\subsection{} % level 2
%\subsubsection{} % level 3
%\paragraph{} % level 4 - equivalent to subsubsubsection
%\subparagraph{} % level 5

%http://tex.stackexchange.com/questions/60209/how-to-add-an-extra-level-of-sections-with-headings-below-subsubsection
\usepackage{titlesec}

\setcounter{secnumdepth}{4}

\titleformat{\paragraph}
{\normalfont\normalsize\bfseries}{\theparagraph}{1em}{}
\titlespacing*{\paragraph}
{0pt}{3.25ex plus 1ex minus .2ex}{1.5ex plus .2ex}

%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Hack for containing figures within sections
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%http://ctan.org/pkg/placeins
\usepackage{placeins}
%De�fines a \FloatBar�rier com�mand, be�yond which floats may not pass; use�ful, for ex�am�ple, to en�sure all floats for a sec�tion ap�pear be�fore the next \sec�tion com�mand.

%%%Hack for centering all figures
%\makeatletter
%\g@addto@macro\@floatboxreset\centering
%\makeatother

%%----------------------------------------------------------------------------%%
%%---------------------------- Formatting Options ----------------------------%%
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%%

%% -------------------------------------------------------------------------- %%
%% Disposition format -- any titles, headings, section titles
%%  These formatting commands affect all headings, titles, headings,
%%  so sizing commands should not be used here.
%%  Formatting options to consider are
%%     +  \sffamily - sans serif fonts.  Dispositions are often typeset in
%%                    sans serif, so this is a good option. 
%%     +  \rmfamily - serif fonts
%%     +  \bfseries - bold face
%\dispositionformat{\sffamily\bfseries}   % bold and sans serif
\dispositionformat{\bfseries}            % bold and serif

%% -------------------------------------------------------------------------- %%
%% Formatting for centered headings - Abstract, Dedication, etc. headings
%%  This is where one might put a sizing command.
%%  \MakeUppercase can be used to typeset all headings in uppercase.
\headingformat{\large\MakeUppercase}   % All letters uppercase
%\headingformat{\large}                % Not all uppercase
%\headingformat{\Large\scshape}        % Small Caps, used with serif fonts.

%% Typographers recommend using a normal inter-word space after
%% sentences. TeX's default is to add an wider space, but \frenchspacing
%% gives a normal spacing. Comment out the following line if you prefer
%% wider spaces between sentences.
\frenchspacing


%% -------------------------------------------------------------------------- %%
%%  Optional packages
%%    A number of compatible packages to improve the look and feel of
%%    your document are available in the file optional.tex 
%%    (For example, hyperlinks, fancy chapter headings, and fonts)
%% To use these options, uncomment the next line and see optional.tex
\include{optional}
%solve bug from fancyhdr in optional
%http://nw360.blogspot.com/2006/11/latex-headheight-is-too-small.html
\setlength{\headheight}{14pt}

%%----------------------------------------------------------------------------%%
%%---------------------------- Content Options -------------------------------%%
%%----------------------------------------------------------------------------%%
%% Size of committee: 3, 4, 5, or 6 -- this number includes the chair
\committeesize{5}

%% Members of committee
%%  Each of the following member commands takes an optional argument
%%   to specify their role on the committee.
%%  For co-chairs, use the commands:
%%      \cochairI{Doug Dodd}
%%      \cochairII{Chris Cox}
%%
\cochairI{Emerson Murphy-Hill}
\cochairII{Sarah Heckman}
\memberI{Tim Menzies}
\memberII{Tiffany Barnes}
\memberIII{Eric Rotenberg}  



%% Student writing thesis, \student{First Middle}{Last}
\student{Brittany Itelia}{Johnson} % a full middle name
%\student{John M.}{Smith} % a middle initial

%% Degree program
\program{Computer Science}

%% Thesis Title
%%  Keep in mind, according to ETD guidelines:
%%    +  Capitalize first letter of important words.
%%    +  Use inverted pyramid shape if title spans more than one line.
%%
%%  Note: To break the title onto multiple lines, use \break instead of \\.
%\thesistitle{A North Carolina State University Sample \LaTeX{} Thesis \break 
%with a Title So Long it Needs a Line Break}
\thesistitle{A Tool (Mis)communication Theory and Adaptive Approach for Supporting Developer Tool Use}

%% Degree year.  Necessary if your degree year doesn't equal the current year.
%\degreeyear{1995}


%%----------------------------------------------------------------------------%%
%%---------------------------- Personal Macros -------------------------------%%
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%% A central location to add your favorite macros.

%% A few examples to get you started.
\newcommand{\uv}[1]{\ensuremath{\mathbf{\hat{#1}}}}
\newcommand{\bo}{\ensuremath{\mathbf{\Omega}}}
\newcommand{\eref}[1]{Eq.~\ref{#1}}
\newcommand{\fref}[1]{Fig.~\ref{#1}}
\newcommand{\tref}[1]{Table~\ref{#1}}
\newcommand{\del}{\nabla}
\renewcommand{\exp}[1]{e^{#1}}
\newcommand{\Conv}{\mathop{\scalebox{1.5}{\raisebox{-0.2ex}{$\ast$}}}}%


\usepackage{color}
%\newcommand{\NEW}[1]{\textcolor{blue}{#1}}
\newcommand{\NEW}[1]{#1}
\newcommand{\COMMENT}[1]{\textcolor{green}{#1}}


