[Rd] Sweave driver extension

From: Terry Therneau <therneau_at_mayo.edu>
Date: Tue, 24 Jan 2012 13:50:15 -0600


Almost all of the coxme package and an increasing amount of the survival package are now written in noweb, i.e., .Rnw files. It would be nice to process these using the Sweave function + a special driver, which I can do using a modified version of Sweave. The primary change is to allow the following type of construction

<<coxme>>
coxme <- function(formula, data, subset, blah blah ){

<<coxme-check-arguments>>
<<coxme-build>>
<<coxme-compute>>
<<coxme-finish>>

}
@

where the parts referred to come later, and will themselves be made up of other parts. Since the point of this file is to document source code, the order in which chunks are defined is driven by "create a textbook" thoughts and won't match the final code order for R. The standard noweb driver only allows one level of recursion, and no references to things defined further down in the file.

  The primary change to the function simply breaks the main loop into two parts: first read through the all the lines and create a list of code chunks (some with names), then go through the list of chunks and call driver routines. There are a couple of other minor details, e.g. a precheck for infinite recursions, but no change to what is passed to the driver routines, nor to anything but the Sweave function itself.

Primary question: who on the core team should I be holding this conversation with?
Secondary: Testing level? I have a few vignettes but not many.

    I'll need a "noweb" package anyway to contain the drivers -- should we just duplicate the modified Sweave under another name?

    Call the package "noweb", "Rnoweb", ...?

And before someone asks: Roxygen is a completely different animal and doesn't address what I need. I have latex equations just above the code that impliments them, an annotated graph of the call tree next to the section parsing a formula, etc. This is stuff that doesn't fit in comment lines. The text/code ratio is >1. On the other hand I've thought very little about integration of manual pages and description files with the code, issues which Roxygen addresses.

Terry Therneau



R-devel_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Tue 24 Jan 2012 - 19:55:57 GMT

This quarter's messages: by month, or sorted: [ by date ] [ by thread ] [ by subject ] [ by author ]

All messages

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Wed 25 Jan 2012 - 04:50:11 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.

list of date sections of archive