From mboxrd@z Thu Jan 1 00:00:00 1970 From: Julian Gehring Subject: Re: Converting Org to Sweave (*.Rnw) Date: Tue, 17 Jul 2012 19:23:15 +0200 Message-ID: <50059F83.6050707@gmail.com> References: <87wr22v0ed.fsf@tajo.ucsd.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([208.118.235.92]:38991) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1SrBUi-0001I4-Qo for emacs-orgmode@gnu.org; Tue, 17 Jul 2012 13:23:34 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1SrBUh-0004nG-3h for emacs-orgmode@gnu.org; Tue, 17 Jul 2012 13:23:32 -0400 Received: from plane.gmane.org ([80.91.229.3]:60378) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1SrBUg-0004nA-P3 for emacs-orgmode@gnu.org; Tue, 17 Jul 2012 13:23:31 -0400 Received: from list by plane.gmane.org with local (Exim 4.69) (envelope-from ) id 1SrBUf-00040d-Jc for emacs-orgmode@gnu.org; Tue, 17 Jul 2012 19:23:29 +0200 Received: from embln.embl.de ([194.94.44.220]) by main.gmane.org with esmtp (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Tue, 17 Jul 2012 19:23:29 +0200 Received: from julian.gehring by embln.embl.de with local (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Tue, 17 Jul 2012 19:23:29 +0200 In-Reply-To: <87wr22v0ed.fsf@tajo.ucsd.edu> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: emacs-orgmode@gnu.org 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 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 > > <>= > 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 >> >> >> >