[R] [slightly off topic] Sweave with markdown

From: baptiste Auguié <ba208_at_exeter.ac.uk>
Date: Fri, 23 May 2008 09:37:45 +0100

DeaR list,

Has anyone tried to mix the Sweave paradigm with the Markdown[*] (and co.) syntax? Would this be hard to implement? My tiny understanding of Sweave is that one can define new drivers for the text part, while some functions that deal with the R code would not require any modification. Here's the reason I'm interested in Mardown for a driver.

I've been orbiting around Sweave for several weeks, and while I understand the great value of this "literate programming", I'm a bit put off by the technical aspect. I'm a LateX user, and a R user (you'd have guessed, albeit fairly novice), so the problem is not to get it working (i got some writings done with Sweave), but more of getting an efficient workflow. I find the LaTeX commands overly intruding in the middle of my R source code, plus the relatively slow compilation of latex makes it quite impractical for quick studies ( I once spent 20 minutes trying to get the graph to be at a sensible scale on the page).

As an alternative, I'm resorting to having a folder per study (I'm physicist, doing data analysis for optical spectroscopy), with one R file per analysis and a text file to keep track of the experimental conditions. When the data is really important / interesting, I've also tried to write a package: great for storing the data, functions and commands in a consistent manner (this works fine, but it cannot be a solution for quick trial experiments. Also, the figures cannot be included in the html doc as far as I know.)

I was considering some alternatives to Sweave, namely R2HTML and odfWeave, but in the former the source syntax is no less disturbing than LaTeX (although the zero compilation time is a plus), while for the latter I do not have a decent compatible editor (on a Mac, I tried Openoffice and Abiword but the fonts look like my handwriting for some obscure reason). Maybe I'll give it another shot at some stage, I just usually prefer plain text files.

Any input welcome,


[*]: http://en.wikipedia.org/wiki/Markdown

Baptiste Auguié

Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,

Phone: +44 1392 264187


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