[R] inheritence in S4

[Martin Morgan]

Hi Christophe --

This is a variant of the problem that Jim Regetz is having in a thread
in R-devel. Here's where the trouble is

> as(c, "A")
Error in .local(.Object, ...) : 
  argument "value" is missing, with no default

By default, 'as(c, "A")' will create a new instance of it's second argument
using new("A"), and then fill the slots of A with appropriate values
from "C". We can see that creating a new "A" without any additional
arguments causes the same error:

> new("A")
Error in .local(.Object, ...) : 
  argument "value" is missing, with no default

Jim has gone down the path of creating coercion methods ('setAs') for
his classes. A different solution is to ensure that 'new' works with
no additional arguments (typically requiring that a prototype, if
present, prodcues valid objects). So for instance

setMethod("initialize","A",function(.Object, value=numeric(0)){
    .Object at x <- value
    return(.Object)
})

and then

> new("A")
A

I find it easier to keep track of prototype and initialize methods,
rather than setAs, so I use a solution like the above.  But a couple
of other quick points. I would have written

setMethod("initialize", "A",
          function(.Object, ..., xValue=numeric(0)){
              callNextMethod(.Object, ..., x=xValue)
          })

Why? this allows the built-in object creation methods to create
.Object, so there's less code for me to maintain (even if it's just
object assignment .Object at x <- value  here). Importantly, when I
create a derived class, the derived class does not have to know in
detail about what the initilalize method for "A" does, e.g.,

setMethod("initialize","B",
          function(.Object, ..., yValue=numeric(0)){
              callNextMethod(.Object, ..., y=yValue)
          })

Here 'initialize' for B just deals with it's slots, and doesn't have
to worry about what to do with A's slots. Also .Object at x <- value
makes a copy of .Object, which can be expensive if .Object is
large. There is some hope that the default method (eventually reached
by callNextMethod) does things relatively efficiently in terms of
copies. Note that each initialize method only deals with its own
slots. 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 when creating
objects with complicated inheritance -- not quite so much need to
follow the method dispatch / argument assignment rules through a
complicated inheritance hierarchy.

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, and instead write

B <- function(xValue=numeric(0), yValue=numeric(0)) {
    new("B", x=xValue, y=yValue)
}

All my slot coercion is in the constructor. The user can figure out
from the signature of the constructor what the appropriate arguments
and their types are, and does not have to know about the details of
the class definition. I can catch common errors and provide
user-friendly messages, rather than getting cryptic messages from the
internals of S4.

Hope that helps.

Martin

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

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