* export from R to tables, possible correction to ob-doc-R.org
@ 2014-01-14 2:09 regcl
2014-01-14 2:27 ` Thomas S. Dye
2014-01-14 2:29 ` John Hendy
0 siblings, 2 replies; 3+ messages in thread
From: regcl @ 2014-01-14 2:09 UTC (permalink / raw)
To: emacs-orgmode
I was looking for an example of the export of R data frames into
tables in html, and the example in ...
http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.org
... did not work for me. I am running ...
GNU Emacs 24.3.1 (x86_64-pc-linux-gnu, GTK+ Version 3.8.4) of 2013-09-26 on trouble, modified by Debian
Org-mode version 8.2.5c (release_8.2.5c @ /home/regcl/.emacs.d/lisp/org-mode/lisp/)
Here is the problematic code ...
### START SNIP ###### START SNIP ###### START SNIP ###
: #+BEGIN_SRC R :results output org
: library(ascii)
: a <- runif(100)
: c <- "Quantiles of 100 random numbers"
: b <- ascii(quantile(a),header=T,include.colnames=T,caption=c)
: print(b,type="org")
: rm(a,b,c)
: #+END_SRC
:
: #+RESULTS:
: #+BEGIN_ORG
: #+CAPTION: Quantiles of 100 random numbers
: | 0% | 25% | 50% | 75% | 100% |
: |------+------+------+------+------|
: | 0.03 | 0.28 | 0.52 | 0.74 | 1.00 |
: #+END_ORG
The output exported to HTML can be quite nice.
#+RESULTS:
#+BEGIN_ORG
#+CAPTION: Quantiles of 100 random numbers
| 0% | 25% | 50% | 75% | 100% |
|------+------+------+------+------|
| 0.03 | 0.28 | 0.52 | 0.74 | 1.00 |
#+END_ORG
### END SNIP ###### END SNIP ###### END SNIP ###
... As you can see, this code is statically "rigged" to export in such
a way that it looks like it is working with R. When I try to make the
code live by removing the markup as shown below ...
#+BEGIN_SRC R :results output org
library(ascii)
a <- runif(100)
c <- "Quantiles of 100 random numbers"
b <- ascii(quantile(a),header=T,include.colnames=T,caption=c)
print(b,type="org")
rm(a,b,c)
#+END_SRC
The html produced by ...
C-c C-e h h
... contains the fontified source code, but no table.
... C-c C-c on the code block produces these results ...
#+RESULTS:
#+BEGIN_SRC org
,#+CAPTION: Quantiles of 100 random numbers
| 0% | 25% | 50% | 75% | 100% |
|------+------+------+------+------|
| 0.02 | 0.30 | 0.49 | 0.70 | 0.99 |
#+END_SRC
By trial and error, I discovered that if I change the header arguments
as shown below ...
#+BEGIN_SRC R :results output raw :exports results
library(ascii)
a <- runif(100)
c <- "Quantiles of 100 random numbers"
b <- ascii(quantile(a),header=T,include.colnames=T,caption=c)
print(b,type="org")
rm(a,b,c)
#+END_SRC
... this produces a table in HTML that matches the table produced by
the static code.
... C-c C-c on this code block produces these results ...
#+RESULTS:
#+CAPTION: Quantiles of 100 random numbers
| 0% | 25% | 50% | 75% | 100% |
|------+------+------+------+------|
| 0.03 | 0.25 | 0.57 | 0.79 | 0.99 |
Can someone tell me if this is how it is supposed to work?
If so, how do I go about submiting a patch to ...
http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.org
Thanks,
regcl
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: export from R to tables, possible correction to ob-doc-R.org
2014-01-14 2:09 export from R to tables, possible correction to ob-doc-R.org regcl
@ 2014-01-14 2:27 ` Thomas S. Dye
2014-01-14 2:29 ` John Hendy
1 sibling, 0 replies; 3+ messages in thread
From: Thomas S. Dye @ 2014-01-14 2:27 UTC (permalink / raw)
To: regcl; +Cc: emacs-orgmode
Aloha regcl,
regcl <regcl@channing.harvard.edu> writes:
> Can someone tell me if this is how it is supposed to work?
Yes, this is how it should work.
> If so, how do I go about submiting a patch to ...
>
> http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.org
You should be able to edit the document directly. See
http://orgmode.org/worg/worg-git.html#contribute-to-worg for the full
instructions.
Thanks for catching this.
