Pretty self explanatory. My PhD thesis is written using a Frankenstein combination of Rmarkdown and LaTeX. A pdf copy of my thesis is available through the University of Melbourne at http://hdl.handle.net/11343/55699.
This repository is mainly for archival purposes. But if you'd like to make the PDF yourself (!?) then this contains all the necessary files. It won't work out of the box, however, because I haven't included all the necessary R packages in the Makefile. I may get to fixing this once I'm back from a much-needed holiday I have no immediate plans to fix this.
There is an acompanying repository containing the analyses for each chapter at https://github.com/PeteHaitch/phd_thesis_analyses.