R help - Aug 2013 - Understanding S4 method dispatch

Hi all,

Any insight into the code below would be appreciated - I don't
understand why two methods which I think should have equal distance
from the call don't.

Thanks!

Hadley

# Create simple class hierarchy
setClass("A", "NULL")
setClass("B", "A")

a <- new("A")
b <- new("B")

setGeneric("f", function(x, y) standardGeneric("f"))
setMethod("f", signature("A", "A"), function(x, y)
"A-A")
setMethod("f", signature("B", "B"), function(x, y)
"B-B")

# These work as I expect
f(a, a)
f(b, b)

setClass("AB", contains = c("A", "B"))
ab <- new("AB")

# Why does this return B-B? Shouldn't both methods be an equal distance?
f(ab, ab)

# These both return distance 1, as I expected
extends("AB", "A", fullInfo=TRUE)@distance
extends("AB", "B", fullInfo=TRUE)@distance
# So why is signature("B", "B") closer than
signature("A", "A")

-- 
Chief Scientist, RStudio
http://had.co.nz/

Hadley,

The class AB inherits from A and from B, but B already inherits from class A. So
actually you only have an object of class B in your object of class AB. When you
call the function f R looks for a method f for AB objects. It does not find such
a method and looks for a method of the object inherited from, B. Such a method
is present and is then executed.

The inheritance structure has to be changed. The behavior is actually desired,
as if this behavior weren't given a diamond class inheritance would be
fatal.


Best

Simon



On Aug 13, 2013, at 3:08 PM, Hadley Wickham <h.wickham at gmail.com>
wrote:
> Hi all,
> 
> Any insight into the code below would be appreciated - I don't
> understand why two methods which I think should have equal distance
> from the call don't.
> 
> Thanks!
> 
> Hadley
> 
> # Create simple class hierarchy
> setClass("A", "NULL")
> setClass("B", "A")
> 
> a <- new("A")
> b <- new("B")
> 
> setGeneric("f", function(x, y) standardGeneric("f"))
> setMethod("f", signature("A", "A"),
function(x, y) "A-A")
> setMethod("f", signature("B", "B"),
function(x, y) "B-B")
> 
> # These work as I expect
> f(a, a)
> f(b, b)
> 
> setClass("AB", contains = c("A", "B"))
> ab <- new("AB")
> 
> # Why does this return B-B? Shouldn't both methods be an equal
distance?
> f(ab, ab)
> 
> # These both return distance 1, as I expected
> extends("AB", "A", fullInfo=TRUE)@distance
> extends("AB", "B", fullInfo=TRUE)@distance
> # So why is signature("B", "B") closer than
signature("A", "A")
> 
> -- 
> Chief Scientist, RStudio
> http://had.co.nz/
> 
> ______________________________________________
> 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.

Hi Hadley,

I suspect that the dispatch algorithm doesn't realize that selection
is ambiguous in your example. For 2 reasons:

   (1) When it does realize it, it notifies the user:

         setClass("A", "NULL")
         setGeneric("f", function(x, y)
standardGeneric("f"))
         setMethod("f", signature("A", "ANY"),
function(x, y) "A-ANY")
         setMethod("f", signature("ANY", "A"),
function(x, y) "ANY-A")
         a <- new("A")

       Then:

         > f(a, a)
         Note: method with signature ?A#ANY? chosen for function ?f?,
          target signature ?A#A?.
          "ANY#A" would also be valid
         [1] "A-ANY"

   (2) When dispatch is ambiguous, the "first method lexicographically in
       the ordering" should be selected (according to ?Methods). So it
       should be A#A, not B#B.

So it looks like a bug to me...

Cheers,
H.


On 08/13/2013 06:08 AM, Hadley Wickham wrote:
> Hi all,
>
> Any insight into the code below would be appreciated - I don't
> understand why two methods which I think should have equal distance
> from the call don't.
>
> Thanks!
>
> Hadley
>
> # Create simple class hierarchy
> setClass("A", "NULL")
> setClass("B", "A")
>
> a <- new("A")
> b <- new("B")
>
> setGeneric("f", function(x, y) standardGeneric("f"))
> setMethod("f", signature("A", "A"),
function(x, y) "A-A")
> setMethod("f", signature("B", "B"),
function(x, y) "B-B")
>
> # These work as I expect
> f(a, a)
> f(b, b)
>
> setClass("AB", contains = c("A", "B"))
> ab <- new("AB")
>
> # Why does this return B-B? Shouldn't both methods be an equal
distance?
> f(ab, ab)
>
> # These both return distance 1, as I expected
> extends("AB", "A", fullInfo=TRUE)@distance
> extends("AB", "B", fullInfo=TRUE)@distance
> # So why is signature("B", "B") closer than
signature("A", "A")
>
-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319