From roebuck at mdanderson.org  Sat Apr 15 10:16:04 2006
From: roebuck at mdanderson.org (Paul Roebuck)
Date: Sat, 15 Apr 2006 03:16:04 -0500 (CDT)
Subject: [Rd] [R] S4 method dispatch matrixOrArray (fwd)
In-Reply-To: <443EC0F9.2060206@r-project.org>
References: <Pine.OSF.4.58.0604122227040.305100@wotan.mdacc.tmc.edu>
	<443EC0F9.2060206@r-project.org>
Message-ID: <Pine.OSF.4.58.0604150243570.402202@wotan.mdacc.tmc.edu>

Thanks for your in-depth explanation. I had noticed the difference
in order in showMethods() output but was unsure whether that was
indicative of the problem or if I was somehow taking advantage of
an undocumented implementation-specific detail.

If I could, I'd like to go back to the original question from
the R-help post here. The original method was doing its real
dispatching on the arguments of the example that were represented
by the dots. The meat of the method was to manipulate array
objects and as such I didn't want to repeat numerous array methods
as matrix methods (code duplication with the only difference being
the first argument). From another recent posting on a similar topic,
I wanted to do something along the lines of

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

but that didn't work as originally presented (probably due to
your comment on matrix/array weirdness). So my other question
would be:

3 - Is there a way to use the class union such that I don't have
to duplicate the code unnecessarily yet avoid the setMethod
ordering issue and clarify the original intention?



On Thu, 13 Apr 2006, John Chambers wrote:

> 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.
> >
> >
> >
> >
>

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SIGSIG -- signature too long (core dumped)



[Rd] [R] S4 method dispatch matrixOrArray (fwd)
Paul Roebuck