knitr + cactus + TwitterBootstrap + Jquery

A few notes and tips from a week of preparing some course notes.

I switched from Sweave to knitr because all the cool kids are doing it. And its better. The caching has already saved me more time than I spent switching from Sweave to knitr, which wasn't much time at all. Win

At first I was building a PDF from .Rnw sources, but then thought maybe HTML would be a better delivery platform. No need to open a PDF reader. So I figured out the .Rhtml syntax and it was done. Win.

But how to do my equations? Mathjax. Problem solved. Almost pixel-perfect equations using LaTeX syntax. Users without Javascript get the LaTeX source so its not all lost on them. Win.

Making a simple HTML file is easy enough, but I want to make a few tutorial sessions, and some other info, so I want to use a template engine. My current fave is cactus.py - you design Django templates, then write your pages to fill in sections such as 'title' or 'content' in the template, then cactus.py will build the static pages. These can then be served by a simple web server or straight from the file system. Win.

So instead of a full HTML file, I just got knitr to process a Django template chunk. However, this didn't give me the CSS for the source code syntax highlighting because there's no HEAD section in the Html. Solved by copying the knitr CSS into a file and serving it up from my template. Works fine, and serving CSS from files rather than inline in HTML is a win because now the server or client can cache it. Win.

For style and structure, I just write my templates to use styles from the Twitter Bootstrap framework. Include the CSS and JS in your template base and you have good-looking responsive pages. Sure, they look like every other Twitter Bootstrap site, but the flexibility to style them is there too. Win.

Then I figured something real cool. The R syntax highlighting wraps all functions with a span of class "functioncall". One line of jQuery can turn all those spans into hyperlinks to information from my current favourite R documentation - the R Graphical Manual. Here's some code which might get mangled by Blogger's formatting and/or my inexperience trying to stick hypertext tags into a Blogger doc:

$("span.functioncall").replaceWith(function(){return '< a href="http://rgm2.lab.nig.ac.jp/RGM2/search.php?query='+$(this).text()+'" >'+$(this).text()+'< /a >'})

Now every function links to the search for that function name. It's probably hard to link directly to the help for that function exactly, since the system would have to know what package each function was in to get to exactly the right help on the RGM, but this is a big help. Win.

So that was my weekend. Also, Chelsea FC. Win.