From: Eric Schulte <eric.schulte@gmx.com>
To: brian powell <briangpowellms@gmail.com>
Cc: emacs-orgmode@gnu.org
Subject: Re: Rsquared for reproductible research
Date: Thu, 12 Jan 2012 13:33:08 -0700 [thread overview]
Message-ID: <87zkdsr797.fsf@gmx.com> (raw)
In-Reply-To: <CAFm0skFi0U-3kN1x-bSu1Xr4d1Th3j=G0OTnyNAb=mHabJdTGQ@mail.gmail.com> (brian powell's message of "Thu, 12 Jan 2012 14:44:27 -0500")
brian powell <briangpowellms@gmail.com> writes:
>>> 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
>
Ah, thank you for linking to this paper. It seems I was missing was the
package-management aspect provided by R2 through CRAN. The instillation
of all software dependencies is a huge benefit exactly as installing
software with apt-get or pacman is simpler than running "./configure &&
make" and manually resolving dependencies.
While such a tool makes sense for a single language system like R, I
fear an Org-mode version of such a system would have too wide of a
scope. Given that code blocks may contain arbitrary languages, and that
sh blocks can freely call any command-line executable such a system
would turn into a system-wide package management tool.
Perhaps there already exists a portable package management system
designed for local installs which could handle most of the heavy
lifting.
As another option, distributing Virtual Machine images are one solution
which I think work well and are increasingly realistic. Or similarly
providing the research environment as a cloud server image (e.g., Amazon
EC2).
Certainly an interesting area for further work!
Best,
--
Eric Schulte
http://cs.unm.edu/~eschulte/
next prev parent reply other threads:[~2012-01-12 20:33 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2012-01-12 19:44 Rsquared for reproductible research brian powell
2012-01-12 20:33 ` Eric Schulte [this message]
[not found] <t5xd3p8qlct.fsf@rgc.damtp.cam.ac.uk>
2010-12-12 3:49 ` Fwd: [RFC] Self-configuring Org-mode files Thomas S. Dye
2012-01-12 12:38 ` Rsquared for reproductible research Stephen Eglen
2012-01-12 15:27 ` brian powell
2012-01-12 15:40 ` Stephen Eglen
2012-01-12 16:29 ` Eric Schulte
2012-01-12 18:24 ` Thomas S. Dye
2012-01-12 20:54 ` Stephen Eglen
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