[R] inheritence in S4

[cgenolin at u-paris10.fr]

Well well well...

To summarize : let assume that A is a class (slot x) and C is a class 
containing A (A and slot y) - as(c,"A") calls new("A"). So new("A") HAS 
TO works, you can not decide to forbid empty object (unless you define 
setAs("C","A") ?)
- In addition, any test that you would like to set in initialize or 
validity have to first check is some field are empty (because 
'if(object at x >0)' will fail if x=numerical(0))
- When you call new("C"), the neither new("A") nor intialize("A") are 
called. (!!!!)

So, all the security test you write in initialize "A", you have to 
rewrite them on "C" ?

I start to undestand why not that much people use S4...

Christophe

> 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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