\documentclass[12pt,a4paper,oneside]{book}
% or use report class for shorter documents
% \documentclass[12pt,a4paper]{report}

% Essential packages
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage[margin=1.5in]{geometry}
\usepackage{setspace}
\usepackage{graphicx}
\usepackage{amsmath,amssymb,amsthm}
\usepackage{hyperref}
\usepackage[backend=biber,style=authoryear]{biblatex}
\addbibresource{references.bib}

% Line spacing
\onehalfspacing % or \doublespacing

% Theorem environments
\newtheorem{theorem}{Theorem}[chapter]
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{corollary}[theorem]{Corollary}
\theoremstyle{definition}
\newtheorem{definition}[theorem]{Definition}
\newtheorem{example}[theorem]{Example}
\theoremstyle{remark}
\newtheorem{remark}[theorem]{Remark}

\begin{document}

% Front matter
\frontmatter
\input{titlepage}
\input{abstract}
\input{acknowledgments}
\tableofcontents
\listoffigures
\listoftables

% Main matter
\mainmatter
\input{chapters/introduction}
\input{chapters/literature_review}
\input{chapters/methodology}
\input{chapters/results}
\input{chapters/discussion}
\input{chapters/conclusion}

% Back matter
\appendix
\input{appendices/appendixA}
\input{appendices/appendixB}

\backmatter
\printbibliography[heading=bibintoc]

\end{document}

% titlepage.tex
\begin{titlepage}
\centering
\vspace*{1cm}

\Huge
\textbf{Your Thesis Title}

\vspace{0.5cm}
\LARGE
Subtitle if Needed

\vspace{1.5cm}

\textbf{Author Name}

\vfill

A thesis presented for the degree of\\
Doctor of Philosophy

\vspace{0.8cm}

\includegraphics[width=0.4\textwidth]{university-logo}

\Large
Department of Computer Science\\
University Name\\
Month Year

\end{titlepage}

% abstract.tex
\chapter*{Abstract}
\addcontentsline{toc}{chapter}{Abstract}

This thesis investigates... [300-500 words summarizing your research]

The main contributions of this work are:
\begin{itemize}
  \item First major contribution
  \item Second major contribution
  \item Third major contribution
\end{itemize}

\textbf{Keywords:} keyword1, keyword2, keyword3, keyword4, keyword5

% chapters/introduction.tex
\chapter{Introduction}
\label{chap:introduction}

\section{Background and Motivation}
\label{sec:background}

The field of study has seen significant developments...

\section{Problem Statement}
\label{sec:problem}

This research addresses the following key problems:
\begin{enumerate}
  \item First problem description
  \item Second problem description
\end{enumerate}

\section{Research Questions}
\label{sec:questions}

This thesis aims to answer:
\begin{itemize}
  \item \textbf{RQ1:} How does...?
  \item \textbf{RQ2:} What is the impact of...?
  \item \textbf{RQ3:} Can we develop...?
\end{itemize}

\section{Contributions}
\label{sec:contributions}

The main contributions are:
\begin{enumerate}
  \item \textbf{Novel algorithm:} We propose...
  \item \textbf{Empirical analysis:} We conduct...
  \item \textbf{Theoretical framework:} We develop...
\end{enumerate}

\section{Thesis Organization}
\label{sec:organization}

The remainder of this thesis is organized as follows:
\begin{itemize}
  \item Chapter~\ref{chap:literature} reviews...
  \item Chapter~\ref{chap:methodology} presents...
  \item Chapter~\ref{chap:results} discusses...
  \item Chapter~\ref{chap:conclusion} concludes...
\end{itemize}

\chapter{Literature Review}
\label{chap:literature}

\section{Theoretical Background}
\label{sec:theory}

The foundational work by \textcite{smith2010} established...

\subsection{Classical Approaches}
Early research by \textcite{jones2005,brown2008} focused on...

\subsection{Recent Developments}
More recently, \textcite{wilson2020} proposed...

