From mboxrd@z Thu Jan 1 00:00:00 1970 From: Sunny Srivastava Subject: Re: Re: Org-mode Code Blocks Manuscript: Request For Comments Date: Mon, 6 Dec 2010 19:13:38 -0500 Message-ID: References: <87lj487z50.fsf@gmail.com> <20101203085837.499fc794@gaia.hsu-hh.de> <5F849514-EDEF-47A0-A059-0389DF230E4E@tsdye.com> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="===============2071520582==" Return-path: Received: from [140.186.70.92] (port=50680 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1PPlBe-0006IH-Qu for emacs-orgmode@gnu.org; Mon, 06 Dec 2010 19:13:44 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1PPlBc-00057M-Vj for emacs-orgmode@gnu.org; Mon, 06 Dec 2010 19:13:42 -0500 Received: from mail-ey0-f177.google.com ([209.85.215.177]:63312) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1PPlBc-00057H-Gs for emacs-orgmode@gnu.org; Mon, 06 Dec 2010 19:13:40 -0500 Received: by eyd9 with SMTP id 9so6679892eyd.36 for ; Mon, 06 Dec 2010 16:13:39 -0800 (PST) In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: "Charles C. Berry" Cc: Detlef Steuer , emacs-orgmode@gnu.org --===============2071520582== Content-Type: multipart/alternative; boundary=0015174be0f061c97c0496c6e085 --0015174be0f061c97c0496c6e085 Content-Type: text/plain; charset=ISO-8859-1 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 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" 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 >>> > > _______________________________________________ >>> > Emacs-orgmode mailing list >>> > Please use `Reply All' to send replies to the list. >>> > Emacs-orgmode@gnu.org >>> > http://lists.gnu.org/mailman/listinfo/emacs-orgmode >>> > >>> >>> >>> _______________________________________________ >>> Emacs-orgmode mailing list >>> Please use `Reply All' to send replies to the list. >>> Emacs-orgmode@gnu.org >>> http://lists.gnu.org/mailman/listinfo/emacs-orgmode >>> >> >> >> _______________________________________________ >> Emacs-orgmode mailing list >> Please use `Reply All' to send replies to the list. >> Emacs-orgmode@gnu.org >> http://lists.gnu.org/mailman/listinfo/emacs-orgmode >> >> > 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 > > > > > _______________________________________________ > Emacs-orgmode mailing list > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > http://lists.gnu.org/mailman/listinfo/emacs-orgmode > --0015174be0f061c97c0496c6e085 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 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 s= hare an example org file that you use for package development? I completely= understand if you can't share the file.=A0

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 =A0and surely I'm biased by my own needs.

Detlef
(a statistician)


Thanks very much for the helpful comments and especially your perspective o= n 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. =A0It wou= ld be great to have an example of your progress on Worg, if you can find th= e time.

Tom,

You might glean something from these links:

ESS and org-mode workflows are discussed here:


http://stackoverflow.co= m/questions/1429907/workflow-for-statistical-analysis-and-report-writing/

http://stackoverflow.com/quest= ions/3027476/ess-workflow-for-r-project-package-development

https://g= ithub.com/Choens/LiterateR


CRAN's reproducible research 'task view' (with 'Related Lin= ks' of some
interest):

=A0 =A0 =A0 http://cran.r-project.org/web/views/Reproduci= bleResearch.html

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

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

=3D=3D=3D=3D=3D=3D

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 bloc= k -
effectively making each operation a point - and - (a little more than
a) click. =A0Those 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 workin= g on a
> paper introducing Org-mode's code block functionality. =A0We plan = to
> submit this paper to the Journal of Statistical Software. =A0As 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 proce= ss
> 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<= br> > following locations.
> > http://cs.unm.edu/~eschulte/org-paper/babel.org
> > http://cs.unm.edu/~eschulte/org-paper/babel.pdf
> > Thanks -- Eric
> > _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmo= de@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>


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


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


Charles C. Berry =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Dep= t of Family/Preventive Medicine
cberry@tajo.ucsd.= edu =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0UC San Diego
ht= tp://famprevmed.ucsd.edu/faculty/cberry/ =A0La Jolla, San Diego 92093-0= 901




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

--0015174be0f061c97c0496c6e085-- --===============2071520582== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode --===============2071520582==--