The highlight package is a simple solution for very nice syntax highlighted code boxes in latex documents. Requires switching the driver, which is best done from within R and requires creating a makefile though. Needs the “highlight” package installed. Here’s a simple makefile.
A wealth/mess of Sweave related packages on the CRAN taskview for Reproducible Research (now what other software platform has a the equivalent of a Reproducible Research task view?)
But why not really do things correctly? The knitr package is beautiful. Abstracts the concept beyond just latex integration. You can write in pure latex, (instead of noweb mix), in pure markdown, or pure html, embedding the R commands in comments. knitr can run the code in those comments to generate a file of the same format, but with the dynamic content embedded. Handles caching, syntax highlighting, and figures in a much more seamless manner. It can also use the package author’s formatRcode to tidy up your code before including it. You can convince R to use this for vignettes with a similar makefile.
[gist id=1470786]
The github markdown integration makes github look like a better and better candidate for a lab notebook. Wonder how it handles mathjax or citations?
Another nice find for bringing my older package documentation into roxygen form: Rd2roxygen.
More ambitious dynamic documentation
These improvements to Sweave are nice, though the dynamic document concept can certainly go much further. Dexy.it is an interesting multi-lingual version, but doesn’t seem to combine source and the documentation in the same file. Guess that can be kinda good, kinda bad. It seem to use a non-standard syntax, and while it’s python easy_install sounds fine, might still be a barrier to adoption among R users…
Meanwhile, some notes form a presentation I saw recently that have a much more ambitious view of what’s possible. Nov 22 (which I’ve recast into the language Tim Berners-Lee uses to describe linked-data on the web:
One star – sweave
two stars - XDynDocs multiple views (alternate analyses, full lab notebook)
three stars - rfirefox - interactive web view
star four - live data sources (self updating)
Some people involved: Deborah Nolan, Thomas Lee, Paul Baines, Wolfgang Polonik, Duncan Temple-Lang, Gabriel Becker.
some of my questions:
In the context of these tools, do we distinguish documenting code from publishing analyses?
Does this make remaining errors the more insidious?