Re: [Rd] Sweave/ESS-like tools for HTML

From: Duncan Temple Lang <>
Date: Wed, 17 Oct 2007 08:59:13 +1300

Hash: SHA1

Hi Doug.

  This is probably more than you want - either to know or to use for your specific task, but I'll throw it out there for general information.

 I write documents using XML, specifically an extended version of Docbook with elements for describing R concepts (e.g. code, plot, output, function name, argument, ...). Then, I use XSL to transform this to either HTML, FO and on to PDF, or to LaTeX (via db2latex). As for processing the R code and inserting the output into the resulting view/document, I use the Sxslt package from within R which allows me to combine XSL rules with those that also call R functions. I author the documents using the nxml mode in emacs and have some basic "gestures" for sending code from the document to R.

Deb Nolan and I use this for creating dynamic and interactive documents which can be transformed to HTML with embedded controls for the reader to control the R computations interactively.

Rather than thinking of the document as being one whose primary purpose is to be displayed to readers, the approach allows us to put arbitrary things into the document as part of our work but render only the bits we want for a particular audience, e.g. mix code, pedagogical material, R documentation, data, code from other languages.

The XML/Docbook-XSL-R approach is very general and flexible with possibly "too" many degrees of freedom. If the document is destined only for HTML, then writing in HTML directly may be best. The generality is useful when there are multiple targets and one wants to extract information programmatically, e.g. extract subsets of the code within the document such as that in section 2, or only Matlab code.

I will be packaging up all the material we have on this soon, so if anyone wants a copy, let me know.


Douglas Bates wrote:
> My university provides me with a powerful course management system for
> the courses that I teach. Among other things I can create a wiki for
> the course, which is very convenient for cross-linking different bits
> of the course.
> Naturally I use R extensively in my teaching and I want to incorporate
> R code, output and graphics in such a wiki. If I were producing LaTeX
> sources instead of HTML sources I create .Rnw files for Sweave and I
> would edit them using ESS in emacs.
> What options do I have for producing HTML with embedded R content and
> what is a good, preferably emacs-based, way of editing the source
> code?
> One basic problem is trying to present mathematical expressions in HTML (see
> but, aside from that, there are
> questions of presenting input R expressions and the corresponding
> output and of incorporating graphics files produced by R. I could try
> to use latex2html or texi2html but the output from latex2html at least
> would be quite inconvenient to use because it generates so many linked
> files. Once they are uploaded it would be horrible trying to get all
> the links straightened out.
> In a sense there are already tools for this type of output from .Rd
> files. Would it be best to use those tools or to use texinfo tools or
> ...?
> ______________________________________________
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