[Rd] S4 class no longer accepts matrix in array slot under 2.0.1

[Giles Heywood]

I see - clearly I had confused the extended superclass with a slot.  I'm not
sure that this correction to my thinking moves me closer to my objective,
however (i.e. extending array and allowing 2D array, as was allowed in
1.9.1).

In such a situation I return to the documentation and examples.  I have a
further question about documentation.  The Green Book, valuable and
frequently cited as it is, is now in many ways increasingly difficult to
relate to R, except at a somewhat abstract level (I fully understand that R
is a separate implementation of the S language etc).  I also have found
Venables and Ripley ch5 most helpful.  Is there in existence documentation
which provides an overview of the methods package as it now stands, rather
like an updated Green Book?  Or are there specific packages or example
packages which illustrate most of, or much of, the functionality (I have
found SparseM useful in this way)?

TIA

Giles


> -----Original Message-----
> From: John Chambers [mailto:jmc at R-project.org]
> Sent: 10 January 2005 22:10
> To: Giles Heywood
> Cc: r-devel at stat.math.ethz.ch
> Subject: Re: [Rd] S4 class no longer accepts matrix in array slot under
> 2.0.1
>
>
> Your example and your subject heading are two different things.  If you
> meant the subject heading, that in fact works.
>
> R> setClass("a1", representation(x="array"))
> [1] "a1"
> R> new("a1", x=matrix(1:12,3,4))
> An object of class "a1"
> Slot "x":
>       [,1] [,2] [,3] [,4]
> [1,]    1    4    7   10
> [2,]    2    5    8   11
> [3,]    3    6    9   12
>
> That's not what your example does.  In your example, the new class
> extends "array", rather than using it as a slot.  It would have been
> clearer if you had said setClass("foo", contains="array"), but your code
> is correct for that purpose.
>
> On first examination, I believe the problem is just what the message
> says it is.  You gave as a new object (and NOT as a slot) an object from
> a subclass of a superclass of "foo".  This is allowed, but has to be
> done by replacing the part of a "foo" object corresponding to the
> "array" contained in a "matrix" object.  Of course, we know that's
> actually the whole object, but nothing has told the software this.  And,
> indeed, it doesn't find the necessary replacement method.
>
> Here's an example similar to what you are doing, but using actual
> classes.  Barring screwups on my part, it shows that the mechanism works
> as asserted.  Classes "c1", "c2", "c3" follow the roles of "array",
> "matrix", and "foo" in your example.
> R> setClass("c1", representation(x="numeric"))
> [1] "c1"
> R> setClass("c2", contains="c1")
> [1] "c2"
> R> setClass("c3", contains = "c1")
> [1] "c3"
> R> x2 = new("c2", x=1)
> R> x3 = new("c3", x2)
> R> x3
> An object of class "c3"
> Slot "x":
> [1] 1
>
> Classes "matrix" and "array" are rather peculiar in R; among other
> things, they act like vector data types in that is.object() is FALSE.
> And you cannot have an "array" with a dimension of length 2.
>
> R> class(array(1:12, dim=c(3,4)))
> [1] "matrix"
>
> Also, because they don't have a consistent set of "slots" (they may or
> may not have a "dimnames), they aren't quite real classes in an S4
> sense.  It would be nice to fix this mess, but not obviously possible
> while being back compatible.
>
> It's possible that there is a fix to get around the particular error
> here, without breaking the more general pattern--I'll take a look.
>
> Otherwise, you may need to follow the approach of your subject heading,
> and define a new class with an array as a slot.
>
> Giles Heywood wrote:
>
> > I have an S4 class with a slot of class "array", and in
> upgrading to 2.0.1
> > (from 1.9.1) I have encountered a change in behaviour. This
> causes me some
> > difficulties if I want to allow 2-dimensional arrays in the slot.
> >
> > The following (in 2.0.1) illustrates the point:
> >
> >
> >>setClass("foo",representation("array"))
> >
> > [1] "foo"
> >
> >>a <- new("foo",array(NA,2:4))
> >>b <- new("foo",matrix(NA,2,3))
> >
> > Error in "as<-"(`*tmp*`, Classi, value = c(NA, NA, NA, NA, NA, NA)) :
> >         No method or default for as() replacement of "foo" with
> > Class="matrix"
> >
> > This last error did not occur under 1.9.1.
> >
> > I conclude that in this context the methods package does not recognise
> > "matrix" as a subclass of "array". However if I use getClass(),
> I see that R
> > recognises "matrix" as a subclass of "array" (and vice-versa).
> So is this
> > new behaviour correct?
>
> You conclude incorrectly, as noted above.
> >
> > [this is a re-posting to R-devel of a question earlier posted to R-help,
> > which attracted limited response]
> >
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> >