From mboxrd@z Thu Jan 1 00:00:00 1970 From: brian powell Subject: Re: Rsquared for reproductible research Date: Thu, 12 Jan 2012 14:44:27 -0500 Message-ID: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=f46d0438931fe44f9404b659f94b Return-path: Received: from eggs.gnu.org ([140.186.70.92]:56166) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RlQZf-00063a-AU for emacs-orgmode@gnu.org; Thu, 12 Jan 2012 14:44:36 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RlQZY-0004fL-SJ for emacs-orgmode@gnu.org; Thu, 12 Jan 2012 14:44:35 -0500 Received: from mail-wi0-f169.google.com ([209.85.212.169]:61999) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RlQZY-0004f9-KY for emacs-orgmode@gnu.org; Thu, 12 Jan 2012 14:44:28 -0500 Received: by wicr5 with SMTP id r5so1163463wic.0 for ; Thu, 12 Jan 2012 11:44:27 -0800 (PST) List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: emacs-orgmode@gnu.org --f46d0438931fe44f9404b659f94b Content-Type: text/plain; charset=ISO-8859-1 >> 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) --f46d0438931fe44f9404b659f94b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
>> Also, I very much agree that a "near exact replica"= of the http://
>> rsquared.stat.uni-muenchen.de/index.rhtml for OrgM= ode would be great.
> Yes! =A0Any takers?!?
>
...
Eric= questioned:=A0
"From looking at the fairly terse web site f= or R^2 it is not clear to me
exactly what the system includes (I&= #39;m sure I'm missing something
obvious). =A0It seems to be the addition of a packaging system over-to= p of
R source files. =A0What would a potential Org-mode based sys= tem provide
which is not already possible with Org-mode text file= s, 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 =A0"Friedrich L= eischa, , Manuel Eugsterb, Torsten Hothornb" put together may make thi= ngs clearer--this paper really seems to be the justification/impetus for th= e R^2 website--it has made things clearer and more exciting for me:


<=3D> "Executable P= apers for the R Community: The R2 Platform for Reproducible Research"<= /div>

** So papers in R (and maybe other languages--maybe lan= guages run thru Babel in OrgMode) could be "executed" by people i= n 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 a= nd data analysis
Sweave: the most popular format for executable p= apers 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/C= WEAVE/CTANGLE=3D>NOWEB (Knuth) comes to mind here--i.e. Literate Program= ming

***** http://www-cs-staff.stanford.edu/~uno/cweb.html =3D>

CTANGLE
converts a source file foo.w to a co= mpilable 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:

?_ob=3DMiamiImageURL&_cid=3D280203&_user=3D10&_pii=3DS1877= 050911001232&\
_check=3Dy&_origin=3Darticle&_zone=3Dt= oolbar&_coverDate=3D\
31-Dec-2011&view=3Dc&originCont= entFamily=3Dserial&wchp=3D\
dGLbVlS-zSkWb&md5=3D4681e5babd7822f321d2a0dd3a9f11cf/\
1= -s2.0-S1877050911001232-main.pdf

* I agree Eric th= at 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 comm= unity might do) the general ideas, the structure of the website's proce= ss "OrgMode=3D>TeX paper in"-->...process...-->Executabl= e/verifiable code interaction a user might experience/stored on-line for re= searchers (one thing I always enjoy a lot when working with e.g. R/S-PLUS a= nd 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 th= e details!

* Thanks for the link Eric to your OrgM= ode "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=A0
&g= t;>for OrgMode would be great.
> Yes! =A0Any takers?!? =A0 =A0---(Stephen Eglen)



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