[Rd] S4 method dispatch

[John Chambers]

On 9/30/11 12:48 AM, Edzer Pebesma wrote:
> Thanks, John!
>
> I did not manage to figure out how the strict= works, but changed class
> inheritance such that simple inheritance did not take place.
>
> I see you're advocating to use the contains= to stress inheritance; back
> in 2005, I followed the green book, which did not yet have this.
>
> If I now would change class definitions from using the representation=
> into contains= to express inheritance, does the binary representation
> also change, i.e. do people relying on sp classes get into problem with
> old, saved objects read by the new software? I'm asking this because
> there's lots of it around, e.g. all the world administrative regions
> available as .RData files from http://gadm.org/

It's just a question of readability: Better to have a clear statement of 
inheritance rather than plowing through the representation list for 
empty name fields.  And easier to discuss (e.g., section 9.3 of SoDA).

You're hardly the only sinner in the flock.  I imagine many packages on 
CRAN would have failed by now if there was a problem.  I only complain 
about it when feeling fussy.

John
.
>
> On 09/18/2011 11:04 PM, John Chambers wrote:
>> The distinction here is "simple inheritance" ("Software for Data
>> Analysis", p. 346). Your first example is simple inheritance (would be
>> clearer if you used the contains= argument). In the second version you
>> supply an explicit coerce method, so method dispatch can no longer just
>> pass in the object from the subclass, but has to call the coerce method
>> explicitly. Details in the reference.
>>
>> If you need to have an explicit coerce method, it's possible to emulate
>> simple inheritance, but the programming may be more subtle than you want
>> to take on. When your method is called, it actually gets also an
>> argument strict= which will be FALSE for method dispatch. You need to
>> take account of the strict= argument in writing your method. See ?setAs
>> for a few more details. Someone on the list may have an example.
>>
>> John
>>
>> On 9/18/11 3:33 AM, Edzer Pebesma wrote:
>>> As a follow-up, I managed to isolate the problem I sent earlier this
>>> week, and reduced it to a small case (I'm using R 2.13.1,
>>> i486-pc-linux-gnu (32-bit)).
>>>
>>> The following script does what I expect:
>>>
>>>
>>> setClass("A", representation(x = "numeric"))
>>> setClass("AB", representation("A"))
>>>
>>> setGeneric("doNothing<-", function(obj, value)
>>> standardGeneric("doNothing<-"))
>>>
>>> setReplaceMethod("doNothing", c("A", "character"),
>>> function(obj, value) obj)
>>>
>>> x = new("AB", x = 10)
>>> doNothing(x) = "irrelevant"
>>> class(x)
>>>
>>> setAs("AB", "A", function(from) new("A", x = from at x))
>>> x = new("AB", x = 10)
>>> doNothing(x) = "irrelevant"
>>> class(x)
>>>
>>>
>>> and results in class(x) being "AB".
>>> However, the following, very similar script:
>>>
>>>
>>> setClass("A", representation(x = "numeric"))
>>> setClass("AB", representation("A"))
>>>
>>> setGeneric("doNothing<-", function(obj, value)
>>> standardGeneric("doNothing<-"))
>>>
>>> setReplaceMethod("doNothing", c("A", "character"),
>>> function(obj, value) obj)
>>>
>>> setAs("AB", "A", function(from) new("A", x = from at x))
>>>
>>> x = new("AB", x = 10)
>>> doNothing(x) = "irrelevant"
>>> class(x)
>>>
>>>
>>> returns "A" as the class of x. Why is this the case? Is this behaviour
>>> intentional?
>>>
>>> Best regards,
>>>
>>>
>>> On 09/14/2011 11:00 PM, Edzer Pebesma wrote:
>>>> List,
>>>>
>>>> In order to get rid of some old, unreadable S3 code in package sp, I'm
>>>> trying to rewrite things using S4 methods. Somewhere I fail, and I
>>>> cannot sort out why. In order to isolate the problem, I created two
>>>> functions, doNothing<- and dosth, and both should do nothing. The issue
>>>> is that in most cases they do nothing, but in some cases dosth(obj)
>>>> changes the class of obj and breaks with the error. I couldn't find a
>>>> pattern when this happens, but have a few cases where it consistently
>>>> breaks. Here's the code snippet:
>>>>
>>>> setGeneric("doNothing<-", function(object, value)
>>>> standardGeneric("doNothing<-"))
>>>>
>>>> setReplaceMethod("doNothing",
>>>> signature(object = "Spatial", value = "ANY"),
>>>> function(object, value) object)
>>>>
>>>> dosth = function(obj) {
>>>> cl1 = class(obj)
>>>> doNothing(obj) = TRUE
>>>> cl2 = class(obj)
>>>> if (!identical(cl1, cl2)) {
>>>> print(paste(cl1, cl2))
>>>> stopifnot(identical(cl1, cl2))
>>>> }
>>>> obj
>>>> }
>>>>
>>>> When things go wrong, dosth and doNothing are called with a subclass of
>>>> Spatial, e.g. an object of class SpatialGrid, but when this gets in
>>>> doNothing, the object is suddenly of class Spatial, and is then
>>>> returned
>>>> as an object of class Spatial, which should never happen.
>>>>
>>>> For instance, I have a case where consistently
>>>>
>>>> setMethod("fullgrid", c("Spatial"),
>>>> function(obj) { is(obj, "SpatialGrid") })
>>>>> class(g)
>>>> [1] "SpatialGrid"
>>>> attr(,"package")
>>>> [1] "sp"
>>>>> fullgrid(g)
>>>> [1] FALSE
>>>>
>>>> is obviously false, but in other cases it works fine.
>>>>
>>>> When I change the signature of doNothing to signature(object = "ANY",
>>>> value = "ANY"), the problem disappears.
>>>>
>>>> I tried to make a self-contained example that reproduced the issue, but
>>>> could only get something that worked as expected.
>>>>
>>>> I would appreciate any help or suggestions.
>>>
>