Re: [R] Re: S4 method inheritance
Ross Boylan wrote:
On Tue, May 24, 2005 at 06:27:56AM -0700, Robert Gentleman wrote:
Duncan Murdoch wrote:
Ross Boylan wrote:
On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote:
Finally, I'm a bit concerned that one article mentioned that S4
inheritance, in practice, is used mostly for data, not methods (Thomas
Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I
shouldn't travel?
Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends
A), how does B's method foo invoke A's foo?
Your question doesn't make sense in S4. In S4, classes don't have
methods, generics have methods. There's no such thing as "B's method"
or "A's method".
You might get what you want with foo(as(bObject, "A")) if bObject is an
instance of class B.
The question assumes that A's foo was defined as an in place function,
so there's no (obvious) named object for it, i.e,
setMethod("A", signature(blah="numeric"), function(x) something)
In general it may be best to think of a generic function as a
dispatching mechanism. For S4 methods are associated with a specific
generic function.
"specific" generic is a reference to the ability to define generics
within the context of a particular package?
Well, more that you can identify one (either explicitly by its package
[ie. fully-qualified name], or implicitly by the fact that it is first
on the search path - the former being prefered). But the notion is that
there is one and you have asked that your method be made available to
that one generic function for dispatch. This is in contrast to S3 -
where no such functionality exists - that I know of; under S3 any method
is a method for all generic functions of the correct name and the
programmer has no (easy) control. Under S4 methods are not really
ordinary functions, should not be called directly and are invoked only
via calls to the generic (you can of course break all of those rules).
A generic knows about all methods that are associated
with it, and about no others.
Presumably setMethod does the association. Is the where argument
intended to identify which generic method to pick? The fact that
there is not a "package" argument to setMethod, as there is to
setGeneric, is a little confusing to me.
I believe that is the documented behavior. Yes the where argument
should allow you complete specificity. I will leave it to the auther to
clarify differences between the where and package arguments in the call
to setGeneric (or you, if you care to explore the code).
Thus in S4, the little tiff over who owns
label goes away - they both do - different packages can define
generic
"They" is two different packages? Or is this a reference to my
original confusion about class vs generic ownership of a method?
It is the two packages. The S langauge allows for the same symbol to
be bound to different values in different namespaces (in R that is
becoming explicit, in SPlus it is less so, but still generally true). I
can think of no good reason to treat generic functions, or any other
first class object, differently.
HTH,
Robert
functions for label, or anything else they care to, and users can write
methods for specific generic
functions and associate them with a
generic.
...
HTH
Robert
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Re: [R] Re: S4 method inheritance
On Tue, May 24, 2005 at 06:27:56AM -0700, Robert Gentleman wrote:
>
>
> Duncan Murdoch wrote:
> >Ross Boylan wrote:
> >
> >>On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote:
> >>
> >>
> >>
> >>>Finally, I'm a bit concerned that one article mentioned that S4
> >>>inheritance, in practice, is used mostly for data, not methods (Thomas
> >>>Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I
> >>>shouldn't travel?
> >>>
> >>
> >>Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends
> >>A), how does B's method foo invoke A's foo?
> >
> >
> >Your question doesn't make sense in S4. In S4, classes don't have
> >methods, generics have methods. There's no such thing as "B's method"
> >or "A's method".
> >
> >You might get what you want with foo(as(bObject, "A")) if bObject is an
> >instance of class B.
> >
> >>The question assumes that A's foo was defined as an in place function,
> >>so there's no (obvious) named object for it, i.e,
> >>setMethod("A", signature(blah="numeric"), function(x) something)
> >
>
> In general it may be best to think of a generic function as a
> dispatching mechanism. For S4 methods are associated with a specific
> generic function.
"specific" generic is a reference to the ability to define generics
within the context of a particular package?
> A generic knows about all methods that are associated
> with it, and about no others.
Presumably setMethod does the association. Is the where argument
intended to identify which generic method to pick? The fact that
there is not a "package" argument to setMethod, as there is to
setGeneric, is a little confusing to me.
> Thus in S4, the little tiff over who owns
> label goes away - they both do - different packages can define
> generic
"They" is two different packages? Or is this a reference to my
original confusion about class vs generic ownership of a method?
> functions for label, or anything else they care to, and users can write
> methods for specific generic functions and associate them with a
> generic.
...
> HTH
>Robert
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Re: [R] Re: S4 method inheritance
On Tue, May 24, 2005 at 07:07:07AM -0400, Duncan Murdoch wrote:
> Ross Boylan wrote:
> >On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote:
> >
> >
> >
> >>Finally, I'm a bit concerned that one article mentioned that S4
> >>inheritance, in practice, is used mostly for data, not methods (Thomas
> >>Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I
> >>shouldn't travel?
> >>
> >
> >Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends
> >A), how does B's method foo invoke A's foo?
