Re: Updating the Babel section of Worg Was: Generating plot with org-babel-R

[tsd@tsdye.com (Thomas S. Dye)]

Hi Eric,

Yes, this is overdue.  I think your plan is a good one.

Perhaps a few of the individual use cases could be moved to FIXME,
instead?  I'm thinking here of Feiming Chen's R setup and some of my
contributions when I was experimenting writing LaTeX inside source
code blocks.  The authors could resurrect these as they see fit.

Hopefully, others will contribute use examples.  My sense from reading
the list is there are many interesting ones.

I'd like it if Org mode users designed a template for the language
specific pages.  Currently, these seem to me a mixed bag and it would be
good to regularize them.  It would also be nice to have one for each of
the supported languages.  There are 11 language specific pages now,
which leaves quite a few languages under-documented.

I'll be happy to work on this as I can.

All the best,
Tom


Eric Schulte <eric.schulte@gmx.com> writes:

> Thanks for raising this point.  The bulk of the content in the Babel
> portion of worg is fairly old, predating the syntax standardization
> efforts this fall.  I've just pushed some minor updates to the main
> babel pages, but updating the language-specific tutorials and the
> individual use cases will be a much larger effort.
>
> I'm not sure how to proceed.  One option would be to go through and add
> a [uses deprecated syntax] tag to the top of each such page, which could
> be removed after the page has been checked and possibly updated to
> ensure consistency with the latest syntax.
>
> Given that the Babel syntax will not be changing significantly moving
> forward now would be a good time to do such a review.  Ideally this
> could be completed before the release of Emacs 24 in a couple of months.
>
> Any other ideas for update/reorganization or volunteers?
>
> Cheers,
>
> tsd@tsdye.com (Thomas S. Dye) writes:
>
>> Hi Riccardo,
>>
>> Thanks for the URL.  Org mode has evolved since this article was
>> written.  It should probably be revised or taken off Worg.  I've copied
>> Eric Schulte, who is better able than me to determine the correct course
>> of action here.
>>
>> In the meantime, an up-to-date description of how Org mode can be used
>> to write literate programs has appeared in the Journal of Statistical
>> Software.  You can find it here: http://www.jstatsoft.org/v46/i03
>>
>> Perhaps you could use the examples in the JSS article to get started?
>> If these don't work for you, or if they raise questions that are difficult
>> to answer, please do come back to the list with your queries.
>>
>> All the best,
>> Tom
>>
>> Riccardo Romoli <ric.romoli@gmail.com> writes:
>>
>>> Hi, this is the URL:
>>>
>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html
>>>
>>> Best
>>> R
>>>
>>> 2012/2/5 Thomas S. Dye <tsd@tsdye.com>
>>>
>>>> Hi Riccardo,
>>>>
>>>> This code appears to be outdated.  I don't recall this code on the org
>>>> site.  Could you send a URL?
>>>>
>>>> All the best,
>>>> Tom
>>>>
>>>> Riccardo Romoli <ric.romoli@gmail.com> writes:
>>>>
>>>> > Hi, I'm trying to generate some figure with R, into an org session.
>>>> Firstly
>>>> > I use the code in the org site. The problem is that the code do not
>>>> > generate any figure.
>>>> >
>>>> > This is the code:
>>>> >
>>>> > #+TITLE:Test
>>>> > #+AUTHOR: Your Name
>>>> > #+EMAIL: your-email@server.com
>>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports
>>>> > both :tangle yes
>>>> >
>>>> > * Example of Org-Babel for R Literate Programming
>>>> > ** R text output
>>>> > A simple summary.
>>>> > #+begin_src R
>>>> >   x <- rnorm(10)
>>>> >   summary(x)
>>>> > #+end_src
>>>> >
>>>> > ** R graphics output
>>>> > Note we use the object =x= generated in previous code block, thanks to
>>>> > the header option =:session *R*=.  The output graphics file is
>>>> > =a.png=.
>>>> >
>>>> > #+begin_src R  :file a.png