\newcommand{\NOTER}[1]{\textcolor{orange}{#1}}
\newcommand{\NOTEC}[1]{\textcolor{blue}{#1}}
\newcommand{\NOTEK}[1]{\textcolor{magenta}{#1}}

\newcommand{\mum}{\ensuremath{{\mu}\text{m}}}

%This makes it so that you can add short paths in your .tex by including the folders where you store your images in the search path
\graphicspath{{./Chapter-1/figs/}{./Chapter-2/figs/}{./Chapter-3/figs/}}%{./Chapter-4/figs/}{./Chapter-5/figs/}{./Chapter-6/figs/}}


%%---------------------------------------------------------------------------%%
\usepackage{calc}
%% Capital letter height
\newlength{\chaptercapitalheight}
\settoheight{\chaptercapitalheight}{D}
\newlength{\chapterfootskip}
\setlength{\chapterfootskip}{\chaptercapitalheight}
\addtolength{\chapterfootskip}{2\baselineskip}
\addtolength{\chapterfootskip}{0.5ex}  % A little extra space to ensure there are 2 full double spaced lines
%\def\chapterfootskipnum{\chapterfootskip}
\renewcommand{\listfigurename}{LIST OF FIGURES}
\renewcommand{\listtablename}{LIST OF TABLES}
\renewcommand{\bibname}{BIBLIOGRAPHY}

%\renewcommand{\cfttoctitlefont}{\centering\ncsu@headingformat}


%http://tex.stackexchange.com/questions/47184/height-of-figure-caption-textheight
\newlength\graphht
\newcommand\calculategraphicstargetheight[1]{%
     \setlength\graphht{\textheight 
                       -\parskip
                       -\abovecaptionskip -\belowcaptionskip
                       -(12pt * #1) % assuming baselineskip of 12pt in caption
                       -\chapterfootskip
                       }}

%\usepackage{titlesec}

%landscape support in fancyhdr from http://tex.stackexchange.com/questions/9071/how-to-translate-and-rotate-the-heading-of-landscaped-pages
\usepackage{pdflscape}
\usepackage{tikz}
\fancypagestyle{lscapedplain}{%
  \fancyhf{}
  \fancyfoot{%
    \tikz[remember picture,overlay]
      \node[outer sep=1cm,above,rotate=90] at (current page.east) {\thepage};}
\renewcommand{\headrulewidth}{0pt} 
\renewcommand{\footrulewidth}{0pt}
}

                      
\begin{document}
\pagestyle{plain}
%%---------------------------------------------------------------------------%%
\frontmatter

\include{front}

%%---------------------------------------------------------------------------%%
\mainmatter



\pagestyle{fancy}
\newgeometry{margin=1in,lmargin=1.25in,footskip=\chapterfootskip, includehead, includefoot}
\include{Chapter-1/Chapter-1}
\include{Chapter-2/Chapter-2}
\include{Chapter-3/Chapter-3}
\include{Chapter-4/Chapter-4}
\include{Chapter-5/Chapter-5}
\include{Chapter-6/Chapter-6}
\include{Chapter-7/Chapter-7}
\include{Chapter-8/Chapter-8}
%\restoregeometry


%%---------------------------------------------------------------------------%%
%%  Bibliography 

%%  You can use the bibitem list.
%\bibliographystyle{unsrt}
%\begin{%thebibliography}{99}
%\bibitem{cb02}
%Casella, G. and Berger, R.L. (2002)
%\newblock {\it Statistical Inference, Second Edition.}
%Duxbury Press, Belmont, CA.
%
%\bibitem{t06}
%Tsiatis, A.A. (2006)
%\newblock {\it Semiparametric Theory and Missing Data.}
%Springer, New York.
%
%\end{thebibliography}

%% or use BibTeX
%\bibliography{Ortiz-thesis}{}
%\bibliographystyle{plain}
%\nociterec{*}

%\bibliographystyle{plainnat}%plainnat is necessary to enable the use of citet. Natbib style file.
%\bibliography{Ortiz-thesis2}
%\ensureoddstart
\begin{spacing}{1}
 \setlength\bibitemsep{11pt} %22pt = 2*11pt, where fontsize is 11pt
 \addcontentsline{toc}{chapter}{{\uppercase{\bibname}}} %\textorpdfstring and \uppercase needed due to hyperref package http://www.latex-community.org/forum/viewtopic.php?f=44&t=16601
 %\vspace{-0.5in}
\titleformat{\chapter}[display]{\bf\filcenter
}{\chaptertitlename\ \thechapter}{11pt}{\bf\filcenter}
\titlespacing*{\chapter}{0pt}{-0.5in-9pt}{22pt}

\printbibliography[heading=myheading]
\end{spacing}
%\bibliographystyle{apalike}


%%---------------------------------------------------------------------------%%
% Appendices
%\ensureoddstart
\restoregeometry
\appendix
\newgeometry{margin=1in,lmargin=1.25in,footskip=\chapterfootskip, includehead, includefoot}


\include{Appendix-A/Appendix-A}
\include{Appendix-B/Appendix-B}
%\include{Appendix-C/Appendix-C}
\include{Appendix-D/Appendix-D}
\include{Appendix-E/Appendix-E}

\restoregeometry

%%---------------------------------------------------------------------------%%
%\ensureoddstart
\backmatter


\end{document}