main.tex

\documentclass[10pt,b5paper,twoside,openany]{memoir}




%%% Packages 
\usepackage[utf8]{inputenc}
\usepackage[danish,english]{babel}
\usepackage{pdfpages}%include pdfs
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{float}
\usepackage{tikz}
\usepackage{blindtext}% dummy text
\usepackage{fancyhdr}
\usepackage{titlesec}
\usepackage[font={small}]{caption}
\usepackage{enumitem}
\usepackage[backend=biber,sorting=none]{biblatex}
\usepackage{csquotes}
\addbibresource{disbib.bib}

\DeclareUnicodeCharacter{0308}{.}

\usepackage{listings}
\usepackage{xcolor}
%% Colors 
\definecolor{codegray}{rgb}{0.5,0.5,0.5}
\definecolor{dtured}{rgb}{0.60, 0.00, 0.00}
\colorlet{thecolor}{dtured!100!}
\definecolor{thechptclr}{gray}{0.6}
\definecolor{thecaptionclr}{gray}{0.6}
\definecolor{gray20}{gray}{0.20}
\definecolor{gray40}{gray}{0.40}
 
\lstdefinestyle{mystyle}{
    keywordstyle=\color{magenta},
    numberstyle=\tiny\color{codegray},
    stringstyle=\color{codepurple},
    basicstyle=\ttfamily\footnotesize,
    breakatwhitespace=true,         
    breaklines=true,                 
    captionpos=b,
    keepspaces=true,                 
    numbers=left,                    
    numbersep=5pt,                  
    showspaces=false,                
    showstringspaces=false,
    showtabs=false,                  
    tabsize=2
}
 
\lstset{style=mystyle}

\pagenumbering{roman}

\title{The Title}

\author{First Last}
\date{22$^{th}$ October, 2022}

%%%%%%%%% WRITE THE SECTION NAME IN THE HEADER %%%%%
%\pagestyle{headings}

\chapterstyle{tandh}

% adjust caption formatting (memoir)
\captionnamefont{\bfseries} 
\captiondelim{. }
\changecaptionwidth
\captionwidth{5in}
\captionsetup{belowskip=0pt}


%%%%%%%%%% customization: formatting for Figure, Table, Equation references
\usepackage{graphicx}
%running fraction with slash - requires math mode.
\newcommand*\rfrac[2]{{}^{#1}\!/_{#2}}
\newcommand{\fig}[2]{\textbf{Figure~\ref{#1}{#2}}} 
\newcommand{\tab}[2]{\textbf{Table~\ref{#1}{#2}}} 
\newcommand{\tabb}{\hspace*{2em}}
\newcommand{\sub}[1]{\mbox{(\textbf{#1})}} % formatting for subfigure label within a caption
\newcommand{\prog}[1]{\texttt{#1}}

\newcommand{\fixme}[1]{\textbf{\underline{#1}}} 
%%%Font size on chapters, sections and subsections
\newcommand*{\justifyheading}{\raggedleft}

\titleformat*{\section}{\LARGE\bfseries}
\titleformat*{\subsection}{\Large\bfseries}
\titleformat*{\subsubsection}{\large\bfseries}
\titleformat*{\paragraph}{\large\bfseries}
\titleformat*{\subparagraph}{\large\bfseries}



%###########################
\begin{document}
%###########################
\setcounter{page}{0}
\include{front/titlepage}

\frontmatter

\include{front/preface}
\include{front/formal}
\include{front/acknowledgements}


%%%%% Table of Content
%\cleardoublepage
\renewcommand*\contentsname{Table of contents}
\tableofcontents*

%% Font stuff 
\include{front/summary_english}
\include{front/summary_danish}

%\cleardoublepage
\include{front/publications}
\include{front/thesisoverview}
\clearpage



%%%%%%% PREFACE CHAPTERS INCLUDE%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\mainmatter
\setcounter{page}{1}

%%%%Put number on subsubsection:
\setcounter{secnumdepth}{3}
\newpage

%%%%%%%%%%% INTRODUCTIOn %%%%%%%%%%%%%%%


%\titlespacing\section{0pt}{0pt}{\parskip}{-\parskip}

%% Header
\makepagestyle{dtu}

\makeoddhead{dtu}{\leftmark}{}{\thepage}
\makeevenhead{dtu}{\thepage}{}{\leftmark}

\makeheadrule{dtu}{\textwidth}{0.3pt}
\pagestyle{dtu}
\aliaspagestyle{chapter}{dtu}

\cleardoublepage
\begingroup

\chapter{Background}
\include{introduction/metagenomics}
\endgroup

\begingroup
\chapter{Methods} 
\include{methods/ML}
\endgroup

%%% Introduction of each Project 
\begingroup
\chapter{Research objectives}
\include{middle/Research_objectives}

\chapter{Description of research projects}
\include{middle/description_research_projects}
\endgroup

%%% Summary and discussion of results 
\begingroup
\chapter{Summary of results and discussion}
\include{middle/2_phamb_results}


\endgroup

%%% Conclusion and Ethics statement
\include{tail/Conclusion}
\include{tail/ethical}


%%%%% APPENDIX %%%%
%\thispagestyle{empty}
\newcommand{\beginsupplement}{%
        \setcounter{table}{0}
        \renewcommand{\thetable}{S\arabic{table}}%
        \setcounter{figure}{0}
        \renewcommand{\thefigure}{S\arabic{figure}}%
     }
\beginsupplement


%%%%%%% Papers 

\begingroup

% Set page layout for papers only
\makepagestyle{papers}
\makeoddhead{papers}{\thepage}{}{\leftmark}
\makeevenhead{papers}{\leftmark}{}{\thepage}
\makeheadrule{papers}{\textwidth}{0.3pt}
\pagestyle{papers}
\aliaspagestyle{chapter}{papers}

\chapter{Manuscripts}

\include{papers/phamb}

\endgroup


%%%%% APPENDIX %%%%
\begingroup

\makepagestyle{papers}
\makeoddhead{papers}{\thepage}{}{\leftmark}
\makeevenhead{papers}{\leftmark}{}{\thepage}
\makeheadrule{papers}{\textwidth}{0.3pt}
\pagestyle{papers}
\aliaspagestyle{chapter}{papers}

\chapter{Appendix}
\include{tail/appendix}
\endgroup


% Giv kapitel nummer. 
\printbibliography[title={References}]


\end{document}