Re: Re: problem with babel and R

From: David Hajage <dhajage@gmail.com>
To: Eric Schulte <schulte.eric@gmail.com>
Cc: emacs-orgmode@gnu.org
Subject: Re: Re: problem with babel and R
Date: Wed, 18 Aug 2010 08:53:33 +0200	[thread overview]
Message-ID: <AANLkTikvYvBDhtjonK_4GRPhLxYWRd6vZe9hQA6eYT7h@mail.gmail.com> (raw)
In-Reply-To: <1668ca$1pq4c@mail.curie.net>

[-- Attachment #1.1: Type: text/plain, Size: 12095 bytes --]

OK, I understand that using ":results org", the results is not altered,
there is no post processing. But I don't want a post processing, I would
like a way to tell babel where is the begining *and the end* of the output
produces by a particular R source block. I think an "#+end_results: foo" at
the end of the output could do the job. Then, the option "replace" could
work in all situation, even if a blank line is inserted somewhere in the org
output. No?
David

On Tue, Aug 17, 2010 at 17:15, Eric Schulte <schulte.eric@gmail.com> wrote:

> Hi David,
>
> David Hajage <dhajage@gmail.com> writes:
>
> > Thank you very much for your answer.
> >
>
> My pleasure
>
> >
> > But when I run the following code directly into R, no extra lines is
> >added
> > by the ascii function:
> >> library(ascii)
> > Le chargement a nécessité le package : proto
> >> options(asciiType = "org")
> >> ascii(head(esoph)) # no extra line
> > |   | 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      |
> >
>
> ah, my fault, this isn't an ascii issue.
>
> >
> > In fact, the solution was to run 'library(ascii)' in another source
> block.
> > When I run only this:
> >
>
> Thanks for pointing this out, I see what's happening now.
>
> The :results output header argument (see [1] for information on header
> arguments) informs Org-mode to collect all of the output of the source
> code block.  This means that when library(ascii) is run, an empty line
> is collected and appended to the output.  Removing the "output" header
> argument should fix this issue.
>
> My I ask why you are using the ascii package for simple table output?
> It seems to me that this would be much simpler using the pure Org-mode
> solution I suggested in my previous email.
>
> >
> > #+begin_src R :session *R* :results output org replace
> >   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 |
> >
> > Everything is then OK.
> > I have no idea why "library(ascii)..." generates an extra empty line in
> the
> > results.
> >
> > If I understand, the results is all the text directly under "#+results:",
> > until the first empty line. But what happens if the result contains empty
> > lines? Here an example with ascii and Hmisc package:
> >
>
> This is not quite right, see [2] for a discussion of results handling.
> The "org" option to results is a special case in which no
> post-processing of the results takes place, and the raw output is
> inserted into the org-mode buffer.
>
> Under normal usage w/o this header argument, results are either tabular
> or are textual.  If tabular a single table can easily be recognized and
> handled, if textual they are normally enclosed in a block (example,
> html, latex, etc...), the block then allows for empty lines while still
> making it clear where the results end.
>

>
> >
> >> library(ascii)
> >> library(Hmisc)
> >> ascii(describe(esoph[, 1:3]))
> > #+CAPTION: esoph[, 1:3]
> > - 3 Variable
> > - 88 Observations
> >
> > *agegp*
> > | n  | missing | unique |
> > | 88 | 0       | 6      |
> >
> > |           | 25-34 | 35-44 | 45-54 | 55-64 | 65-74 | 75+ |
> > | Frequency | 15    | 15    | 16    | 16    | 15    | 11  |
> > | %         | 17    | 17    | 18    | 18    | 17    | 12  |
> >
> > *alcgp*
> > | n  | missing | unique |
> > | 88 | 0       | 4      |
> >
> >  0-39g/day (23, 26%), 40-79 (23, 26%), 80-119 (21, 24%), 120+ (21, 24%)
> >
> > *tobgp*
> > | n  | missing | unique |
> > | 88 | 0       | 4      |
> >
> >  0-9g/day (24, 27%), 10-19 (24, 27%), 20-29 (20, 23%), 30+ (20, 23%)
> >
> > As you can see, describe() generate a description of my data, and ascii
> > generate org-mode markup as result. The result contains empty rows. Since
> > there is no special characters indicating the end of the results in
> babel,
> > replace option will not work in this case. Is there any workaround?
> >
>
> When using ":results org" there is no workaround, as the explicit
> purpose of this setting is for your results to be inserted directly into
> the Org-mode buffer w/o any interpretation or alteration.
>

>
> In general I would recommend keeping a 1-to-1 mapping between code
> blocks and result items, which should resolve this issue.
>
> >
> > Of course, ascii is not usefull in this case, but it can coerce into
> > org-mode markup many other R objects (see my previous example and
> > http://orgmode.org/worg/org-contrib/babel/examples/ascii.php)
> >
>
> I see, that answers my question from above. Thanks
>
> Hope this helps -- Eric
>
> >
> > David
> >
> >
> > On Tue, Aug 17, 2010 at 15:57, Eric Schulte <schulte.eric@gmail.com>
> wrote:
> >
> >> 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
> >> >>
> >> > _______________________________________________
> >> > 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
> >>
>
> Footnotes:
> [1]  http://orgmode.org/manual/Header-arguments.html#Header-arguments
>
> [2]
> http://orgmode.org/manual/Results-of-evaluation.html#Results-of-evaluation
>
>
> L'intégrité de ce message n'étant pas assurée sur Internet, l'Institut
> Curie ne peut être tenu responsable de son contenu.
> Si vous n'êtes pas destinataire de ce message confidentiel, merci de le
> détruire et d'avertir immédiatement l'expéditeur.
> Afin de contribuer au respect de l'environnement, merci de n'imprimer ce
> mail qu'en cas de nécessité.
>

[-- Attachment #1.2: Type: text/html, Size: 16111 bytes --]

[-- Attachment #2: Type: text/plain, Size: 201 bytes --]

_______________________________________________
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