To convert Markdown files to html in R two packages are currently available: markdown and rmarkdown (note there is an extra r to the last one).

Both are very similar but for my actual project I had to choose and master one. Then I compared them in the table above.

Comparison table

markdown rmarkdown  
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
Main function markdownToHTML render
YAML No Yes
Table of Content Yes
(with option = "toc")
Yes
(specified in the YAML header of the .md)
Documentation Internal Internal + Website

Choice

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.