Paper.tex

\documentclass[a4paper,11pt,bibliography=totoc,numbers=noenddot]{scrartcl}\usepackage[]{graphicx}\usepackage[]{color}
%% maxwidth is the original width if it is less than linewidth
%% otherwise use linewidth (to make sure the graphics do not exceed the margin)
\makeatletter
\def\maxwidth{ %
  \ifdim\Gin@nat@width>\linewidth
    \linewidth
  \else
    \Gin@nat@width
  \fi
}
\makeatother

\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%

\usepackage{framed}
\makeatletter
\newenvironment{kframe}{%
 \def\at@end@of@kframe{}%
 \ifinner\ifhmode%
  \def\at@end@of@kframe{\end{minipage}}%
  \begin{minipage}{\columnwidth}%
 \fi\fi%
 \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
 \colorbox{shadecolor}{##1}\hskip-\fboxsep
     % There is no \\@totalrightmargin, so:
     \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
 \MakeFramed {\advance\hsize-\width
   \@totalleftmargin\z@ \linewidth\hsize
   \@setminipage}}%
 {\par\unskip\endMakeFramed%
 \at@end@of@kframe}
\makeatother

\definecolor{shadecolor}{rgb}{.97, .97, .97}
\definecolor{messagecolor}{rgb}{0, 0, 0}
\definecolor{warningcolor}{rgb}{1, 0, 1}
\definecolor{errorcolor}{rgb}{1, 0, 0}
\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX

\usepackage{alltt}
\usepackage[english]{babel}
\usepackage{amsmath,amssymb}
\usepackage{enumerate}
\usepackage{blindtext}
\usepackage{listings}
%\usepackage{xcolor} % knitr automatically adds this
\usepackage{graphicx}
\usepackage{float}
\usepackage{rotating} % allows for rotation of tables
\usepackage{dcolumn} % aligns numbers regarding decimal point in tables
\usepackage{pdfpages}
\usepackage[onehalfspacing]{setspace}
\usepackage[left=3cm,right=2.5cm,top=2.5cm,bottom=2.5cm
  %,includeheadfoot
  ]{geometry}
\usepackage{varioref} % use \vref{} instead of \ref
\usepackage{pgf,tikz}
\usepackage[pdfborder={0 0 0}]{hyperref}
\usepackage{apacite}
\usepackage{appendix}

%%%%%%%%%%%%%%% Define some commands: %%%%%%%%%%%%%%%%
\newcommand{\R}{\textrm{R}} % for correct writing of R, write \R

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%% Check and edit this: %%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newcommand{\theAuthor}{Your Name}
\newcommand{\theDate}{\today}
\newcommand{\theAddress}{Your Address}
\newcommand{\theZip}{ZIP Code}
\newcommand{\theCity}{Your City}
\newcommand{\theMatriculation}{09-xyz-xyz}
\newcommand{\theTitle}{Some Title}
\newcommand{\theSubtitle}{Some Subtitle}
\newcommand{\theSupervisor}{Prof.\,PhD~Jon Doe}
\newcommand{\theType}{Master's Thesis}
\newcommand{\theSemester}{Fall 2016}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\labelformat{section}{section~#1}
\labelformat{subsection}{subsection~#1}
\labelformat{equation}{(#1)}
\labelformat{table}{table~#1}
\labelformat{figure}{figure~#1}
% penalty for line break over pages
\clubpenalty = 10000
\widowpenalty = 10000

% Distance Toc-Title and first entry
\usepackage{tocloft}
%\setlength\cftaftertoctitleskip{30pt}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}

% Front page:
\include{FrontBack/Frontpage}

% Abstract:
\include{FrontBack/Abstract}

\pagenumbering{Roman} % Change pagenumbering to capital roman numbers
% Preface:
\include{FrontBack/Preface}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Lists %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% TOC
\newpage
\tableofcontents
\newpage
% List of Tables
%\phantomsection
%\addcontentsline{toc}{section}{List of Tables}
%\addtocontents{toc}{\protect\vspace{-5pt}}
\listoftables
\newpage
% List of Figrues
%\phantomsection
%\addtocontents{toc}{\protect\vspace{-5pt}}
%\addcontentsline{toc}{section}{List of Figures}
\listoffigures
%\lstlistoflistings

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Load relevant things into R's memory, such as functions, data and packages %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Content %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Introduction:

\newpage
\pagenumbering{arabic}
\section{Introduction}
\label{sec:Introduction}
\blindtext

% Data:

\newpage
\section{Data}
\label{sec:Data}
\blindtext[1]

Useful package: \texttt{stargazer} produced \vref{tab:summarystats} \cite{stargazer}. One can see that the mean of sepal length is 5.8433333. You can install required packages on the fly, using the function shown in \vref{app:code}.
\subsection{Summary Statistics}
\label{sub:Stats}
\blindtext

% Table created by stargazer v.5.2 by Marek Hlavac, Harvard University. E-mail: hlavac at fas.harvard.edu
% Date and time: Fre, Aug 05, 2016 - 09:59:03
% Requires LaTeX packages: dcolumn 
\begin{table}[!htbp] \centering 
  \caption{Summary statistics of the iris database} 
  \label{tab:summarystats} 
\begin{tabular}{@{\extracolsep{5pt}}lD{.}{.}{-3} D{.}{.}{-3} D{.}{.}{-3} D{.}{.}{-3} D{.}{.}{-3} } 
\\[-1.8ex]\hline 
\hline \\[-1.8ex] 
Statistic & \multicolumn{1}{c}{N} & \multicolumn{1}{c}{Mean} & \multicolumn{1}{c}{St. Dev.} & \multicolumn{1}{c}{Min} & \multicolumn{1}{c}{Max} \\ 
\hline \\[-1.8ex] 
Sepal.Length & 150 & 5.843 & 0.828 & 4.300 & 7.900 \\ 
Sepal.Width & 150 & 3.057 & 0.436 & 2.000 & 4.400 \\ 
Petal.Length & 150 & 3.758 & 1.765 & 1.000 & 6.900 \\ 
Petal.Width & 150 & 1.199 & 0.762 & 0.100 & 2.500 \\ 
\hline \\[-1.8ex] 
\end{tabular} 
\end{table} 

\blindtext[3]

\subsection{Further Statistics}
\blindtext
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{figure}

{\centering \includegraphics[width=\maxwidth]{figure/boxplots-1} 

}

\caption[Boxplots of the iris data for all three species]{Boxplots of the iris data for all three species}\label{fig:boxplots}
\end{figure}


\end{knitrout}
\blindtext[4]

For the boxplots, see \vref{fig:boxplots}.


% Conclusion:

\newpage
\section{Conclusion}
\label{sec:Conclusion}

\blindtext[4]

% References
\newpage
\setlength{\bibitemsep}{.45\baselineskip}
\bibliographystyle{apacite}
\interlinepenalty=10000  %prevent splited bibitems
\bibliography{References}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Appendix %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\labelformat{section}{appendix~#1} % following sections are called appendix when refered to
\begin{appendices}
\include{Appendices/DataDeclaration}



\newpage
\section{\R-Code}
\label{app:code}
\lstinputlisting[nolol=true,basicstyle=\scriptsize\tt,breaklines=true]{Code/functions.R}
\end{appendices}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Academic Honesty %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\include{FrontBack/Honesty}

\end{document}