Stephen Eglen S@J@Eg|en @end|ng |rom d@mtp@c@m@@c@uk
Mon Feb 16 08:13:14 CET 2015

>> Right now, I can open an Rmd file in Emacs, M-x markdown-mode, the correct
>> menus appear. However when I try to compile something, I get the minibuffer
>> error
>
> That sounds like a pretty clear hint that you should install markdown.
> But that will only give you .md --> .html, you will still need a way
> to convert .Rmd --> .md. One way or another most people are using
> pandoc for this, so you should probably install that too (if you don't

markdown-mode has a variable "markdown-command" which should point to
the binary (normally "markdown") that makes the html.  Get markdown or
try hooking pandoc in.

http://kieranhealy.org/blog/archives/2014/01/23/plain-text/

which shows how you can get citations into markdown.  I'm currently
writing a journal article with it, and the workflow is pretty nice.
LaTeX is still king but pandoc is great if ever you need html or .docx
from your source files.  One thing markdown currently misses is \label{}
and \ref{} equivalents, but there's discussion about implementing that.

Stephen