Re: [O] export from R to tables, possible correction to ob-doc-R.org

[John Hendy]

On Mon, Jan 13, 2014 at 8:09 PM, regcl <address@hidden> 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