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Appendices.tex
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Appendices.tex
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\addcontentsline{toc}{chapter}{Appendices}
% The \appendix command resets the chapter counter, and changes the chapter numbering scheme to capital letters.
%\chapter{Appendices}
\appendix
% I switched the order so chapter 2 \includes chapter3
\chapter{Appendix: A comparative test of the role of population structure in determining pathogen richness}
\chaptermark{Appendix: A comparative test of population structure and pathogen richness}
\label{empirAppendix}
\input{Appendix3}
% Chapter 3 Appendix
\chapter{Appendix: Understanding how population structure affects pathogen richness in a mechanistic model of bat populations}
\chaptermark{Appendix: Population structure and pathogen richness: a mechanistic model}
\label{sims1Appendix}
\input{Appendix2}
% Chapter 4 Appendix
\chapter{Appendix: A mechanistic model to compare the importance of interrelated population measures: population size, population density and colony size}
\chaptermark{Appendix: A comparison of population size, population density and colony size}
\label{sims2Appendix}
\input{Appendix4}
% Chapter 5 Appendix
\chapter{Appendix: A generalised random encounter model for estimating animal density with remote sensor data}
\chaptermark{Appendix: A generalised random encounter model for estimating animal density}
\label{gremAppendix}
\input{lucas_et_al_supplementarymaterial_2015-01-20.tex}
\chapter{Colophon}
\label{appendixlabel3}
This thesis was set using \LaTeX, \XeLaTeX\vspace{1mm} and Bib\LaTeX. \vspace{-0.12cm}
The formatting is defined by the \href{https://github.com/robjstan/latex-phdthesis}{\emph{phdthesis}} class by Robert Stanley.
The TeX Gyre Pagella typeface is used in the main text while {\usefont{T1}{fla}{l}{n} Lato Light} and {\usefont{T1}{fla}{eb}{n} \color[rgb]{0.75,0.75,0.75} Lato Black} are used in the figures.
Chapters \ref{ch:empirical}, \ref{ch:sims1} and \ref{ch:sims2} are entirely reproducible \href{http://yihui.name/knitr/}{\emph{knitr}} documents \cite{knitr}.
Code for the simulations in Chapter \ref{ch:grem} is not combined into a \emph{knitr} document but code for creating figures is.
All code is available on Github at \url{https://github.com/timcdlucas/PhDThesis}. %TODO add dois for thesis and MetapopEpi
Plots were created with a combination of \href{www.inkscape.org}{\emph{Inkscape}}, \emph{ggplot2} \cite{ggplot2}, \emph{palettetown} \cite{palettetown}, \emph{ggtree} \cite{ggtree}, \emph{cowplot} \cite{cowplot} and base \emph{R} \cite{R}.
References were handled with \emph{JabRef} \cite{JabRef_software}.
% description of document, e.g. type faces, TeX used, TeXmaker, packages and things used for figures. Like a computational details section.
% e.g. http://tex.stackexchange.com/questions/63468/what-is-best-way-to-mention-that-a-document-has-been-typeset-with-tex#63503