From: Julian Gehring <julian.gehring@gmail.com>
To: emacs-orgmode@gnu.org
Subject: Re: Converting Org to Sweave (*.Rnw)
Date: Tue, 17 Jul 2012 19:23:15 +0200 [thread overview]
Message-ID: <50059F83.6050707@gmail.com> (raw)
In-Reply-To: <87wr22v0ed.fsf@tajo.ucsd.edu>
Hi Chuck,
thanks, what you describe seems to me like a already quite elaborated
solution. I would be very interested in your existing implementation
for this.
As you mentioned, there will probably have to be a trade-off between the
syntax/functionality of Org-mode/babel and Sweave. But already a
solution being able to handle to obvious cases of header argumnets would
be step forward in bringing Org-mode even closer to R Sweave.
Best
Julian
On 07/17/2012 06:05 PM, cberry@tajo.ucsd.edu wrote:
> 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
>>
>>
>>
>
next prev parent reply other threads:[~2012-07-17 17:23 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
2012-07-17 17:23 ` Julian Gehring [this message]
2012-07-18 3:19 ` cberry
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