\section{Related Work}
\label{sec:related}

\begin{table}[htbp]
\centering
\caption{Comparison of existing approaches}
\label{tab:comparison}
\begin{tabular}{lcccc}
\toprule
Method & Accuracy & Speed & Scalability & Year \\
\midrule
\citeauthor{smith2010} & High & Low & Limited & 2010 \\
\citeauthor{jones2015} & Medium & High & Good & 2015 \\
\citeauthor{brown2018} & High & Medium & Excellent & 2018 \\
Our approach & Very High & High & Excellent & 2024 \\
\bottomrule
\end{tabular}
\end{table}

\section{Research Gap}
\label{sec:gap}

Despite these advances, several limitations remain:
\begin{enumerate}
  \item No existing work addresses...
  \item Current methods fail to consider...
  \item The scalability issue remains unsolved...
\end{enumerate}

thesis/
├── main.tex
├── references.bib
├── preamble/
│   ├── packages.tex
│   ├── commands.tex
│   └── settings.tex
├── frontmatter/
│   ├── titlepage.tex
│   ├── abstract.tex
│   ├── acknowledgments.tex
│   └── dedication.tex
├── chapters/
│   ├── introduction.tex
│   ├── literature_review.tex
│   ├── methodology.tex
│   ├── results.tex
│   ├── discussion.tex
│   └── conclusion.tex
├── appendices/
│   ├── appendixA.tex
│   └── appendixB.tex
└── figures/
    ├── chapter1/
    ├── chapter2/
    └── ...

\documentclass[12pt,a4paper]{book}

% Load all packages and settings
\input{preamble/packages}
\input{preamble/commands}
\input{preamble/settings}

\begin{document}

% Use \includeonly for faster compilation during writing
% \includeonly{chapters/methodology}

\frontmatter
\include{frontmatter/titlepage}
\include{frontmatter/abstract}
\include{frontmatter/acknowledgments}
\tableofcontents
\listoffigures
\listoftables

\mainmatter
\include{chapters/introduction}
\include{chapters/literature_review}
\include{chapters/methodology}
\include{chapters/results}
\include{chapters/discussion}
\include{chapters/conclusion}

\appendix
\include{appendices/appendixA}
\include{appendices/appendixB}

\backmatter
\printbibliography[heading=bibintoc]

\end{document}

% In preamble/packages.tex
\usepackage{graphicx}
\usepackage{subcaption}
\usepackage{float}

% Set figure path
\graphicspath{{figures/}{figures/chapter1/}{figures/chapter2/}}

% In chapters
\begin{figure}[htbp]
  \centering
  \includegraphics[width=0.8\textwidth]{experiment-setup}
  \caption[Short caption for list]{Detailed caption explaining the experimental setup and all relevant parameters for understanding the figure.}
  \label{fig:experiment-setup}
\end{figure}

% Multiple subfigures
\begin{figure}[htbp]
  \centering
  \begin{subfigure}[b]{0.45\textwidth}
    \centering
    \includegraphics[width=\textwidth]{result1}
    \caption{First result}
    \label{fig:result1}
  \end{subfigure}
  \hfill
  \begin{subfigure}[b]{0.45\textwidth}
    \centering
    \includegraphics[width=\textwidth]{result2}
    \caption{Second result}
    \label{fig:result2}
  \end{subfigure}
  \caption{Comparison of results under different conditions}
  \label{fig:results-comparison}
\end{figure}

\usepackage{booktabs}
\usepackage{multirow}
\usepackage{array}
\usepackage{siunitx}

\begin{table}[htbp]
\centering
\caption{Experimental results across different datasets}
\label{tab:results}
\begin{tabular}{l*{4}{S[table-format=2.1]}}
\toprule
\multirow{2}{*}{Method} & \multicolumn{2}{c}{Dataset A} & \multicolumn{2}{c}{Dataset B} \\
\cmidrule(lr){2-3} \cmidrule(lr){4-5}
& {Precision} & {Recall} & {Precision} & {Recall} \\
\midrule
Baseline & 82.3 & 79.1 & 75.6 & 81.2 \\
Method 1 & 85.7 & 83.4 & 79.2 & 84.5 \\
Method 2 & 87.2 & 85.9 & 81.8 & 86.3 \\
\textbf{Proposed} & \textbf{91.4} & \textbf{89.6} & \textbf{86.7} & \textbf{90.1} \\
\bottomrule
\end{tabular}
\end{table}

% In preamble
\usepackage[
  backend=biber,
  style=authoryear, % or numeric, alphabetic, etc.
  sorting=nyt,
  maxbibnames=99,
  maxcitenames=2,
  uniquelist=false,
  url=false,
  doi=true,
  isbn=false
]{biblatex}

\addbibresource{references.bib}

% Custom citation commands
\DeclareCiteCommand{\citeauthor}
  {\boolfalse{citetracker}%
   \boolfalse{pagetracker}%
   \usebibmacro{prenote}}
  {\ifciteindex
     {\indexnames{labelname}}
     {}%
   \printnames{labelname}}
  {\multicitedelim}
  {\usebibmacro{postnote}}

% Different citation styles
According to \textcite{smith2020thesis}, the problem...
This was confirmed by recent studies \parencite{jones2021,wilson2022}.
\citeauthor{brown2019} argues that...
In \citeyear{taylor2023}, researchers demonstrated...

