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

From: Sunny Srivastava <research.baba@gmail.com>
To: "Charles C. Berry" <cberry@tajo.ucsd.edu>
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 19:13:38 -0500	[thread overview]
Message-ID: <AANLkTikjjn=HWNmnMWiavSyDtX7HLgG2-Rm8JSuH=2iS@mail.gmail.com> (raw)
In-Reply-To: <Pine.LNX.4.64.1012061107040.28663@tajo.ucsd.edu>

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Hello Chuck:

Your idea is very interesting. I am curious to make use of your ideas. If it
is not too much trouble, can you please share an example org file that you
use for package development? I completely understand if you can't share the
file.

Your help is highly appreciated.

Thank you in advance.

Best Regards,
S.

On Mon, Dec 6, 2010 at 2:52 PM, Charles C. Berry <cberry@tajo.ucsd.edu>wrote:

> 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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>>> > Please use `Reply All' to send replies to the list.
>>> > Emacs-orgmode@gnu.org
>>> > http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>>> >
>>>
>>>
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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
>
>
>
>
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