%Manuscript Style Thesis Template modified for Overleaf by Babatunde S. Adejumobi.
% 2018-05-18 v. 0.0.2
%% Copyright 2018 by Babatunde S. Adejumobi. <adejumobibabatunde@gmail.com>
% A simple UKZN PhD thesis template (collection of papers).
% 2016-11-20 v.
% Copyright 2016 by Remmy Musumpuka <musumpuka@ukzn.ac.za>
%
% This is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% This is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You can find the GNU General Public License at <http://www.gnu.org/licenses/>.
%
\documentclass[11pt,oneside,openright]{book}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Language, Encoding and Fonts
% http://en.wikibooks.org/wiki/LaTeX/Internationalization
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Select encoding of your inputs. Depends on
% your operating system and its default input
% encoding. Typically, you should use
% Linux : utf8 (most modern Linux distributions)
% latin1
% Windows: ansinew
% latin1 (works in most cases)
% Mac : applemac
% Notice that you can manually change the input
% encoding of your files by selecting "save as"
% an select the desired input encoding.
\usepackage[utf8]{inputenc}
\usepackage{blindtext}
\usepackage{float}
\usepackage{amsmath} %
\usepackage{parskip}
\usepackage{dsfont}
\usepackage{graphics}
\usepackage{tabstackengine}
\usepackage{multicol}
%\setcitestyle{square}
\usepackage{dsfont}
% Make latex understand and use the typographic
% rules of the language used in the document.
\usepackage[danish,english]{babel}
% Use the palatino font
\usepackage{times}
%\usepackage[sc]{mathpazo}
%\usepackage{mathptmx}
\usepackage{ragged2e}
%\doublespacing
\linespread{1.5} %{1.5} % Palatino needs more leading (space between lines)
% Choose the font encoding
% Choose the font encoding
\usepackage[T1]{fontenc}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Graphics and Tables
% http://en.wikibooks.org/wiki/LaTeX/Importing_Graphics
% http://en.wikibooks.org/wiki/LaTeX/Tables
% http://en.wikibooks.org/wiki/LaTeX/Colors
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\usepackage{graphicx}
%\usepackage[pdftex]{graphicx}
\usepackage{caption}
%\usepackage{subcaption}
\usepackage{cases}
\usepackage{lipsum}
\usepackage{hyperref}
\usepackage{theorem}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{mathtools}
%\usepackage[retainorgcmd]{IEEEtrantools}
%\usepackage{algorithm}
%\usepackage{algorithmic}
%\usepackage[nottoc]{tocbibind}
\usepackage{algorithmicx}
\usepackage[noend]{algpseudocode}
\usepackage{algorithm}
\renewcommand{\algorithmicrequire}{\textbf{Input:}}
\renewcommand{\algorithmicensure}{\textbf{Output:}}
\usepackage{float}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{subfig}
\usepackage{array}
\usepackage{lipsum}
\usepackage[]{acronym} %list of symbols
\newcounter{MYtempeqncnt} %added by remmy
% load a colour package
\usepackage{xcolor}
% UniPrint prefers that no colours are used in the template by default.
% However, if you want some colours, then you can easily change the following
\definecolor{aaublue}{RGB}{0,0,0}% black
%\definecolor{aaublue}{RGB}{33,26,82}% dark blue
% The standard graphics inclusion package
%\usepackage{graphicx}
%\ifCLASSOPTIONcompsoc
%\usepackage[caption=false, font=normalsize,labelfont=sf, textfont=sf]{subfig}
%\else
%\usepackage[caption=false, font=footsizenote]{subfig}
%\fi
%\usepackage{multirow}
%\usepackage{subfig}
% Set up how figure and table captions are displayed
\usepackage{caption}
\captionsetup{%
font=footnotesize,% set font size to footnotesize
labelfont=bf % bold label (e.g., Figure 3.2) font
}
% Make the standard latex tables look so much better
\usepackage{array,booktabs}
\usepackage{tabularx}
\usepackage{multirow}
\usepackage{csquotes}
\usepackage{array}
\newcolumntype{L}[1]{>{\raggedright\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
\newcolumntype{C}[1]{>{\centering\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
\newcolumntype{R}[1]{>{\raggedleft\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
% Enable the use of frames around, e.g., theorems
% The framed package is used in the example environment
\usepackage{framed}
% Create beautiful plots using TikZ and PGFPLOTS
%\usepackage{tikz,pgfplots}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Mathematics
% http://en.wikibooks.org/wiki/LaTeX/Mathematics
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Defines new environments such as equation,
% align and split
%\usepackage{eqnarry,amsmath}
% Adds new math symbols
%\usepackage{amssymb}
\usepackage{pdfpages}
% Use theorems in your document
% The ntheorem package is also used for the example environment
% When using thmmarks, amsmath must be an option as well. Otherwise \eqref doesn't work anymore.
