figure captions, references using knitr and markdown to html

Question

I\'m writing an Rmd file, to be processed by knitr into HTML. It contains some R chunks that generate figures, which get stored as data URIs in HTML.

1) How do I add

Answer 1

One way to do both of these is described here: http://rmflight.github.io/posts/2012/10/papersinRmd.html

Another is described here (but I don't know if it does your #2). http://gforge.se/2014/01/fast-track-publishing-using-knitr-part-iii/