This is a repo containing my PhD Thesis.
The template is taken from here. The style file is taken from Robert Stanley here. There was a few edits to get the template and Rob's style to work together. The style file requires xelatex (or lautex) so the thesis is now compiled with xelatex.
The main file is tim-lucas-thesis.tex and tim-lucas-thesis.pdf is the compiled pdf which should render in github (maybe slowly).
The following files contain the main content of the thesis.
NB The file Chapter3.Rtex is in fact Chapter 2 in the thesis and Chapter2.Rtex is Chapter3.
I don't think I want to rename them as this will mess up the git history (lesson learned, don't use numbered files like this...)
Data chapters are written as .Rtex files with embedded R code.
These files are Chapter*.Rtex.
These files are compiled to create files Chapter*.tex which does not include R code.
Text only chapters are written directly in a .tex file.
While tim-lucas-thesis.pdf is the full thesis pdf, most chapters are also compiled seperately. These files are
- drafts/intro_draft.pdf
- drafts/Chapter_2_draft.pdf
- drafts/Chapter_3_draft.pdf
- drafts/Chapter_4_draft.pdf
- drafts/Chapter_5_draft.pdf
- drafts/discussion_draft.pdf
Chapter5DataReformat.R takes data from simulations for Chapter 5 and reformats them ready for plotting.
chapter3functions.R and chapter4functions.R contain additional files used in these chapters and are pulled out to keep the .Rtex files more tidy.
Appendix3.Rtex contains code and text for appendices for Chapter 2.
lucas_et_al_supplementarymaterial_2015-01-20.tex, REM-methods.tex and files in latexFiles/ make up additional methods for Chapter 5 and are included as an appendix.
data/ contains all raw and processed data for each chapter in seperate folders. Each folder should contain a README describing the data files in more detail.
Figures created directly from Chapter analyses by knitr are in figure/. Figures created by older analyses and manually with inkscape are in imgs/
misc/ contains additional files such as my ggplot2 themes and global knitr options.
The thesis is largely reproducible. Chapters 2 and 4 require my R package MetapopEpi which is only available on github. The simulations in Chapter 5 are not reproducible. They were written by a coauthor and I haven't gotten round to getting the code and working out how to run it. Sorry.
Most of the simulations are run using my R package MetapopEpi. While this isn't particularly well written for reusability, feel free to have a go.
If you want to use knitr in your thesis there is a barebones thesis here. This repo also explains some of the issues and benefits with using knitr in this way.
As the required formatting for a UCL thesis is rather uninspiring I am also creating a file that is formatted in a way that I think is attractive and readable. Since including Rob's style file, the pretty thesis is much less necessary. But I'll still play with it.
The files for this version are in PrettyThesis/ and the combined pdf is PrettyThesis/tim-lucas-pretty-thesis.pdf.
