I prefer to store the data somewhere safe and link to it with something like
./data -> /Users/syounkin/data/Box/HOT/bvarick/data/
Thius keeps the repo light and avoids making any data public.
Created a Makefile to be used to run R markdown scripts. See README for more info. Also created R and html subdirectories. The repo should contain the html subdirectory but not the files in it.