All the best,
Tom
--
Thomas S. Dye
http://www.tsdye.com
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: export from R to tables, possible correction to ob-doc-R.org
2014-01-14 2:09 export from R to tables, possible correction to ob-doc-R.org regcl
2014-01-14 2:27 ` Thomas S. Dye
@ 2014-01-14 2:29 ` John Hendy
1 sibling, 0 replies; 3+ messages in thread
From: John Hendy @ 2014-01-14 2:29 UTC (permalink / raw)
To: regcl; +Cc: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 3804 bytes --]
On Mon, Jan 13, 2014 at 8:09 PM, regcl <regcl@channing.harvard.edu> wrote:
> I was looking for an example of the export of R data frames into
> tables in html, and the example in ...
>
> http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.org
>
> ... did not work for me. I am running ...
>
> GNU Emacs 24.3.1 (x86_64-pc-linux-gnu, GTK+ Version 3.8.4) of 2013-09-26
> on trouble, modified by Debian
>
> Org-mode version 8.2.5c (release_8.2.5c @
> /home/regcl/.emacs.d/lisp/org-mode/lisp/)
>
> Here is the problematic code ...
>
> ### START SNIP ###### START SNIP ###### START SNIP ###
>
> : #+BEGIN_SRC R :results output org
> : library(ascii)
> : a <- runif(100)
> : c <- "Quantiles of 100 random numbers"
> : b <- ascii(quantile(a),header=T,include.colnames=T,caption=c)
> : print(b,type="org")
> : rm(a,b,c)
> : #+END_SRC
> :
> : #+RESULTS:
> : #+BEGIN_ORG
> : #+CAPTION: Quantiles of 100 random numbers
> : | 0% | 25% | 50% | 75% | 100% |
> : |------+------+------+------+------|
> : | 0.03 | 0.28 | 0.52 | 0.74 | 1.00 |
> : #+END_ORG
>
> The output exported to HTML can be quite nice.
>
> #+RESULTS:
> #+BEGIN_ORG
> #+CAPTION: Quantiles of 100 random numbers
> | 0% | 25% | 50% | 75% | 100% |
> |------+------+------+------+------|
> | 0.03 | 0.28 | 0.52 | 0.74 | 1.00 |
> #+END_ORG
>
> ### END SNIP ###### END SNIP ###### END SNIP ###
>
> ... As you can see, this code is statically "rigged" to export in such
> a way that it looks like it is working with R. When I try to make the
> code live by removing the markup as shown below ...
>
> #+BEGIN_SRC R :results output org
> library(ascii)
> a <- runif(100)
> c <- "Quantiles of 100 random numbers"
> b <- ascii(quantile(a),header=T,include.colnames=T,caption=c)
> print(b,type="org")
> rm(a,b,c)
> #+END_SRC
>
> The html produced by ...
>
> C-c C-e h h
>
> ... contains the fontified source code, but no table.
>
> ... C-c C-c on the code block produces these results ...
>
> #+RESULTS:
> #+BEGIN_SRC org
> ,#+CAPTION: Quantiles of 100 random numbers
> | 0% | 25% | 50% | 75% | 100% |
> |------+------+------+------+------|
> | 0.02 | 0.30 | 0.49 | 0.70 | 0.99 |
> #+END_SRC
>
> By trial and error, I discovered that if I change the header arguments
> as shown below ...
>
> #+BEGIN_SRC R :results output raw :exports results
> library(ascii)
> a <- runif(100)
> c <- "Quantiles of 100 random numbers"
> b <- ascii(quantile(a),header=T,include.colnames=T,caption=c)
> print(b,type="org")
> rm(a,b,c)
> #+END_SRC
>
> ... this produces a table in HTML that matches the table produced by
> the static code.
>
> ... C-c C-c on this code block produces these results ...
>
> #+RESULTS:
> #+CAPTION: Quantiles of 100 random numbers
> | 0% | 25% | 50% | 75% | 100% |
> |------+------+------+------+------|
> | 0.03 | 0.25 | 0.57 | 0.79 | 0.99 |
>
> Can someone tell me if this is how it is supposed to work?
>
Yup. I think you stumbled on a "bug" (though probably just more of an
oversight). I looked around a bit for the default babel header arguments
and think this looks accurate:
-
http://orgmode.org/manual/System_002dwide-header-arguments.html#System_002dwide-header-arguments
This, with nothing set for `:exports something`, the default is `:exports
code`.
What you did instead is correct -- you want to export results. I get the
same behavior: code only with no value set, results with `:exports results`
added. To "patch," that page, you would follow the procedure for
contributing to Worg:
- http://orgmode.org/worg/worg-git.html
You submit a key to Bastien, clone Worg, edit the file, and push your
changes.
Best regards,
John
>
> If so, how do I go about submiting a patch to ...
>
> http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.org
>
> Thanks,
> regcl
>
>
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2014-01-14 2:09 export from R to tables, possible correction to ob-doc-R.org regcl
2014-01-14 2:27 ` Thomas S. Dye
2014-01-14 2:29 ` John Hendy
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