R devel - Feb 2006 - S4 classes and methods with optional arguments

Hi,

i have used S4 classes to implement a unified access to random number generators
(package rstream on CRAN).

I have used a construct to allow optional arguments:

if(!isGeneric("rstream.sample"))
        setGeneric("rstream.sample", function(stream,...)
standardGeneric("rstream.sample"))

setMethod("rstream.sample",
c("rstream","numeric"),
          function(stream,n=1) { ... [ code ] ... } )

Thus if rs is an instance of an rstream object one can a random
sample of size 10 using 

rstream.sample(rs, 10)

for a sample of size 1 one can use equivalently

rstream.sample(rs,1) 
rstream.sample(rs) 

however, with R-devel the above construct does not work any more, due to
more stringent checkings. It can be fixed by replacing it by

if(!isGeneric("rstream.sample"))
        setGeneric("rstream.sample", function(stream,n)
standardGeneric("rstream.sample"))

setMethod("rstream.sample",
c("rstream","numeric"),
          function(stream,n=1) { ... [ code ] ... } )

then rstream.sample(rs) does not work any more.

Is there still a way to allow optional arguments for methods of
S4 classes?

Josef

Hi Josef,

On 14 Feb 2006, leydold at statistik.wu-wien.ac.at
wrote:
> I have used a construct to allow optional arguments:
>
> if(!isGeneric("rstream.sample"))
setGeneric("rstream.sample",
> function(stream,...) standardGeneric("rstream.sample"))
First, a question:
  Is this idiom of testing for the generic before defining it still
  "recommended"?  It seems to me that one should either define
one's
  own generic in the package namespace or define a method for a
  *particular* generic defined elsewhere.  Otherwise, one could end up
  defining a method for the wrong generic.
> setMethod("rstream.sample",
c("rstream","numeric"),
> function(stream,n=1) { ... [ code ] ... } )
This will work if you remove the second arg in the signature.  That
is,

  setMethod("rstream.sample", signature(stream="rstream"),
            function(strea, n=1) { ... })

Putting an arg in the signature means dispatching on that arg.  You
cannot dispatch on an arg that is not named in the definition of the
generic.
> however, with R-devel the above construct does not work any more,
> due to more stringent checkings. It can be fixed by replacing it by
>
> if(!isGeneric("rstream.sample"))
setGeneric("rstream.sample",
> function(stream,n) standardGeneric("rstream.sample"))
>
> setMethod("rstream.sample",
c("rstream","numeric"),
> function(stream,n=1) { ... [ code ] ... } )
>
> then rstream.sample(rs) does not work any more.
>
> Is there still a way to allow optional arguments for methods of S4
> classes?
Here's an approach that works for me:

1. You have to specify a default value to args *in the generic*.  This
   doesn't make a whole lot of sense to me, but it does seem to be
   needed.

   setGeneric("rstream.sample", 
              function(stream, n=0) standardGeneric("rstream.sample"))

2. Then define a method with a signature that matches the default
   case:

   setMethod("rstream.sample", signature(stream="rstream",
n="missing"),
             function(stream, n=1) { ... })

   Note that you could also use signature(stream="rstream"), but then
   a call like rstream.sample(s, "foo") could match... Leaving out the
   arg is like saying n="ANY".

HTH,

+ seth

The problem is not the optional argument, but the attempt to dispatch on 
an argument not in the generic.

setGeneric("rstream.sample", function(stream, ...)
            standardGeneric("rstream.sample"))
setMethod("rstream.sample", "rstream", function(stream,n=1)
{ print(n) } )
rstream.sample(rs, 10)
[1] 10
rstream.sample(rs)
[1] 1

works, and seems to work as you intended.

On Tue, 14 Feb 2006, Josef Leydold wrote:
> Hi,
>
> i have used S4 classes to implement a unified access to random number
generators
> (package rstream on CRAN).
>
> I have used a construct to allow optional arguments:
>
> if(!isGeneric("rstream.sample"))
>        setGeneric("rstream.sample", function(stream,...)
standardGeneric("rstream.sample"))
>
> setMethod("rstream.sample",
c("rstream","numeric"),
>          function(stream,n=1) { ... [ code ] ... } )
>
> Thus if rs is an instance of an rstream object one can a random
> sample of size 10 using
>
> rstream.sample(rs, 10)
>
> for a sample of size 1 one can use equivalently
>
> rstream.sample(rs,1)
> rstream.sample(rs)
>
> however, with R-devel the above construct does not work any more, due to
> more stringent checkings. It can be fixed by replacing it by
>
> if(!isGeneric("rstream.sample"))
>        setGeneric("rstream.sample", function(stream,n)
standardGeneric("rstream.sample"))
>
> setMethod("rstream.sample",
c("rstream","numeric"),
>          function(stream,n=1) { ... [ code ] ... } )
>
> then rstream.sample(rs) does not work any more.
>
> Is there still a way to allow optional arguments for methods of
> S4 classes?
>
> Josef
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Echoing similar suggestions, but with a bit of philosophy... How about:

setGeneric("rstream.sample",
           function( stream, ... ) standardGeneric("rstream.sample"))

setMethod("rstream.sample", c( "numeric" ),
          function( stream, n = 1, ... ) { code }  )

It seems to me like the generic should (always?) just have arguments
used for dispatch -- stream, in this case -- and that methods then
specify default values. To also dispatch on the second argument, one
might

setGeneric("rstream.sample",
           function( stream, n, ... )
standardGeneric("rstream.sample"))

setMethod("rstream.sample", c( "rstream.sample",
"numeric" ),
          function( stream, n, ... ) { code } )

setMethod("rstream.sample", c( "rstream.sample",
"missing" ),
          function( stream, n, ... ) rstream.sample( stream, n = 1 ))

setMethod("rstream.sample", c( "rstream.sample",
"otherclass" ),
          function( stream, n, ... ) n )

Martin

"Josef Leydold" <leydold at statistik.wu-wien.ac.at> writes:
> Hi,
>
> i have used S4 classes to implement a unified access to random number
generators
> (package rstream on CRAN).
>
> I have used a construct to allow optional arguments:
>
> if(!isGeneric("rstream.sample"))
>         setGeneric("rstream.sample", function(stream,...)
standardGeneric("rstream.sample"))
>
> setMethod("rstream.sample",
c("rstream","numeric"),
>           function(stream,n=1) { ... [ code ] ... } )
>
> Thus if rs is an instance of an rstream object one can a random
> sample of size 10 using 
>
> rstream.sample(rs, 10)
>
> for a sample of size 1 one can use equivalently
>
> rstream.sample(rs,1) 
> rstream.sample(rs) 
>
> however, with R-devel the above construct does not work any more, due to
> more stringent checkings. It can be fixed by replacing it by
>
> if(!isGeneric("rstream.sample"))
>         setGeneric("rstream.sample", function(stream,n)
standardGeneric("rstream.sample"))
>
> setMethod("rstream.sample",
c("rstream","numeric"),
>           function(stream,n=1) { ... [ code ] ... } )
>
> then rstream.sample(rs) does not work any more.
>
> Is there still a way to allow optional arguments for methods of
> S4 classes?
>
> Josef
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel