Both are very similar but for my actual project I had to choose and master one. Then I compared them in the table above.
|Title||Markdown rendering for R||Dynamic Documents for R|
|Maintainer||Yihui Xie||JJ Allaire|
|Creator||JJ Allaire||JJ Allaire|
|Date of last version||2014-08-24||2015-01-26|
|Project is active on GitHut||Not since december 2014||Yes|
|Depends on or imports||mime||tools, utils, knitr, yaml, htmltools, caTools|
|Require Pandoc installed||No||Yes|
|Is imported by Knitr||Yes||No|
|Convert to HTML||Yes||Yes|
|Convert to PDF||No||Yes|
|Convert to Docx||No||Yes|
|Size without dependencies in MacOS X||417 Ko||3184 Ko|
|Table of Content||Yes
(specified in the YAML header of the .md)
|Documentation||Internal||Internal + Website|
The main obstacle to using rmarkdown is its requirement of Pandoc installed in the system.
I’m working on a reporting tool that have to work in various of platforms, including PC’s under Windows XP without admin access. Then we could install R and packages but not easily Pandoc.
Furthermore, this report tool must have the minimum dependencies, and I have to use knitr that include markdown package.
As a conclusion, rmarkdown is the default choice when you can use Pandoc, and you can have a lot of dependancies. markdown package is a good choice for lightweight applications that have to produce only simple HTML files.