Is there a way to configure Emacs so that it recognizes (and allows execution of) R code chunks within R markdown (.Rmd) files similar to the way it recognizes code chunks in .Rnw (Sweave) or .org (org-mode) files?
polymode is being developed which does/will allow you to write markdown with R chunks (for processing with
Instructions for setting up polymode+rmarkdown are in the README
Update: polymode has been released on MELPA, simplifying the installation process by using emacs' existing package mechanism. See the announcement on the ESS mailing list here.