\documentclass[12pt, a4paper]{book}
%\documentclass[a4paper,12pt,oneside]{report}
\usepackage{graphicx}
%%%%% For titlepage %%%%%
\usepackage[protrusion=true,expansion=true]{microtype}
\usepackage{commath}
\usepackage{wrapfig}
\usepackage[utf8]{inputenc}
\usepackage[greek, english]{babel}
\usepackage{alphabeta}
\usepackage[margin=1in]{geometry}
\setlength{\parskip}{2mm}
\setlength{\parindent}{1cm}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{color}
\usepackage{booktabs}
\usepackage{verbatim}
\usepackage{spverbatim}
\usepackage{bm}
\usepackage{booktabs}
\usepackage{subfigure}
\usepackage{natbib}
\usepackage{multirow}
\usepackage{array}
\usepackage{graphicx}
\usepackage{subcaption}
\usepackage{mathalfa}
\usepackage{appendix}
\usepackage{tabularx}
\usepackage{lipsum}
\usepackage{rotating}
\usepackage{adjustbox}
\usepackage{pdflscape}
\usepackage{lscape}
\newcolumntype{L}{>{\centering\arraybackslash}m{3cm}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% END OF PREAMBLE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
\input{0_titlepage.tex}
\newpage
\input{acknowledgments}
\newpage
\input{abstract}
\tableofcontents
\listoftables
\listoffigures
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Introduction %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Introduction}
\setcounter{page}{1}
\input{1_intoduction}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% chapter1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Survival analysis}
\section{Definitions}
\input{2_SURVIVAL ANALYSES/1_definitions}
\section{Distributions of failure time}
\input{2_SURVIVAL ANALYSES/2_distributionsSURV}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% chapter2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{The theory of everyhting}
\section{Definition of something}
Another chapter here. Note that you can have (As we did for chapter 1) as a separate tex file.
\section{The answer is 42}
\subsection{And one subsection}
\subsection{A second one}
\chapter{Simulations}
\section{Simulation for estimating something}
\input{4_SIMULATION/A_simulation}
\newpage
%\nocite{}
\bibliographystyle{apalike} % bibliography style is unsrt: numbered in order of appearance
\bibliography{references} % this is the .bib file that holds the bibliography records
\end{document}
