I'm working on the next iteration of coxme. (Rather slowly during the summer). This is the most subtle code I've done in S, both mathematically and technically, and seems a perfect vehicle for the "literate programming" paradym of Knuth. The Sweave project is pointed at S output however, not source code. I would appreciate any pointers to an noweb type client that was R-aware. Other suggestions are welcome as well. At the end of the day I'd like to have a good user guide, technical reference, and solid enough code documentation that others can begin to participate as well. (Retirement in 10 years -- I don't expect to maintain this forever!) Terry Therneau therneau.terry at mayo.edu
Hi Terry,
You can do this with Sweave (and something smart like emacs with ESS
installed as your editor), but you have to work at it a little. The key
is the fact that a couple of releases ago they added options for
"keep.source" and "expand". For example, you do the
following:
First, describe the various steps in the algorithm. (Unless you are
defining functions to use later, you probably do not want to evaluate
these.)
<<extractParameters,eval=FALSE>># code here to get the parameters
@
<<selectTrainingSet,eval=FALSE>># code here to split data into
training and test sets
@
<<trainModel,eval=FALSE>># code here to fit a model to training data
@
<<testModel,eval=FALSE>># code here to see how well the model works
@
Then you can put the pieces together, doing something like
<<runSplits,keep.source=TRUE,expand=FALSE>>for (i in
1:numberOfSplits) {
<<extractParameters>>
<<selectTrainingSet>>
<<trainModel>>
<<testModel>>
}
@
The "expand=FALSE" makes sure that the final report does not re-expand
the lines of code in the displayed output, which allows you to focus on
the structure of the algorithm.
There are still two weaknesses compared to Knuth's original idea:
[1] You cannot describe the overall algorithm first but wait until later
to define the pieces. (Actually, I could be wrong about this; it just
occurred to me that you might be able to manage this with yet another
clever use of "eval=FALSE", but I haven't tried that.)
[2] The names that you assign to the code chunks do not appear in the
report automatically, so you have to write text in front of them to make
them show up. Without these, the references in the final piece do not
necessarily make sense to the reader trying to follow the action.
Best,
Kevin
Terry Therneau wrote:> I'm working on the next iteration of coxme. (Rather slowly during the
summer).
>
> This is the most subtle code I've done in S, both mathematically and
> technically, and seems a perfect vehicle for the "literate
programming" paradym
> of Knuth. The Sweave project is pointed at S output however, not source
code.
> I would appreciate any pointers to an noweb type client that was R-aware.
>
> Other suggestions are welcome as well. At the end of the day I'd
like to have
> a good user guide, technical reference, and solid enough code documentation
that
> others can begin to participate as well. (Retirement in 10 years -- I
don't
> expect to maintain this forever!)
>
> Terry Therneau
> therneau.terry at mayo.edu
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
G'day Terry, On Tue, 5 Aug 2008 09:38:23 -0500 (CDT) Terry Therneau <therneau at mayo.edu> wrote:> I'm working on the next iteration of coxme. (Rather slowly during > the summer). > This is the most subtle code I've done in S, both mathematically > and technically, and seems a perfect vehicle for the "literate > programming" paradym of Knuth. The Sweave project is pointed at S > output however, not source code. I would appreciate any pointers to > an noweb type client that was R-aware.I would suggest you look at relax: http://www.wiwi.uni-bielefeld.de/~wolf/software/relax/relax.html Cheers, Berwin =========================== Full address ============================Berwin A Turlach Tel.: +65 6515 4416 (secr) Dept of Statistics and Applied Probability +65 6515 6650 (self) Faculty of Science FAX : +65 6872 3919 National University of Singapore 6 Science Drive 2, Blk S16, Level 7 e-mail: statba at nus.edu.sg Singapore 117546 http://www.stat.nus.edu.sg/~statba
>>>>> On Tue, 5 Aug 2008 09:38:23 -0500 (CDT), >>>>> Terry Therneau (TT) wrote:> I'm working on the next iteration of coxme. (Rather slowly during > the summer). This is the most subtle code I've done in S, both > mathematically and technically, and seems a perfect vehicle for > the "literate programming" paradym of Knuth. The Sweave project > is pointed at S output however, not source code. I would > appreciate any pointers to an noweb type client that was > R-aware. > Other suggestions are welcome as well. At the end of the day > I'd like to have a good user guide, technical reference, and solid > enough code documentation that others can begin to participate as > well. (Retirement in 10 years -- I don't expect to maintain this > forever!) Why not use the original noweb in the first place? You can even maintain Sweave files with it, the Sweave latex syntax was written for exactly that purpose ... ESS supported noweb before Sweave existed. In fact the emacs noweb mode was the main reason I chose that syntax for Sweave, and the latex syntax was added lateron because some people write whole packages using noweb and would have had a syntax conflict in their vignettes. Best, Fritz
"ESS supported noweb before Sweave existed." That is the bit I didn't know. What I was rather looking for was a noweb mode that knows about S formatting, and here it was available all along. I've used a version of ESS for a loooong time - probably should re-read the documentation one of these days to catch up on all the new features! "and the latex syntax was added lateron because some people write whole packages using noweb and would have had a syntax conflict in their vignettes" I'm not quite sure what this means. Thanks much, Terry Therneau