From mboxrd@z Thu Jan 1 00:00:00 1970 From: cberry@tajo.ucsd.edu Subject: Re: Converting Org to Sweave (*.Rnw) Date: Tue, 17 Jul 2012 09:05:14 -0700 Message-ID: <87wr22v0ed.fsf@tajo.ucsd.edu> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from eggs.gnu.org ([208.118.235.92]:47180) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1SrAHJ-0001N5-Ur for emacs-orgmode@gnu.org; Tue, 17 Jul 2012 12:05:43 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1SrAHD-0007Oc-O9 for emacs-orgmode@gnu.org; Tue, 17 Jul 2012 12:05:37 -0400 Received: from plane.gmane.org ([80.91.229.3]:40621) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1SrAHD-0007Nm-E1 for emacs-orgmode@gnu.org; Tue, 17 Jul 2012 12:05:31 -0400 Received: from list by plane.gmane.org with local (Exim 4.69) (envelope-from ) id 1SrAHA-0002Yp-8s for emacs-orgmode@gnu.org; Tue, 17 Jul 2012 18:05:28 +0200 Received: from tajo.ucsd.edu ([137.110.122.165]) by main.gmane.org with esmtp (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Tue, 17 Jul 2012 18:05:28 +0200 Received: from cberry by tajo.ucsd.edu with local (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Tue, 17 Jul 2012 18:05:28 +0200 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 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 > > > -- 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