[R] setMethod confusion -best reference for S4 programming

[Berton Gunter]

You might also wish to read the relevant chapter of V&R's S PROGRAMMING.

-- 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 
> Stephen Henderson
> Sent: Wednesday, March 15, 2006 4:28 AM
> To: r-help at stat.math.ethz.ch
> Cc: Henrik Bengtsson; Martin Maechler
> Subject: Re: [R] setMethod confusion -best reference for S4 
> programming
> 
> Thanks I think you have both answered my question (reckon Ill go S3 on
> that). As an adjunct to this do you know what might be the best
> reference to the S4 methods current implementation.
> 
> I have ordered the Chambers book "Programming with Data", and I have a
> short tutorial-- "S4 Classes in 15 pages, more or less".
> 
> Have I missed any other useful resources?
> 
> Stephen Henderson
> Wolfson Inst. for Biomedical Research
> Cruciform Bldg., Gower Street
> University College London
> United Kingdom, WC1E 6BT
> +44 (0)207 679 6827
> 
> 
> -----Original Message-----
> From: henrik.bengtsson at gmail.com 
> [mailto:henrik.bengtsson at gmail.com] On
> Behalf Of Henrik Bengtsson
> Sent: 15 March 2006 10:59
> To: Martin Maechler
> Cc: Stephen Henderson; r-help at stat.math.ethz.ch
> Subject: Re: [R] setMethod confusion
> 
> On 3/15/06, Martin Maechler <maechler at stat.math.ethz.ch> wrote:
> > >>>>> "Stephen" == Stephen Henderson <s.henderson at ucl.ac.uk>
> > >>>>>     on Tue, 14 Mar 2006 16:32:56 -0000 writes:
> >
> >     Stephen> Hello I've checked through previous postings but
> >     Stephen> don't see a fully equivalent problem-just a few
> >     Stephen> hints.  I have been trying to set a new method for
> >     Stephen> the existing function "table" or
> >     Stephen> "as.data.frame.table" for my class "tfSites".
> >     Stephen> Taking out all the useful code and just returning
> >     Stephen> the input class I get the error
> >
> >     >> setMethod("table", "tfSites", function(.Object) .Object)
> >
> >     Stephen> Error in conformMethod(signature, mnames, fnames,
> >     Stephen> f) : In method for function "table": formal
> >     Stephen> arguments omitted in the method definition cannot
> >     Stephen> be in the signature (exclude = "tfSites")
> >
> >
> >     >> setMethod("as.data.frame.table", "tfSites",
> >     >> function(.Object) .Object )
> >
> >     Stephen> Error in conformMethod(signature, mnames, fnames,
> >     Stephen> f) : In method for function "as.data.frame.table":
> >     Stephen> formal arguments omitted in the method definition
> >     Stephen> cannot be in the signature (x = "tfSites")
> >
> >     Stephen> What does this mean? Is there something peculiar
> >     Stephen> about the table function? Is it because it takes
> >     Stephen> arguments beginning table(..., etc)
> >
> > Yes.  Since table's  argument list starts with "..."
> > you cannot directly write S4 methods for it.
> 
> Although not fully tested, but a workaround could be to i) define an
> S4 method tableS4(), then ii) rename table() to table.default() and
> iii) make table() an S3 generic function, and finally iv) define
> table.tfSites() to call tableS4(). Would this work?  If so, step
> (ii)-(iv) can be done in one step using the R.oo package. Example:
> 
> library(R.oo)
> setClass("fSites", representation(x="numeric", y="numeric"))
> setGeneric("tableS4", function(.Object, ...) 
> standardGeneric("tableS4"))
> setMethod("tableS4", "fSites", function(.Object) .Object)
> setMethodS3("table", "fSites", function(.Object, ...) tableS4(.Object,
> ...))
> 
> Test;
> > x <- new("fSites")
> > table(x)
> An object of class "fSites"
> Slot "x":
> numeric(0)
> 
> Slot "y":
> numeric(0)
> 
> > X <- rpois(20, 1)
> > table(X)
> X
>  0  1  2  3
> 10  7  2  1
> 
> But, what's wrong with S3 in the first place? ;)
> 
> /Henrik
> 
> 
> 
> 
> > One could consider changing table's argument list to become
> >   (x, ..., exclude = c(NA, NaN), dnn = list.names(...), 
> deparse.level
> = 1)
> > but that's not entirely trivial to do back compatibly, since
> > table() produces *named* dimnames from its arguments in "..."
> > and we'd want to make sure that this continues to work as now
> > even when the first argument is formally named 'x'.  E.g.,
> >
> >  > X <- rpois(20, 1)
> >  > table(X)
> >  X
> >   0  1  2  3
> >   7 10  2  1
> >  >
> >
> > should continue to contain "X" as  names(dimnames(.)).
> >
> > Of course this has now become a topic for R-devel rather
> > than R-help.
> >
> > Martin Maechler,
> > ETH Zurich
> >
> > ______________________________________________
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> >
> 
> 
> --
> Henrik Bengtsson
> Mobile: +46 708 909208 (+1h UTC)
> 
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