That sounds like a nice way to do it, too. I heard about it before, but don't know R, so I didn't really consider it.
The reason I chose lmt is that it correctly keeps the markdown language syntax of the code blocks. That means I can put my literate config into my Zettelkasten [1] or [2] and watch it pretty-print in the browser.
There are also literate [3] and org-babel [4], but I don't think they are future proof. .lit is a random format and .org basically requires Emacs+orgmode.
1: https://github.com/srid/emanote