Re: [R] inheritence in S4

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Tue, 04 Mar 2008 06:23:03 -0800

cgenolin_at_u-paris10.fr writes:

> Hi Martin, thanks for your answer
>
>> But a couple
>> of other quick points. I would have written
>>
>> setMethod("initialize", "A",
>> function(.Object, ..., xValue=numeric(0)){
>> callNextMethod(.Object, ..., x=xValue)
>> })
>>
>
> I am not that much familiar with S3... In our way of writing this
> method, 'initialize' for 'A' will call the next method for A, which is
> initialise' for 'numeric', is that right ?

from below,

>>> setClass("A", representation(x="numeric"))

The 'next' method refers to arguments in the signature of the generic, i.e., the 'next' method relevant to .Object. For "A", the next method is the default "initialize" method, which will use all named arguments to fill the slots of .Object (and perhaps call validObject, among other things). You can see the code with

> showMethods("initialize", classes="ANY", includeDef=TRUE)

S3 is not relevant here.

>> And finally, the position of 'xValue' and 'yValue' means that
>> the arugment has to be named, e.g., new("B", yValue=12). This seems a
>> little awkward at first, but seems like a best practice
>
> I agree with you. But I do not like the use of ... , it lets us to
> make many mistake like in :
>
> print(3.5165,digitts=2)
>
> There is a typo in digitts, but since print works with ... , R does
> not detect the mistake.
> So I agree with the importance of naming argument, I always do it but
> without 'forcing' it

If this were "initialize", and you had provided an invalid named argument, the default method would have failed because there is no slot of that name.

>> And finally, in Jim's thread I mention using a constructor. So in
>> practice for a case like the above I would not define any initialize
>> methods,
>
> Interesting. Will you still define a validity method or not even ?

For a simple case like this there is no extra validity to check beyond that ensured by S4 (e.g., slots of the correct type). If there were constraints, e.g., only positive values, or length one vectors, then I would define a validity function.

Martin

>
> Christophe
>
>
>>
>> Christophe Genolini <cgenolin_at_u-paris10.fr> writes:
>>
>>> Thanks Martin
>>>
>>> Well it works except that "as" seems to not like the "initialize"
>>> method : the following code (that is the same than yours with some
>>> initialize for A B and C) does not compile. It seems that as(c,"A")
>>> does not work if we definie a initialize for A...
>>>
>>> --- 8< --------------
>>> setClass("A", representation(x="numeric"))
>>> setMethod("initialize","A",function(.Object,value){.Object_at_x <-
>>> value;return(.Object)})
>>> a <- new("A",4)
>>>
>>> setClass("B", representation(y="numeric"))
>>> setMethod("initialize","B",function(.Object,value){.Object_at_y <-
>>> value;return(.Object)})
>>> b <- new("B",5)
>>>
>>> setClass("C", contains=c("A", "B"))
>>> setMethod("initialize","C",function(.Object,valueA, valueB){
>>> .Object_at_x <- valueA
>>> .Object_at_y <- valueB
>>> return(.Object)
>>> })
>>> c <- new("C",valueA=10,valueB=12)
>>>
>>> setMethod("show", "A", function(object) cat("A\n"))
>>> setMethod("show", "B", function(object) cat("B\n"))
>>> setMethod("show", "C", function(object) {
>>> callGeneric(as(object, "A"))
>>> callGeneric(as(object, "B"))
>>> cat("C\n")
>>> })
>>> c
>>> --- 8< --------------------
>>>
>>> Is there something wrong with the use of 'as' between class and father
>>> class?
>>>
>>> Christophe
>>>> Hi Christophe --
>>>>
>>>> I don't know whether there's a particularly elegant way. This works
>>>>
>>>> setClass("A", representation(x="numeric"))
>>>> setClass("B", representation(y="numeric"))
>>>> setClass("C", contains=c("A", "B"))
>>>>
>>>> setMethod("show", "A", function(object) cat("A\n"))
>>>> setMethod("show", "B", function(object) cat("B\n"))
>>>> setMethod("show", "C", function(object) {
>>>> callGeneric(as(object, "A"))
>>>> callGeneric(as(object, "B"))
>>>> cat("C\n")
>>>> })
>>>>
>>>>
>>>>> new("C")
>>>>>
>>>> A
>>>> B
>>>> C
>>>>
>>>> but obviously involves the developer in making explicit decisions
>>>> about method dispatch when there is multiple inheritance.
>>>>
>>>> Martin
>>>>
>>>> cgenolin_at_u-paris10.fr writes:
>>>>
>>>>
>>>>> Hi the list
>>>>>
>>>>> I define a class A (slot a and b), a class C (slot c and d) and a
>>>>> class E that inherit from A and B.
>>>>> I define print(A) and print(B). For print(C), I would like to use
>>>>> both of them, but I do not see how...
>>>>>
>>>>> Thanks for your help...
>>>>>
>>>>> Christophe
>>>>>
>>>>> ----------------------------------------------------------------
>>>>> Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
>>>>>
>>>>> ______________________________________________
>>>>> R-help_at_r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>
>>>>
>>>
>>
>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M2 B169
>> Phone: (206) 667-2793
>>
>
>
>
> ----------------------------------------------------------------
> Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
>
>
>

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

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Received on Tue 04 Mar 2008 - 14:31:06 GMT

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