>
> Your question doesn't make sense in S4. In S4, classes don't have
> methods, generics have methods. There's no such thing as "B's method"
> or "A's method".
Oops, I keep taking the references to "objects" too literally. Thanks.
>
> You might get what you want with foo(as(bObject, "A")) if bObject is an
> instance of class B.
>
> >The question assumes that A's foo was defined as an in place function,
> >so there's no (obvious) named object for it, i.e,
> >setMethod("A", signature(blah="numeric"), function(x) something)
There's my confusion: the first argument should be the name of the
generic, not the class.
>
> I don't know what you mean by "in place function", but I hope my answer
> helps anyway.
Just for clarification, "in place function" was in contrast to a
function defined elsewhere with an explicit name, e.g.,
fforA<-function(x) something
setMethod("foo", signature(blah="numeric"), fforA)
In that case I could just refer to fforA directly. (Trying to avoid
the S3ish f.A).
Is sounds as if the use of as() or callNextMethod() will get me what I
want. And the docs seem clear that callNextMethod() returns control
(and a value) to the calling function.
Thanks to everyone for their help.
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Re: [R] Re: S4 method inheritance
On Mon, 23 May 2005, Ross Boylan wrote: On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: Finally, I'm a bit concerned that one article mentioned that S4 inheritance, in practice, is used mostly for data, not methods (Thomas Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I shouldn't travel? Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends A), how does B's method foo invoke A's foo? You may be looking for callNextMethod, or foo(as(object, "A")). The comment about inheritance in my R News article has nothing to do with S3 vs S4. It is just that extensions of data structures typically happen by specialisation (for which inheritance is appropriate) whereas models are typically extended by generalisation (for which inheritance isn't appropriate). The only relevance to the S3 vs S4 discussion is that it provides an explanation for the lack of appreciation of S4. Since most statisticians don't use inheritance when programming they don't see the benefit in a system that gets inheritance right. -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Re: S4 method inheritance
Duncan Murdoch wrote:
Ross Boylan wrote:
On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote:
Finally, I'm a bit concerned that one article mentioned that S4
inheritance, in practice, is used mostly for data, not methods (Thomas
Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I
shouldn't travel?
Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends
A), how does B's method foo invoke A's foo?
Your question doesn't make sense in S4. In S4, classes don't have
methods, generics have methods. There's no such thing as "B's method"
or "A's method".
You might get what you want with foo(as(bObject, "A")) if bObject is an
instance of class B.
The question assumes that A's foo was defined as an in place function,
so there's no (obvious) named object for it, i.e,
setMethod("A", signature(blah="numeric"), function(x) something)
In general it may be best to think of a generic function as a
dispatching mechanism. For S4 methods are associated with a specific
generic function. A generic knows about all methods that are associated
with it, and about no others. Thus in S4, the little tiff over who owns
label goes away - they both do - different packages can define generic
functions for label, or anything else they care to, and users can write
methods for specific generic functions and associate them with a
generic. [Note that in the S3 system there is no real mechanism for
saying that foo.bar is a method for one generic named foo, and not for
another - but the language does allow for multiple generics named foo -
one of the very many reasons that S3 does not really do what you want it
to, but many seem convinced otherwise].
The class hierarchy of the actual supplied arguments, is used to
determine the dispatch order (a linearization of the available methods)
once the generic is invoked. The most specific method is used first. It
may intiate a call to callNextMethod (S4) or NextMethod (S3) to transfer
control to the next most specific method - the manual pages provide more
specific details.
As Duncan said - classes do not own methods in this paradigm. Generic
functions do.
HTH
Robert
I don't know what you mean by "in place function", but I hope my answer
helps anyway.
Duncan Murdoch
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Re: [R] Re: S4 method inheritance
Ross Boylan wrote:
On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote:
Finally, I'm a bit concerned that one article mentioned that S4
inheritance, in practice, is used mostly for data, not methods (Thomas
Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I
shouldn't travel?
Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends
A), how does B's method foo invoke A's foo?
Your question doesn't make sense in S4. In S4, classes don't have
methods, generics have methods. There's no such thing as "B's method"
or "A's method".
You might get what you want with foo(as(bObject, "A")) if bObject is an
instance of class B.
The question assumes that A's foo was defined as an in place function,
so there's no (obvious) named object for it, i.e,
setMethod("A", signature(blah="numeric"), function(x) something)
I don't know what you mean by "in place function", but I hope my answer
helps anyway.
Duncan Murdoch
__
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https://stat.ethz.ch/mailman/listinfo/r-help
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[R] Re: S4 method inheritance
On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote:
> Finally, I'm a bit concerned that one article mentioned that S4
> inheritance, in practice, is used mostly for data, not methods (Thomas
> Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I
> shouldn't travel?
>
Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends
A), how does B's method foo invoke A's foo?
The question assumes that A's foo was defined as an in place function,
so there's no (obvious) named object for it, i.e,
setMethod("A", signature(blah="numeric"), function(x) something)
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