I have an S4 class which extends array and has other slots, 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
(which I do).
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.
This becomes a practical consideration in an extract method:
> setMethod("[", c("foo"), function(x, i, j, ..., drop)
+ {
+ if(missing(i)) {i <- min(1,nrow(x)):nrow(x)}
+ if(missing(j)) {j <- min(1,ncol(x)):ncol(x)}
+ if(missing(drop)) {drop <- TRUE}
+ subx <- x at .Data[i, j, ..., drop = drop]
+ new("foo",subx)
+ })
[1] "["> a[,,1]
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 is changed behaviour from 1.9.1, for the reason above.
I can try to assign the matrix an array class, but the 2-dimensional object
has a special status, viz:
> class(as(1,"array"))
[1] "array"> dim(as(1,"array"))
[1] 1
but:
> class(as(matrix(1,1,1),"array"))
[1] "matrix"
I have checked using extends(), and matrix and array still extend one
another (hence there is a trivial but unhelpful answer to the title of this
posting).
getClass() shows some differences, but I am not sure whether they are
related to this issue:
1.9.1
>getClass("matrix")
No Slots, prototype of class "matrix"
Extends: "structure", "array"
Known Subclasses:
Class "array", directly, with explicit test and coerce
2.0.1
>getClass("matrix")
No Slots, prototype of class "matrix"
Extends:
Class "structure", directly
Class "array", directly
Class "vector", by class "structure", with explicit coerce
Class "vector", by class "array", with explicit coerce
Known Subclasses:
Class "array", directly, with explicit test and coerce
My question is: how can I get a 2-dimensional object into the slot in my S4
class, or into the class "foo" in the minimal example above?
[OS = Windows XP]
