Re: Rsquared for reproductible research

[brian powell <briangpowellms@gmail.com>]

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>> 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:

http://www.sciencedirect.com/science/article/pii/S1877050911001232

<=> "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 =>

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

* Exactly the paper can be found at:

http://www.sciencedirect.com/science\
?_ob=MiamiImageURL&_cid=280203&_user=10&_pii=S1877050911001232&\
_check=y&_origin=article&_zone=toolbar&_coverDate=\
31-Dec-2011&view=c&originContentFamily=serial&wchp=\
dGLbVlS-zSkWb&md5=4681e5babd7822f321d2a0dd3a9f11cf/\
1-s2.0-S1877050911001232-main.pdf

* 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:

http://eschulte.me/org-scraps/

* 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
http://rsquared.stat.uni-muenchen.de/index.rhtml
>>for OrgMode would be great.
> Yes!  Any takers?!?    ---(Stephen Eglen)

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