Welcome to my dissertation code dump. For the time being, this is the only route to reproducing my results and I apologize if it's a labyrinth!
It does NOT include three folders, which are not tracked, and which therefore do not appear here, but that are also integral parts of the workflow:
/Data/ (files are nearly all in .Rdata format, so not good to track with git. Download separately as stated above)
/DiagnosticPlots/ (these are not in the dissertation. These figures were early looks at the data)
/latex/Figures/ (folder to hold pdfs for inclusion in the main latex document. You can reproduce its contents with the R scripts and data)
All figures can be reproduced by using the R script files if you have the data, which you need to download separately from Google Drive under the following link:
https://drive.google.com/folderview?id=0B2b7NmVR77Q1bDdSNkVaVGxJZVE&usp=sharing
This will give you a folder called 'Data', which should be placed in /DISS/ at the same level as /R/ (and friends)
Once you have the data, R scripts will (hopefully) be able to grab it and use it to make Figures, or to help you test functions. All R functions are undocumented, though some are lightly annotated (but not thoroughly at this time). I'll be trickle-grooming this code, so either make a request or be patient. In general, you'll need to tinker to make sense of things, sorry.
Each R script begins by setting the working directory with, with setwd(), so you need to change that appropriately
DO NOT mindlessly run an entire script without looking at it first, as it may contain a simulation that will dominate your computer resources.
thesisMain.tex is the mother tex document, pulling in chunks from /latex/ The structure of \thesisMain.tex is what gives the dissertation its part/chapter/section structure If you want to find how functions were implemented, the best way (for now) is to either 1) intuit via script names, or 2) to find a figure in the dissertation that used this code, then find the .tex file that makes that section. In the latex chunk where the figure is included you'll (usually) see the name of the script that produced it.
wish me luck