%\usepackage[framed,amsmath,amsthm,thmmarks]{ntheorem}
\setcounter{secnumdepth}{5}
\setcounter{tocdepth}{3}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Page Layout and appearance
% http://en.wikibooks.org/wiki/LaTeX/Page_Layout
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Change margins, papersize, etc of the document
\usepackage[
paperwidth=21cm, %17 width of a page
paperheight=29.7cm, %24 height of a page
outer=2.7cm, % right margin on an odd page
inner=2.7cm, % left margin on an odd page
top=2.7cm, % top margin
bottom=2.7cm % bottom margin
]{geometry}
% Enable the crop package if you want to print on a4 paer
\usepackage[a4,cam,center]{crop}
% Modify how \chapter, \section, etc. look
\renewcommand{\thesection}{\arabic{section}}
% The titlesec package is very configureable
\usepackage{titlesec}
\titleformat*{\section}{\normalfont\Large\bfseries\color{aaublue}}
\titleformat*{\subsection}{\normalfont\large\bfseries\color{aaublue}}
\titleformat*{\subsubsection}{\normalfont\normalsize\bfseries\color{aaublue}}
\titleformat*{\paragraph}{\normalfont\normalsize\bfseries\color{aaublue}}
\titleformat*{\subparagraph}{\normalfont\normalsize\bfseries\color{aaublue}}
% Change some default names
\addto\captionsenglish{%this line is required when using the babel package
\renewcommand\appendixname{Paper} % change Appendix to Paper
\renewcommand\bibname{References} % change Bibliography to references
\renewcommand\figurename{Fig.} % change Figure to Fig.
}
% Change the headers and footers
\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhf{} %delete everything
\renewcommand{\headrulewidth}{1pt} %remove the horizontal line in the header
\fancyhead[CE]{\color{aaublue}\small\nouppercase\leftmark} %even page - chapter title
\fancyhead[R]{\color{aaublue}\small\nouppercase\bfseries\rightmark} %uneven page - section title
\fancyfoot[CE,CO]{\thepage} %page number on all pages
% Do not stretch the content of a page. Instead,
% insert white space at the bottom of the page
\raggedbottom
% Enable arithmetics with length. Useful when
% typesetting the layout.
