[R] Too generic with S4 methods?

[Berton Gunter]

Yes, you're correct. From the Green book ("Programming with Data"):

(p.323) "Strictly speaking, the [specific] method supplied [for a generic]
must have the exact same formal argument list as the generic ... However, if
you do supply a function with different arguments, setMethod will construct
a valid method that calls the function you supplied, passing down all the
arguments of the generic."

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
 
"The business of the statistician is to catalyze the scientific learning
process."  - George E. P. Box
 
 

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Ross Boylan
> Sent: Thursday, June 02, 2005 2:44 PM
> To: r-help
> Subject: [R] Too generic with S4 methods?
> 
> I tried the following (relevant excerpt only)
> setMethod("likelihood",
>            signature(spec="Specification", covs="vector",
>                      states="vector"),
>           function(spec, covs, states) {
> ####
> setMethod("likelihood",
>            signature(model="Model", path="matrix"),
>            function(model, path) {
> 
> This fails with the message
> arguments in definition changed from (spec) to (object)
> Error in match.call(fun, fcall) : unused argument(s) (model ...)
> 
> I'll note in passing that it would be helpful to have a line 
> number for
> the error, and  that the error didn't mean much to me.
> 
> After study, my guess is that generics are not supposed to work this
> way.  All the definitions need to have the same named arguments
> (exceptions: some can be "missing", and ... is allowed).  So the error
> above is a complaint that my second signature uses different names (or
> is it different classes?).  And the "unused argument" is triggered by
> the fact that the original signature had 3 args named spec, covs, and
> states, and the new signature has none of them.  Is that about right?
> 
> It looks as if I might get away by not naming the arguments, so the
> first signature could be signature("Specification", "vector", 
> "vector")
> and the 2nd signature("Model", "matrix", "missing").
> 
> Among other problems, the lack of identifiers makes the 
> semantics of the
> signature obscure in this case.
> 
> Basically, would it be advisable to use different generic 
> names for the
> two functions listed above?
> -- 
> Ross Boylan                                      wk:  (415) 502-4031
> 530 Parnassus Avenue (Library) rm 115-4          ross at biostat.ucsf.edu
> Dept of Epidemiology and Biostatistics           fax: (415) 476-9856
> University of California, San Francisco
> San Francisco, CA 94143-0840                     hm:  (415) 550-1062
> 
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