>>>> >   y <- rnorm(10)
>>>> >   plot(x, y)
>>>> > #+end_src
>>>> >
>>>> > Same plot with larger dimension:
>>>> >
>>>> > #+begin_src R  :file b.png :width 800 :height 800
>>>> >   plot(x, y)
>>>> > #+end_src
>>>> >
>>>> >
>>>> > Where do I wrong?
>>>> >
>>>> > Best
>>>> > Riccardo
>>>> > Hi, I&#39;m trying to generate some figure with R, into an org session.
>>>> Firstly I use the code in the org site. The problem is that the code do not
>>>> generate any figure. This is the code:
>>>> > #+TITLE:Test
>>>> > #+AUTHOR: Your Name
>>>> > #+EMAIL: mailto:your-email@server.com
>>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports both
>>>> :tangle yes
>>>> >
>>>> > * Example of Org-Babel for R Literate Programming
>>>> > ** R text output
>>>> > A simple summary.
>>>> > #+begin_src R
>>>> >   x <- rnorm(10)
>>>> >   summary(x)
>>>> > #+end_src
>>>> >
>>>> > ** R graphics output
>>>> > Note we use the object =x= generated in previous code block, thanks to
>>>> > the header option =:session *R*=.  The output graphics file is
>>>> > =a.png=.
>>>> >
>>>> > #+begin_src R  :file a.png
>>>> >   y <- rnorm(10)
>>>> >   plot(x, y)
>>>> > #+end_src
>>>> >
>>>> > Same plot with larger dimension:
>>>> >
>>>> > #+begin_src R  :file b.png :width 800 :height 800
>>>> >   plot(x, y)
>>>> > #+end_src
>>>> > Where do I wrong?BestRiccardo
>>>>
>>>> --
>>>> Thomas S. Dye
>>>> http://www.tsdye.com
>>>>
>>> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.htmlBestR
>>> 2012/2/5 Thomas S. Dye <span dir="ltr"><mailto:tsd@tsdye.com></span>Hi Riccardo,
>>>
>>>
>>> This code appears to be outdated.  I don&#39;t recall this code on the org
>>> site.  Could you send a URL?
>>>
>>> All the best,
>>> Tom
>>>
>>> Riccardo Romoli <mailto:ric.romoli@gmail.com> writes:
>>>
>>>> Hi, I&#39;m trying to generate some figure with R, into an org session. Firstly
>>>> I use the code in the org site. The problem is that the code do not
>>>> generate any figure.
>>>>
>>>> This is the code:
>>>>
>>>> #+TITLE:Test
>>>> #+AUTHOR: Your Name
>>>> #+EMAIL: mailto:your-email@server.com
>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports
>>>> both :tangle yes
>>>>
>>>> * Example of Org-Babel for R Literate Programming
>>>> ** R text output
>>>> A simple summary.
>>>> #+begin_src R
>>>>   x <- rnorm(10)
>>>>   summary(x)
>>>> #+end_src
>>>>
>>>> ** R graphics output
>>>> Note we use the object =x= generated in previous code block, thanks to
>>>> the header option =:session *R*=.  The output graphics file is
>>>> =a.png=.
>>>>
>>>> #+begin_src R  :file a.png
>>>>   y <- rnorm(10)
>>>>   plot(x, y)
>>>> #+end_src
>>>>
>>>> Same plot with larger dimension:
>>>>
>>>> #+begin_src R  :file b.png :width 800 :height 800
>>>>   plot(x, y)
>>>> #+end_src
>>>>
>>>>
>>>> Where do I wrong?
>>>>
>>>> Best
>>>> Riccardo
>>>> Hi, I&#39;m trying to generate some figure with R, into an org
>>>> session. Firstly I use the code in the org site. The problem is
>>>> that the code do not generate any figure. This is the code:
>>>> #+TITLE:Test
>>>> #+AUTHOR: Your Name
>>>> #+EMAIL: mailto:mailto:your-email@server.com
>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes
>>>>
>>>> * Example of Org-Babel for R Literate Programming
>>>> ** R text output
>>>> A simple summary.
>>>> #+begin_src R
>>>>   x <- rnorm(10)
>>>>   summary(x)
>>>> #+end_src
>>>>
>>>> ** R graphics output
>>>> Note we use the object =x= generated in previous code block, thanks to
>>>> the header option =:session *R*=.  The output graphics file is
>>>> =a.png=.
>>>>
>>>> #+begin_src R  :file a.png
>>>>   y <- rnorm(10)
>>>>   plot(x, y)
>>>> #+end_src
>>>>
>>>> Same plot with larger dimension:
>>>>
>>>> #+begin_src R  :file b.png :width 800 :height 800
>>>>   plot(x, y)
>>>> #+end_src
>>>> Where do I wrong?BestRiccardo
>>>
>>> <span class="HOEnZb">--
>>> Thomas S. Dye
>>> http://www.tsdye.com
>>> </span>

-- 
Thomas S. Dye
http://www.tsdye.com