This template gives a basic introduction to \(\mathrm{\LaTeX}\) and provides a template for the Creighton University Master's thesis, especially as pertains to the MS in physics and medical physics degrees.
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%This is the main file. This is where you set up your preferences, name the packages you need, and use the "input" command to order the chapters and other major components of your thesis, most of which are set up as separate .tex files. To see other project files, click the "Project" tab on the upper left. If you click on a section in the pdf preview, you will jump to that file (Overleaf).
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\documentclass[12pt]{report} %12 point font is set - Times New Roman is the default
%These are a bunch of packages that may or may not be needed for features I use later
\usepackage{graphicx}
\usepackage[table]{xcolor}
\usepackage{amsmath}
\usepackage{hyperref}
\usepackage{url}
\usepackage{multicol}
\usepackage{booktabs}
\usepackage[toc,page]{appendix}
\usepackage{glossaries}
\input{glossary}
\renewcommand\bibname{References}
\usepackage{setspace}
\usepackage[letterpaper,left=1.5in,right=1in,top=1in,bottom=1in]{geometry} %margin of bound side 1.5 in, rest of margins 1 in, per Creighton Thesis guideline formats
\usepackage{pdflscape}
\usepackage{subfigure}
\usepackage{pdfpages}
\widowpenalty10000% This automatically groups lines so there is at least 2 from each paragraph on a page. Optional
\clubpenalty10000 %see above comment
\usepackage{indentfirst} %This makes the first paragraph of a section indented. Optional.
\usepackage{breqn}
\begin{document}
\newpage
\thispagestyle{empty}
\mbox{}
\clearpage %blank page at beginning of pdf. not numbered
\input{approval} %Have this page printed and signed, then delete from your thesis and insert the signed version.
%\includepdf[scale=1.0]{Sig2.pdf} % After the dean signs the approval page, LuAnn Schwery sends you a pdf, which you insert into your thesis
\pagenumbering{roman} %begin roman numeral page numbers for the front matter
\input{cover} %title page
\doublespacing
\newpage %insert blank page, counted in page numbers
\thispagestyle{empty} % do not display page number
\mbox{}
\clearpage
\addcontentsline{toc}{chapter}{Abstract} %include abstract in table of contexts. Chicago Manual of Style argues against having any front matter before the TOC included in the TOC
\input{abstract} %Abstract is the first thing in the thesis after the title
\clearpage
\addcontentsline{toc}{chapter}{Acknowledgments} %includes abstract in table of contexts. Chicago Manual of Style argues against listing front matter that is before the TOC in the TOC
\input{acknowledgments} %optional
\clearpage
\addcontentsline{toc}{chapter}{Dedication}%includes dedication in table of contexts. Chicago Manual of Style argues against listing front matter that is before the TOC in the TOC
\input{dedication} %optional
\clearpage
\tableofcontents %automatically generate TOC
\clearpage
\listoftables %automatically generates list of tables
\clearpage
\listoffigures%automatically generates list of figures
\clearpage
\pagenumbering{arabic} % start normal numbering on the first page of chapter 1
\input{chapter1}
\input{chapter2}
\input{chapter3}
\input{chapter4}
\input{chapter5}
%\clearpage
\appendix %begin appendix section
\chapter{Style guide} \label{sec:appa}% Input Appendix titles as chapters. \label{sec:appa} is a section label, which makes it easy to reference the section with the command \ref{sec:appa}
\input{appendixa}
%\clearpage
\chapter{Copyright permissions}\label{sec:appb}
\input{appendixb}
%\clearpage
\addcontentsline{toc}{chapter}{Glossary}
\printnoidxglossaries
%\clearpage
%.tex method to make a references section
\addcontentsline{toc}{chapter}{References}
\input{biblio}
%.bib method for a references section
\bibliography{biblio}
%\bibliographystyle{IEEEtran}
\bibliographystyle{plain}
\end{document}