This document was compiled using LyX 2.2.1 for LaTeX (including KnitR)
master.lyx contains the main document (master.lyx), with the other 
chapters as child documents.

Also in this folder are some R scripts required for the reading of some
data formats as well as the "library.bib" BibTex file, "gibson.bst"
bibstyle file and "preamble.tex" which contains the LaTeX preable.

To compile the master document in LyX you will need the sidecap package
from http://theorie.physik.uni-konstanz.de/jrioux/lyx/
You will also need to make sure R and knitr are installed, and that
the PATH is set to the R installation dirctory, see this link for more 
info http://stackoverflow.com/questions/9645451/how-to-install-the-knitr-module-in-lyx-2-0-3

The "compiled" folder contains most of the output from the pdfLaTeX
and KnitR conversion (tex files and Rnw files), but does not contain
any of the image files or data which are in the "figure", "images" and
"data" folders in this directory. All the plots in the figure folder
are produced when the LyX document is "knited" using the R chunks and
the data (in the data folder).

A number of images have been removed in this version as although
I have permission to reproduce them in my thesis, I do not have
permission to store them in ORA. A list can be found in the
"MissingImages.txt" file. I suggest these are rendered in the
LaTeX "draft mode" to avoid problems.

A J London August 2016