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 __ 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 __ 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 __ 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
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
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. __ 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
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 __ 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
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 __ 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
[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) __ 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
