Now Yuhui from Rstudio (who's been prolific in this area) has written bookdown for authoring books with rmarkdown. It's not for authoring statistical papers (as the other comments stated - that's rmarkdown's realm) it's for books like Hadley Wickham's R4DS and Advanced R. Other examples can be found on the bookdown website.
I'd also add that, regardless of inserting R code, bookdown is a class authoring format and personally I would write a book or large document in bookdown even if it was just pure prose.