To those interested in working with big project templates, deployment and R applications distribution, I just made available in Github a variation of r4ds, @hadleywickham book.
It is a variation because it has been built using #rsuite, a neat rstats application for deployment and distribution, including Docker and standalone python.
The code of r4ds remains untouched but you place the bookdown under the rsuite folder structure, which includes a deployment folder where the OS dependent sources and binaries are installed.
You can find the code here:
Enjoy!