% For numeric styles
As shown in \cite{ref1}, the algorithm...
Multiple studies \cite{ref1,ref2,ref3} confirm...

% Footnote citations
Some researchers claim this\footcite{smith2020thesis}.

% Full citations in text
\fullcite{jones2021}

% Load packages
\usepackage{hyperref}
\usepackage{cleveref}

% Configure hyperref
\hypersetup{
  colorlinks=true,
  linkcolor=blue,
  citecolor=blue,
  urlcolor=blue,
  bookmarks=true,
  bookmarksopen=true,
  pdftitle={Your Thesis Title},
  pdfauthor={Your Name},
  pdfsubject={PhD Thesis},
  pdfkeywords={keyword1, keyword2, keyword3}
}

% Configure cleveref
\crefname{figure}{Figure}{Figures}
\crefname{table}{Table}{Tables}
\crefname{equation}{Equation}{Equations}
\crefname{chapter}{Chapter}{Chapters}
\crefname{section}{Section}{Sections}

% Usage examples
As shown in \cref{fig:results}, the performance...
\Cref{chap:methodology} describes our approach...
The results in \cref{tab:comparison,tab:results} demonstrate...
\Cref{eq:main,eq:secondary,eq:tertiary} define...

% Range references
\crefrange{fig:first}{fig:last} show the progression...
Chapters~\ref{chap:intro}--\ref{chap:conclusion} cover...

% Page margins (check your university's requirements)
\usepackage[
  top=1.5in,
  bottom=1.5in,
  left=1.5in,
  right=1in,
  headheight=15pt
]{geometry}

% Line spacing
\usepackage{setspace}
\doublespacing % Most universities require double spacing

% Page numbering
\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhf{}
\fancyhead[R]{\thepage}
\renewcommand{\headrulewidth}{0pt}

% Chapter heading format
\usepackage{titlesec}
\titleformat{\chapter}[display]
  {\normalfont\huge\bfseries}{\chaptertitlename\ \thechapter}{20pt}{\Huge}
\titlespacing*{\chapter}{0pt}{0pt}{40pt}

% Table of contents depth
\setcounter{tocdepth}{3}
\setcounter{secnumdepth}{3}

\chapter*{Declaration}
\addcontentsline{toc}{chapter}{Declaration}

I declare that this thesis is my own work and has not been submitted in any form for another degree or diploma at any university or other institution of tertiary education. Information derived from the published or unpublished work of others has been acknowledged in the text and a list of references is given.

\vspace{2cm}
\noindent
\begin{tabular}{@{}ll}
Signature: & \makebox[3in]{\hrulefill} \\[0.5cm]
Date: & \makebox[3in]{\hrulefill}
\end{tabular}

\newpage

\chapter*{Copyright}
\addcontentsline{toc}{chapter}{Copyright}

\textcopyright\ \the\year\ Author Name

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means without the prior written permission of the author.

% appendices/appendixA.tex
\chapter{Mathematical Proofs}
\label{app:proofs}

\section{Proof of Theorem~\ref{thm:main}}

\begin{proof}
Let $X$ be a compact metric space and $f: X \to X$ be continuous...
[detailed mathematical proof]
\end{proof}

% appendices/appendixB.tex
\chapter{Supplementary Data}
\label{app:data}

\section{Dataset Description}

\begin{longtable}{lp{8cm}r}
\caption{Detailed dataset characteristics} \\
\toprule
Dataset & Description & Size \\
\midrule
\endfirsthead
\multicolumn{3}{c}{\tablename\ \thetable\ -- \textit{Continued from previous page}} \\
\toprule
Dataset & Description & Size \\
\midrule
\endhead
\midrule
\multicolumn{3}{r}{\textit{Continued on next page}} \\
\endfoot
\bottomrule
\endlastfoot
% Table data
Dataset A & Collection of text documents from... & 10,000 \\
Dataset B & Images collected from... & 50,000 \\
% ... more rows
\end{longtable}