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Re: [O] Rsquared for reproductible research

From: brian powell
Subject: Re: [O] Rsquared for reproductible research
Date: Thu, 12 Jan 2012 14:44:27 -0500

>> Also, I very much agree that a "near exact replica" of the http://
>> rsquared.stat.uni-muenchen.de/index.rhtml for OrgMode would be great.
> Yes!  Any takers?!?
Eric questioned: 
"From looking at the fairly terse web site for R^2 it is not clear to me
exactly what the system includes (I'm sure I'm missing something
obvious).  It seems to be the addition of a packaging system over-top of
R source files.  What would a potential Org-mode based system provide
which is not already possible with Org-mode text files, Org-mode
publishing and a version control repository."

* I mostly agree with your statements. Good challenges. I did more investigation: This link to the paper that  "Friedrich Leischa, , Manuel Eugsterb, Torsten Hothornb" put together may make things clearer--this paper really seems to be the justification/impetus for the R^2 website--it has made things clearer and more exciting for me:


<=> "Executable Papers for the R Community: The R2 Platform for Reproducible Research"

** So papers in R (and maybe other languages--maybe languages run thru Babel in OrgMode) could be "executed" by people in the community--one could verify research studies and papers interactively, ad hoc.

*** They mention in the paper that they use several key tools:

"R: the lingua franca of statistics and data analysis
Sweave: the most popular format for executable papers in the R community
CRAN: package building and checking system has been developed for more then a decade and copes successfully
with the exponential growth of the number of packages"

**** Weave/CWEB/CWEAVE/CTANGLE=>NOWEB (Knuth) comes to mind here--i.e. Literate Programming

***** http://www-cs-staff.stanford.edu/~uno/cweb.html =>

converts a source file foo.w to a compilable program file foo.c;
converts a source file foo.w to a prettily-printable and cross-indexed document file foo.tex.

* Exactly the paper can be found at:


* I agree Eric that the website is a bit terse; but, for the most part I was excited about (and I think Stephen is interested in--he suggested it is something the community might do) the general ideas, the structure of the website's process "OrgMode=>TeX paper in"-->...process...-->Executable/verifiable code interaction a user might experience/stored on-line for researchers (one thing I always enjoy a lot when working with e.g. R/S-PLUS and PYTHON's interactive CLI, etc.)

** They even publish the minute details of the settings on the machines--the local environment variables, etc.--the devil is in the details!

* Thanks for the link Eric to your OrgMode "scraps"--they could be very useful:


* Lastly, most importantly I'll repeat the link and query to the community:
>> Also, I very much agree that a "near exact replica" of the 
>>for OrgMode would be great.
> Yes!  Any takers?!?    ---(Stephen Eglen)

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