\usepackage{calc}
% fix the marginpar command so it is always on the correct side
\usepackage{mparhack}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Bibliography
% http://en.wikibooks.org/wiki/LaTeX/Bibliography_Management
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Bibliography for each chapter
\usepackage[sectionbib]{chapterbib}
% Custom bibliograhy - used in the list of papers
\usepackage{multibib}
\newcites{main}{Main References}
\newcites{other}{Bibliography}
% Change [1,2,3,4] into [1-4]
\usepackage{cite}
\usepackage{enumerate}
\usepackage[inline]{enumitem}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Misc
\usepackage{algorithm,algcompatible,amsmath}
\DeclareMathOperator*{\argmax}{\arg\!\max}% https://tex.stackexchange.com/q/83169/5764
\algnewcommand\INPUT{\item[\textbf{Input:}]}%
\algnewcommand\OUTPUT{\item[\textbf{Output:}]}%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Add bibliography and index to the table of
% contents
\usepackage[nottoc,section]{tocbibind}
% Enable subappendices
\usepackage{appendix}
\renewcommand{\setthesection}{\Alph{section}} % remove the chapter numbering
% Add the command \pageref{LastPage} which refers to the
% page number of the last page
\usepackage{lastpage}
% Add notes to in your document
\usepackage[
% disable, %turn off todonotes
colorinlistoftodos, %enable a coloured square in the list of todos
textwidth=2cm, %set the width of the todonotes
textsize=scriptsize, %size of the text in the todonotes
]{todonotes}
\setlength{\marginparwidth}{2cm}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Hyperlinks
% http://en.wikibooks.org/wiki/LaTeX/Hyperlinks
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Enable hyperlinks and insert info into the pdf
% file. Hypperref should be loaded as one of the
% last packages
\usepackage{hyperref}
\hypersetup{%
% pdfpagelabels=true,%
plainpages=false,%
pdfauthor={Author},%
pdftitle={Title},%
pdfsubject={Subject},%
bookmarksnumbered=true,%
colorlinks=true,%
citecolor=aaublue,%
filecolor=aaublue,%
linkcolor=aaublue,% you should probably change this to black before printing
urlcolor=aaublue,%
pdfstartview=FitH%
}
\tolerance=1
\emergencystretch=\maxdimen
\hyphenpenalty=10000
\hbadness=10000
\usepackage{balance}
\usepackage{etoolbox}
\input{all/hyphenations.tex}%
\input{all/macros.tex}% my new macros
%%%%%%%%
\AtBeginDocument{\AtBeginShipoutNext{\AtBeginShipoutDiscard}}
% \graphicspath{{introduction/figures/}{papers/paperA/figures/}{papers/paperB/figures/}{papers/paperC/figures/}}%{onclusion}} %Importing the graphics from subfolder {papers/paperB-to-C/figures/}
%
%\renewcommand{\chaptername}{Lecture}
\begin{document}
\justify
%frontmatter
\frontmatter
\pagestyle{empty} %disable headers and footers
\pagenumbering{roman} %use roman page numbering in the frontmatter
\input{frontmatter/frontpage}
\input{frontmatter/examiners-copy}
\input{frontmatter/supervisor-signature}
\input{frontmatter/declaration-plagiarism}
\input{frontmatter/declaration-publication}
\input{frontmatter/dedication}
\input{frontmatter/acknowledgments}
\input{frontmatter/abstract}
%\input{frontmatter/acknowledgments}
\cleardoublepage
\pdfbookmark[0]{Table of Contents}{label:contents}
\pagestyle{fancy} %enable headers and footers again
\tableofcontents
\input{frontmatter/list-of-figures}
\input{frontmatter/list-of-tables}
\input{frontmatter/acronyms}
\cleardoublepage
%\listoftodos
\input{frontmatter/preface}
\cleardoublepage
%mainmatter
\titleformat{%command
\chapter
}[%shape
display%
]{%format
\normalfont\huge
}{%label
\begin{center}\color{aaublue}\chaptertitlename\ \thechapter\end{center}
}{%style
1cm
}{%code before title
\thispagestyle{plain}\begin{center}\Large
%code after title
\end{center}
}
%\cleardoublepage
%\backmatter
%\renewcommand{\partname}{Experiment}
\mainmatter
\part{Introduction}
\include{introduction/introduction}
\appendix
\part{Included Chapters}
\includepaper{papers/paperA/paperA}%chapter2
\part{Included Chapters}
\includepaper{papers/paperB/paperB}%chapter3
\part{Included Chapters}
\includepaper{papers/paperC/paperC}%chapter4
\part{Included Chapters}
\includepaper{papers/paperD/paperD}%chapter5
\cleardoublepage
\setcounter{part}{2}
\part{Conclusion}
\setcounter{section}{0}
\includepaper{conclusion/conclusion}
%\cleardoublepage
\backmatter
%\include{conclusion/conclusion}
\appendix
\part{Bibliography}
\includepaper{bibChap}
\end{document}%%missing {document}
