S4 method dispatch matrixOrArray (fwd)

You have two questions, presumably:

1 - how could the order of the setMethod calls make a difference in the
results?
2 - what's causing the infinite loop & how could it be avoided, reliably?

Second question first.  The danger sign is the "vector" method:

setMethod("foo",
           signature(A = "vector"),
           function(A, ...) {
               foo(matrix(A, nrow = 1), ...)
           })

This handles a vector by recalling the generic with a matrix.  But
"vector" is a superclass of "matrix" (see getClass("matrix")) and you
DON'T have an explicit method defined for "matrix".  So for sure if
"vector" was the only method, you would be in immediate trouble.
Coercing down the inheritance tree is potentially bad news.

Generally, if you're going to take over dispatch by coercing an argument
& then recalling the generic, the result is simplest if you have an
exact match for the new call, not relying on inheritance.  After all, if
you're doing the work to coerce the argument, might as well pick one
that works right away.   Not a universal rule, but other things being
equal ...

There's an additional issue with methods for  "matrix" and "array"
because R never allows 2-way arrays to have class "array", which means
using array() here with the same dimensions would not have helped.
Also, matrix and array objects are weird in that they are not basic
vectors but also have no class attribute, and is.object() is FALSE for them.

More interesting though--how can the order of the setMethod() calls
matter?  To see that we need to look at the methods list object.  (The
discussion is simplified to the case that only one argument is involved,
which doesn't affect the result.)

The MethodsList object has a slot containing a named list of methods,
with the names being those of the classes that appeared in the setMethod
calls, in the order that the calls occurred(note!).  All classes are
essentially equal from the view of the generic function, so there's no
ordering favoring the "more relevant".

When method dispatch occurs, the code first looks for an exact match to
the class of the actual argument--that's a quick search in the names of
the list.

If the direct search fails, the code now looks for an inherited method.
The key point is that this second search is "greedy"--the first
inherited method found is used.

NOW it should be clear why the order of the setMethod() calls matters.
You have two potential inherited methods here for "matrix"; namely,
"array" and "vector".  WE know that the "array" method is `closer', and
the R dispatcher could decide this also, if it were willing to look
through all possible inheritance paths and drop one possibility if a
better one was found.

It currently doesn't do any further search, and doing so would be a
modest efficiency hit.  I'm inclined to think the cost would be worth it
to eliminate unpleasant suprises like this one, but opinions may
differ.  (Once found, the inherited method is stored directly in the
list used for the first lookup,  so the hit is only the first time a
particular signature turns up.)

To make the difference clearer, I added to your example another generic
"bar" with the same methods as "foo", but with the order of the
setMethod calls reversed.
By looking at the "methods" slot in the two cases, we can see why the
bad ("vector") method is selected for bar() but not for foo():

 > names(getMethods("foo")@methods)

[1] "array"  "vector"

 > names(getMethods("bar")@methods)

[1] "vector" "array"

After running foo(1:10) and trying to run bar(1:10):

 > showMethods("foo")

Function "foo":
 A = "array"
 A = "vector"
 A = "integer"
    (inherited from A = "vector")
 A = "matrix"
    (inherited from A = "array")

 > showMethods("bar")

Function "bar":
 A = "vector"
 A = "array"
 A = "integer"
    (inherited from A = "vector")
 A = "matrix"
    (inherited from A = "vector")

But including setMethod("bar", "matrix", ...) in the source code makes
bar() work fine.



Paul Roebuck wrote:

Sorry to bother but could you shed some light on this?
I don't understand why order of setMethod calls makes
any difference. Since it obviously does, it has shaken
the foundations of what I thought I understood about
S4 methods. Even Gabor was surprised...


---------- Forwarded message ----------
Date: Wed, 12 Apr 2006 18:24:46 -0400
From: Gabor Grothendieck <ggrothendieck at gmail.com>
To: Paul Roebuck <roebuck at mdanderson.org>
Cc: R Help Mailing List <r-help at stat.math.ethz.ch>
Subject: Re: [R] S4 method dispatch matrixOrArray

On 4/12/06, Paul Roebuck <roebuck at mdanderson.org> wrote:

On Wed, 12 Apr 2006, Gabor Grothendieck wrote:

On 4/12/06, Paul Roebuck <roebuck at mdanderson.org> wrote:

I have some code where the primary dispatching is on
other parameters so I'd like not to have to create a
set of functions for "matrix" and another duplicate
set for "array". But the class union technique isn't
working as implemented below and I don't have my Green
book with me. How do I fix my infinite recursion problem?


##--------------------------------------------------------
library(methods)

setGeneric("foo",
         function(A, ...) {
             cat("generic", match.call()[[1]], "\n")
             standardGeneric("foo")
         })

setMethod("foo",
        signature(A = "vector"),
        function(A, ...) {
            callGeneric(matrix(A, nrow = 1), ...)
        })

setClassUnion("matrixOrArray", c("matrix", "array"))

setMethod("foo",
        signature(A = "matrixOrArray"),
        function(A, ...) {
            cat("A =", A, "\n")
        })

## Test
foo(1:4)
foo(matrix(1:4, 1, 4))
foo(array(1:4, c(1, 4, 1)))

I think its good enough to just define an array method, i.e. you
don't need the matrix method or the matrixOrArray class, and the
vector method can call foo(matrix(A,1), ...) so:

setGeneric("foo",
         function(A, ...) {
             cat("generic", match.call()[[1]], "\n")
             standardGeneric("foo")
         })

setMethod("foo",
        signature(A = "array"),
        function(A, ...) {
            cat("A =", A, "\n")
        })

setMethod("foo",
        signature(A = "vector"),
        function(A, ...) {
            foo(matrix(A, nrow = 1), ...)
        })

Something didn't seem right here. That was pretty close
to what I had started with, before trying to go the
classUnion route. Matter of fact, the vector method can
retain use of callGeneric.

The solution has to do with the order in which calls to
setMethod are made. Adding foo-vector after foo-array
works fine; the other way around causes infinite recursion.

This is surprising.  I would have thought that the
parent/child relationships determine the order that
dispatched methods are invoked, not the order that
the setMethod commands are issued in.