Re: Re: problem with babel and R

From: "Eric Schulte" <schulte.eric@gmail.com>
To: David Hajage <dhajage@gmail.com>
Cc: emacs-orgmode@gnu.org
Subject: Re: Re: problem with babel and R
Date: Tue, 17 Aug 2010 07:57:05 -0600	[thread overview]
Message-ID: <87tymtnxzi.fsf@gmail.com> (raw)
In-Reply-To: <AANLkTimGG+0GycTXbZ3N93v1K2BD7Pwq-AofGMaQCiYb@mail.gmail.com> (David Hajage's message of "Tue, 17 Aug 2010 14:01:03 +0200")

Hi David,

It seems that the problem here is in the ascii package.  It is inserting
an empty line at the beginning of your table, so that the table is not
snugly sitting under the #+results foo tag, because of this the table
isn't seen as results and is not replaced -- if you delete that space
then re-run the code block you'll notice that the table is replaced.

Org-mode is very capable of inserting tabular data into Org-mode
documents without using the ascii package.  For example the following
would be a more idiomatic example of using Org-mode to create a table
from R code.

--8<---------------cut here---------------start------------->8---
#+begin_src R
  numbers <- matrix(c(51,43,22,92,28,21,68,22,9),ncol=3,byrow=TRUE)
  numbers
#+end_src

#+results:
| 51 | 43 | 22 |
| 92 | 28 | 21 |
| 68 | 22 |  9 |

#+begin_src R :colnames yes
  numbers <- matrix(c(51,43,22,92,28,21,68,22,9),ncol=3,byrow=TRUE)
  numbers
#+end_src

#+results:
| V1 | V2 | V3 |
|----+----+----|
| 51 | 43 | 22 |
| 92 | 28 | 21 |
| 68 | 22 |  9 |
--8<---------------cut here---------------end--------------->8---

or applied to your example, the following code block should generate the
desired results.

--8<---------------cut here---------------start------------->8---
#+srcname: foo
#+begin_src R :session *R*
  head(esoph)
#+end_src
--8<---------------cut here---------------end--------------->8---

One last small note: the "replace" argument to :results is normally the
default value, and doesn't need to be explicitly added (although I can
see why you would have added it in this case since it wasn't working as
expected).

Cheers -- Eric

David Hajage <dhajage@gmail.com> writes:

> I tried the code with the last development version of org-mode:
>
> #+srcname: foo
> #+begin_src R :session *R* :results output org replace
>   library(ascii)
>   options(asciiType = "org")
>   ascii(head(esoph))
> #+end_src
>
> #+results: foo
>
>  |   | agegp | alcgp     | tobgp    | ncases | ncontrols |
> |---+-------+-----------+----------+--------+-----------|
> | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00   | 40.00     |
> | 2 | 25-34 | 0-39g/day | 10-19    | 0.00   | 10.00     |
> | 3 | 25-34 | 0-39g/day | 20-29    | 0.00   | 6.00      |
> | 4 | 25-34 | 0-39g/day | 30+      | 0.00   | 5.00      |
> | 5 | 25-34 | 40-79     | 0-9g/day | 0.00   | 27.00     |
> | 6 | 25-34 | 40-79     | 10-19    | 0.00   | 7.00      |
>
>  |   | agegp | alcgp     | tobgp    | ncases | ncontrols |
> |---+-------+-----------+----------+--------+-----------|
> | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00   | 40.00     |
> | 2 | 25-34 | 0-39g/day | 10-19    | 0.00   | 10.00     |
> | 3 | 25-34 | 0-39g/day | 20-29    | 0.00   | 6.00      |
> | 4 | 25-34 | 0-39g/day | 30+      | 0.00   | 5.00      |
> | 5 | 25-34 | 40-79     | 0-9g/day | 0.00   | 27.00     |
> | 6 | 25-34 | 40-79     | 10-19    | 0.00   | 7.00      |
>
> There is no more ">", but an extra space.
> But, the replace option doesn't work: results are still appended. I am not
> an org-mode guru (far, far away), but I think this is because when output is
> org, there is no indication about the "end" of the results.
>
> David
>
>
> On Tue, Aug 17, 2010 at 10:17, David Hajage <dhajage@gmail.com> wrote:
>
>> Hello,
>>
>> I am trying to use babel with R. Here the code:
>>
>> #+srcname: foo
>> #+begin_src R :session *R* :results output org replace
>>   library(ascii)
>>   options(asciiType = "org")
>>   ascii(head(esoph))
>> #+end_src
>>
>> #+results: foo
>>
>> > |   | agegp | alcgp     | tobgp    | ncases | ncontrols |
>> |---+-------+-----------+----------+--------+-----------|
>> | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00   | 40.00     |
>> | 2 | 25-34 | 0-39g/day | 10-19    | 0.00   | 10.00     |
>> | 3 | 25-34 | 0-39g/day | 20-29    | 0.00   | 6.00      |
>> | 4 | 25-34 | 0-39g/day | 30+      | 0.00   | 5.00      |
>> | 5 | 25-34 | 40-79     | 0-9g/day | 0.00   | 27.00     |
>> | 6 | 25-34 | 40-79     | 10-19    | 0.00   | 7.00      |
>>
>> > |   | agegp | alcgp     | tobgp    | ncases | ncontrols |
>> |---+-------+-----------+----------+--------+-----------|
>> | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00   | 40.00     |
>> | 2 | 25-34 | 0-39g/day | 10-19    | 0.00   | 10.00     |
>> | 3 | 25-34 | 0-39g/day | 20-29    | 0.00   | 6.00      |
>> | 4 | 25-34 | 0-39g/day | 30+      | 0.00   | 5.00      |
>> | 5 | 25-34 | 40-79     | 0-9g/day | 0.00   | 27.00     |
>> | 6 | 25-34 | 40-79     | 10-19    | 0.00   | 7.00      |
>>
>> With org-mode 7.01g in emacs 23, there is two problems:
>>  - an extra ">" is added in the first line while output is "org"
>>  - when I run the code twice, the new results is appended, while I have the
>> option "replace".
>>
>> Is there any problem with my header?
>>
>> Thank you very much for your help.
>> David
>>
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