S4 classes and methods with optional arguments

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S4 classes and methods with optional arguments

Josef Leydold
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

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Re: S4 classes and methods with optional arguments

Seth Falcon-2
Hi Josef,

On 14 Feb 2006, [hidden email] 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

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Re: S4 classes and methods with optional arguments

Brian Ripley
In reply to this post by Josef Leydold
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
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

--
Brian D. Ripley,                  [hidden email]
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

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Re: S4 classes and methods with optional arguments

Martin Morgan
In reply to this post by Josef Leydold
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" <[hidden email]> 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
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: S4 classes and methods with optional arguments

Seth Falcon-2
On 14 Feb 2006, [hidden email] wrote:

> 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.

There are advantages to adding named arguments to a generic to define
the expected interface.  These 'extra' args may not be *needed* for
dispatch in the sense that the first arg may be enough to decide what
method you want.

So IMO, there are two reasons to put an arg in a generic:

1. You really want to dispatch on it.
2. You want to define an interface and can handle the fact that you
   will have to also dispatch on it.

I guess my point is that for downstream developers extending your
generic and for the sake of documentation, relying too much on '...'
can make things difficult.

> 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 ))

And here I might offer a slight improvement.  Putting the default
value in the signature of the function will give automated tools a
chance to document:

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

+ seth

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