The Orgmode extension to Emacs has quite an elegant, flexible, and powerful way of doing what you want. Can be hard to wrap your mind around at the beginning b

The Orgmode extension to Emacs has quite an elegant, flexible, and powerful way of doing what you want. Can be hard to wrap your mind around at the beginning but has good payoff once you're up to speed. Here's a video showing how one guy uses it with Python (though it integrates with multitude of languages, including R): http://www.youtube.com/watch?v=1-dUkyn_fZA http://www.youtube.com/watch?v=1-dUkyn_fZA Here's paper (itself from LaTeX generated by Orgmode) describing use of Orgmode for this kind of "reproducible research": http://www.jstatsoft.org/v46/i03/paper http://www.jstatsoft.org/v46/i03/paper