From: cberry@tajo.ucsd.edu
To: emacs-orgmode@gnu.org
Subject: Re: Converting Org to Sweave (*.Rnw)
Date: Tue, 17 Jul 2012 09:05:14 -0700 [thread overview]
Message-ID: <87wr22v0ed.fsf@tajo.ucsd.edu> (raw)
In-Reply-To: ju3l8d$ta9$1@dough.gmane.org
Julian Gehring <julian.gehring@gmail.com> writes:
> Hi,
>
> is there a way to convert Org-mode files with R code blocks to the
> Sweave ('*.Rnw') [1] file format or has anyone planned to work on
> this?
First, there is this thread:
http://comments.gmane.org/gmane.emacs.orgmode/7931
and then there is this
http://yihui.name/knitr/demo/org/
====
But I wanted more, and I think the new exporter provides some awesome
possibilities, so...
I have put together a rudimentary exporter for Sweave and for brew style
chunks and hope to have several of the knitr chunk flavors supported
soon. I've not looked closely, but I think pander can be supported, too.
The basic idea is to use the new export engine. See
http://orgmode.org/worg/dev/org-export-reference.html
for background.
The e-latex, e-html, and other modes are used as parent backends and
e-latex-rnw, e-html-brew, etc are *derived* backends. It is pretty easy
to hitch a ride on the work done to make a parent backend and then add a
minimal definition of the chunk formatting.
The only tricky bit is getting Babel to help in the process, but not
interfere. I want Babel to porcess non-R src blocks and clean out R
#+RESULTS blocks, but not strip out the header args, as these may be
wanted (as you suggest below) to inform the chunk arguments. I've
managed this by advise'ing org-babel-exp-do-export to do special
handling of R src blocks.
I've not yet delved into translating the headers into code chunk
arguments. Some like 'width' seem pretty obvious. Others like the
:exports + :results translation may take some thought. And there are
some idioms in Sweave and kntir that have not corresponding idiom in org
(which is a strong motive for doing this work) like 'dev' in knitr as
well as ':cache yes' versus 'cache=T', which are false cognates, so to
speak
So far, what I've done is do add a header arg like this:
Here is an inline chunk: src_R{ rnorm(1) } which the brew export
renders as <%= rnorm(1) -%> (i.e. print the result, but do not place
a line break after the result), making a non-printing version of this
is done by using this src_R[ :ravel <% -%> ]{ rnorm(1) }, which
renders as <% rnorm(1) -%>.
or this
: #+name: aCachedChunk
: #+begin_src R :ravel cache=T
: x <- rnorm(1e7)
: #+end_src
which is rendered as
<<aCachedChunk, cache=T>>=
x <- rnorm(1e7)
@ %def
when using the Sweave style exporters.
However, Nicolas *just* added support for #+ATTR_SOMETHING, where
SOMETHING is a user defined key. And I incline to the view that using
something like
: #+attr_ravel: cache=T
: #+name: aCachedChunk
: #+begin_src R
: x <- rnorm(1e7)
: #+end_src
might be preferred.
Anyway, I'll try to get a version up where you can have a look at it
sometime today.
I am keen to collaborate on this.
Chuck
>
> Sweave is heavily used in the R community in terms of literate
> programming, and has a tight integration into current package building
> workflows. Essentially, the file format is a latex document, with
> designated code chunks.
>
> Since Org/Org-babel offers a very similar feature set, and already
> covers the export to latex, I was wondering whether anyone is working
> on some code that would rewrite the code block headers in the export?
> In the R community, I have seen a lot of interest in such an exporter,
> that would allow to write the documentation in Org itself and later
> export it to several backends, including Sweave to integrate it in the
> R package.
>
> If anyone has some comments regarding this or is interested in working
> on this, please let me know. My colleagues and I would be very
> interested in contributing in projects in this direction.
>
>
> Best
> Julian
>
>
> [1] http://en.wikipedia.org/wiki/Sweave
>
>
>
--
Charles C. Berry Dept of Family/Preventive Medicine
cberry at ucsd edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
next prev parent reply other threads:[~2012-07-17 16:05 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2012-07-17 12:19 Converting Org to Sweave (*.Rnw) Julian Gehring
2012-07-17 16:05 ` cberry [this message]
2012-07-17 17:23 ` Julian Gehring
2012-07-18 3:19 ` cberry
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