Re: Re: Org-mode Code Blocks Manuscript: Request For Comments

From: "Charles C. Berry" <cberry@tajo.ucsd.edu>
To: "Thomas S. Dye" <tsd@tsdye.com>
Cc: Detlef Steuer <detlef.steuer@gmx.de>, emacs-orgmode@gnu.org
Subject: Re: Re: Org-mode Code Blocks Manuscript: Request For Comments
Date: Mon, 6 Dec 2010 11:52:44 -0800	[thread overview]
Message-ID: <Pine.LNX.4.64.1012061107040.28663@tajo.ucsd.edu> (raw)
In-Reply-To: <5F849514-EDEF-47A0-A059-0389DF230E4E@tsdye.com>

On Sat, 4 Dec 2010, Thomas S. Dye wrote:

> Aloha Detlef,
>
> On Dec 2, 2010, at 9:58 PM, Detlef Steuer wrote:
>
>> Hi!
>> 
>> I very much appreciate your article as a nice introduction to org-babel
>> and its uses. As I'm going to introduce my colleagues into the nice
>> world of org-babel giving a talk sometime next term I'll shamelessly
>> steal from your work. (Of course giving attribution!)
>> 
>> Some remarks:
>> If you send it to Journal of _Statistical_ Software may be you should
>> be a little bit more focused on statistics. You article introduces
>> org-babel as a multi-language frontend to literate programming. What it
>> is, but there is little statistics in it.
>> 
>> In their article Gentleman and Lang introduced the "statistical
>> compendium". In my opinion emacs + org-mode + babel +
>> all-programming-languages-we-know + LaTeX + HTML export build the first
>> incarnation of a tool to really create such a compendium, org-babel
>> being central in that chain.
>> May be you can use some of Tom Dye's data to give an example of a
>> self-contained statistical workflow. I used his introduction given in
>> Worg to do my first steps in that direction. (Thx again Tom!)
>> Doing everything beginning with data-cleaning over data analysis to
>> template generating and report publishing and presentation in one
>> text-file.
>> That feature was, what caught me immediately as a statistician.
>> 
>> If you want to focus on the simulation side (may be more focused on
>> academics) I would stress the "always-correctness" of graphs in
>> articles. You all know what I mean...
>> 
>> Just my 2 cents. Of course it is great as it stands  and surely I'm
>> biased by my own needs.
>> 
>> Detlef
>> (a statistician)
>> 
>
> Thanks very much for the helpful comments and especially your perspective on 
> the Journal of Statistical Software.
>
> I'm interested to learn how you've developed a statistical workflow with 
> Org-mode beyond my first tentative steps in that direction.  It would be 
> great to have an example of your progress on Worg, if you can find the time.

Tom,

You might glean something from these links:

ESS and org-mode workflows are discussed here:

http://stackoverflow.com/questions/1429907/workflow-for-statistical-analysis-and-report-writing/

http://stackoverflow.com/questions/3027476/ess-workflow-for-r-project-package-development

https://github.com/Choens/LiterateR

CRAN's reproducible research 'task view' (with 'Related Links' of some
interest):

        http://cran.r-project.org/web/views/ReproducibleResearch.html

If you want to reach the R community, 'The R Journal' might be worth a try:

http://journal.r-project.org/

======

Let me just add my $0.02 worth to what others have already said and
say, that I really find org-babel useful in my R related work.

Currently, I am making use of it an environment for developing
R-packages. An org-mode file sits in the top level source directory of
an R package; it contains src blocks to fire up speedbar, list files
(for navigation w/o speedbar), do version control operations, check,
build, install, load the package, and do other routine tasks. Each
operation has its own headline, so I need only put the point on the
headline and 'C-c C-v C-s y' to run the subtree containing the block -
effectively making each operation a point - and - (a little more than
a) click.  Those source blocks are nearly the same for each package.

Additional blocks display help pages in the org file, load sample
data, let me work on new package features, and try out R idioms I
might want to use.

Then there are all the usual org-mode features that let me keep notes
and ideas and track the status of the package. org-mode has made this
part of my life a good deal simpler!

Chuck

>
> All the best,
> Tom
>
>> On Thu, 02 Dec 2010 12:28:27 -0700
>> "Eric Schulte" <schulte.eric@gmail.com> wrote:
>> 
>> > Hi,
>> > 
>> > Dan Davison, Tom Dye, Carsten Dominik and myself have been working on a
>> > paper introducing Org-mode's code block functionality.  We plan to
>> > submit this paper to the Journal of Statistical Software.  As both
>> > Org-mode and the code block functionality are largely products of this
>> > mailing list community, and in the spirit of an open peer review process
>> > we are releasing the current draft of the paper here to solicit your
>> > review and comments.
>> > 
>> > Both the .org and .pdf formats of the paper are available at the
>> > following locations.
>> > 
>> > http://cs.unm.edu/~eschulte/org-paper/babel.org
>> > 
>> > http://cs.unm.edu/~eschulte/org-paper/babel.pdf
>> > 
>> > Thanks -- Eric
>> > 
>> > _______________________________________________
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>> > 
>> 
>> 
>> 
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Charles C. Berry                            Dept of Family/Preventive Medicine
cberry@tajo.ucsd.edu			    UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901