Re: Org-mode and ESS

From: Austin Frank <austin.frank@gmail.com>
To: emacs-orgmode@gnu.org
Subject: Re: Org-mode and ESS
Date: Wed, 12 Nov 2008 14:42:24 -0500	[thread overview]
Message-ID: <m0d4h0loin.fsf@gmail.com> (raw)
In-Reply-To: 2c75873c0811111000m3c80e8e4rf08b742e80300cd0@mail.gmail.com

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On Tue, Nov 11 2008, Graham Smith wrote:

> Is any one using Org-mode with ESS.  ESS seems to need a file with a
> *.R name to work, but it would be really useful to use Org-mode
> features to keep notes of comments and code, before sending to R, and
> of course to copy results back into an Org-Mode file from R.
>
> As a search here and a google hasn't thrown up anything obvious, I
> assume not, but I thought I would ask.

In my local git repo of the org sources I have a pretty nice setup for
using R or S inside org-mode.  I liked the in-file native editing of
source code so much that I decided that I wanted to use org files as
source files with Sweave (instead of using .Rtex or .Rnw files).  My
goal was to export documents with embedded R code, rather than to use
org within the comments of R files.  I can certainly see a use for the
latter approach (which seems to be what you have in mind), as well.

There was recently a thread where someone created a preprocessing system
for specific types of blocks.  That would be another possible strategy
for evaluating blocks of R code before export.  Since that facility
didn't exist yet and there was already the extensible Sweave
pre-processor, I took the route of making Sweave org-aware.

Basically, in the workflow I've developed, I create a file with the
extension .Rorg, say homework_key.Rorg.  Within that file, I can embed
blocks of R code, and can refer to variables defined in the R code
contained in the document.

--8<---------------cut here---------------start------------->8---
#+BEGIN_R
a <- 3
a
#+END_R

* the value of a is \R{a}
* the value of a + 3 is \R{a + 3}  
--8<---------------cut here---------------end--------------->8---

Executing C-c ' inside the block takes you into a temporary buffer
that's in ESS mode, with full support for interactive evaluation.

When I'm ready to export, I run the R command

  Sweave("homework_key.Rorg", driver=RweaveOrgLatex, syntax=SweaveSyntaxOrg).

(I've defined those driver and syntax functions locally).  This creates
a new file, homework_key.org.  In the new file, the above text would be
translated into

--8<---------------cut here---------------start------------->8---
#+BEGIN_LATEX
\begin{Schunk}
\begin{Sinput}
> a <- 3
> a
\end{Sinput}
\begin{Soutput}
[1] 3
\end{Soutput}
\end{Schunk}
#+END_LATEX

* the value of a is 3
* the value of a + 3 is 6
--8<---------------cut here---------------end--------------->8---

The plain homework_key.org file could then be exported into \LaTeX.  It
even works with the new pdf export.

I haven't put the code anywhere public because there are several things
I still need to do:

- test graphic creation and export
- improve generation of latex headers
- automate processing from .Rorg to .tex (or .pdf) (currently at least 3
  steps, should be 1)
- come up with suggested keybindings for inserting the #+BEGIN/END_R
  blocks
- create a driver to generate HTML instead of \LaTeX

Still, it is in a works-for-me state at the moment, and I could send a
pull request to Carsten or could push it worg if folks were interested.

Let me know,
/au

-- 
Austin Frank
http://aufrank.net
GPG Public Key (D7398C2F): http://aufrank.net/personal.asc

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