
216 R Programming for Bioinformatics
compendium is essentially a collection of code, data and text that can be used
to recreate a specific analysis in complete detail. One implementation of a
compendium is as an R package, where there are structured ways to include
code, data and a literate document, such as an Sweave document.
The vignette function has a print method that will open the PDF version
of a vignette for reading. It also has an edit method that will extract the code
chunks from the vignette and open them in an editor, thereby facilitating cut
and paste operations.
In the tools package, there is a function pkgVignettes, which can be used
to ...