dissertation.tex

\documentclass[print]{dissertation}
%\documentclass{dissertation}

%\usepackage{microtype}

\usepackage[acronym]{glossaries}

\usepackage{amsmath}
\usepackage{gensymb}

\usepackage{physics}

\usepackage[nodisplayskipstretch]{setspace}

\usepackage{listings}

\usepackage{rotating}
\usepackage{tabularx} 
\usepackage{multirow}
\usepackage{booktabs}
\newcolumntype{C}[1]{>{\raggedright\arraybackslash}p{#1}}

\usepackage{afterpage}

\usepackage{wrapfig}

\usepackage[inline]{enumitem}

\usepackage{mathtools}

\usepackage{contour}

\usepackage{hyperref}
\usepackage{float}
\usepackage[export]{adjustbox}
\usepackage{footnote}

\usepackage[utf8]{inputenc}

\usepackage[english]{babel}
\usepackage{natbib}
\bibliographystyle{abbrvnat}
%\setcitestyle{authoryear}

\usepackage{bibentry}
\nobibliography*

\usepackage{comment}

% show sources
\usepackage[source]{optional}

% no sources
% \usepackage[no_source]{optional}

\usepackage{tikz}

\usetikzlibrary{shadows.blur}
\usetikzlibrary{shapes.symbols}

\usepackage{tcolorbox}
\newtcolorbox{highlighted}{colback=yellow}

\usepackage{graphicx}
%% \usepackage{pgfplots}

\usepackage{xcolor}

% Select what to do with todonotes: 
% \usepackage[disable]{todonotes} % notes not showed
\usepackage[draft]{todonotes}   % notes showed


\newcounter{mycomment}
\newcommand{\mycomment}[2][]{%
	% initials of the author (optional) + note in the margin
	\refstepcounter{mycomment}%
	{%
		\setstretch{0.7}% spacing
		\todo[color={red!100!green!33},size=\small]{%
			\textbf{Comment [\uppercase{#1}\themycomment]:}~#2}%
}}

% JS for strikethrough
\usepackage{soul}

\setlength{\marginparwidth}{2cm}    

% abbreviations:
\newacronym{HAND}{HAND}{Height above the nearest drainage}
\newacronym{SRTM}{SRTM}{Shuttle Radar Topography Mission}
\newacronym{NED}{NED}{National Elevation Dataset}
\newacronym{NDWI}{NDWI}{Normalized Difference Water Index}
\newacronym{MNDWI}{MNDWI}{Modified Normalized Difference Water Index}
\newacronym{NDVI}{NDVI}{Normalized Difference Vegetation Index}
\newacronym{NDSI}{NDSI}{Normalized Difference Snow Index}
\newacronym{SAR}{SAR}{Synthetic Aperture Radar}
\newacronym{InSAR}{InSAR}{Interferometric Synthetic Aperture Radar}
\newacronym{AWEI}{AWEI}{Automated Water Extraction Index}
\newacronym{HSV}{HSV}{Hue Saturation Value}
\newacronym{LOWESS}{LOWESS}{Locally Weighted Scatterplot Smoothing}
\newacronym{OSM}{OSM}{OpenStreetMap}
\newacronym{VGI}{VGI}{Volunteered Geographic Information}
\newacronym{EO}{EO}{Earth Observation}
\newacronym{CART}{CART}{Classification And Regression Tree}
\newacronym{IPCC}{IPCC}{Intergovernmental Panel on Climate Change}
\newacronym{SDG}{SDGs}{Sustainable Development Goals}
\newacronym{KDE}{KDE}{Kernel Density Estimation}
\newacronym{PGM}{PGM}{Probabilistic Graphical Model}
\newacronym{CPD}{CPD}{Conditional Probability Distribution}
\newacronym{BN}{BN}{Bayesian Network}
\newacronym{MRF}{MRF}{Markov Random Field}
\newacronym{CRF}{CRF}{Conditional Random Field}
\newacronym{DAG}{DAG}{Directed Acyclic Graph}
\newacronym{MCMC}{MCMC}{Markov Chain Monte Carlo}
\newacronym{EM}{EM}{Expectation Minimization}
\newacronym{PDF}{PDF}{Probability Distribution Functions}

\makeglossaries


\begin{document}

%% Specify the title and author of the thesis. This information will be used on
%% the title page (in title/title.tex) and in the metadata of the fi\dfrac{num}{den}l PDF.
\title{Planetary-scale surface water detection from space}
\author{Gennadii}{Donchyts}

%% Use Roman numerals for the page numbers of the title pages and table of contents.
\frontmatter

\include{00.1-title/title}

\dedication{
	\epigraph{
		``Entia non sunt multiplicanda praeter necessitatem.`` \\
		``Entities should not be multiplied beyond necessity.``
	}{\textit{--- William of Occam}}
}

\tableofcontents

\addcontentsline{toc}{chapter}{Acronyms}
\setheader{Acronyms}
\printglossary[type=\acronymtype,title=Acronyms]

\include{00.2-summary/summary}

%% Use Arabic numerals for the page numbers of the chapters.
\mainmatter

%% Turn on thumb indices.
\thumbtrue

\include{01.1-introduction/introduction}
\include{01.1-remote-sensing/remote-sensing}
\include{01.2-water-detection/water-detection}
\include{01.3-prob/prob}
\include{01.4-change-detection/change-detection}
\include{01.8-aqua-monitor/aqua-monitor}
\include{01.9-water-murray-darling/water-australia-osm}

\include{02.1-conclusions/conclusion}

\include{02.2-acknowledgments/acknowledgments}

\appendix % Use letters for the chapter numbers of the appendices.
\include{01.2-water-detection/appendix-a}

% see website
% \include{01.8-aqua-monitor/appendix-a}

\include{03.1-publications/publications}
% \include{propositions}

%\bibliographystyle{apa}
\bibliographystyle{dissertation}
\bibliography{dissertation}


%% Turn off thumb indices for unnumbered chapters.
\thumbfalse

\end{document}













\begin{comment}
* talk to Lourens on IPCC, big issues and trends


* check "we ...", change to "I ..." or "it ..." where appropriate

* check Chapter <> chapter 
+ check \ref{ch2} where Chapter needs to be added
* check Figure <> figure
* check \ref{fig:} where Figure needs to be added

* rename ch1 to ch1-introduction, etc.


* human-made vs man-made? 

* data sets vs datasets?
* water body / water bodies vs waterbody / waterbodies?

* in order to -> to

* A, m3 -> m2

* Introduction IVVV --> 10

* Landsat <> LANDSAT

* Figure 3.2 freuency

\end{comment}