aperm() was designed for multidimensional arrays, but is also useful for
table objects, particularly
with the lattice, vcd and vcdExtra packages. But aperm() was designed
and implemented before other
related object classes were conceived, and I propose a small tune-up to
make it more generally useful.
The problem is that aperm() always returns an object of class 'array',
which causes problems for methods
designed for table objects. It also requires some package writers to
implement both .array and .table
methods for the same functionality, usually one in terms of the other.
Some examples of unexpected, and initially perplexing results (when only
methods for one class are implemented)
are shown below.
> library(vcd)
> pairs(UCBAdmissions, shade=TRUE)
> UCB <- aperm(UCBAdmissions, c(2, 1, 3))
>
> # UCB is now an array, not a table
> pairs(UCB, shade=TRUE)
There were 50 or more warnings (use warnings() to see the first 50)
>
> # fix it, to get pairs.table
> class(UCB) <- "table"
> pairs(UCB, shade=TRUE)
>
Of course, I can define a new function, tperm() that does what I think
should be the expected behavior:
# aperm, for table objects
tperm <- function(a, perm, resize = TRUE) {
result <- aperm(a, per, resize)
class(result) <- class(a)
result
}
But I think it is more natural to include this functionality in aperm()
itself. Thus, I propose the following
revision of base::aperm(), at the R level:
aperm <- function (a, perm, resize = TRUE, keep.class=TRUE)
{
if (missing(perm))
perm <- integer(0L)
result <- .Internal(aperm(a, perm, resize))
if(keep.class) class(result) <- class(a)
result
}
I don't think this would break any existing code, except where someone
depended on coercion to an array.
The drop-in replacement for aperm would set keep.class=FALSE by default,
but I think TRUE is more
natural.
FWIW, here are the methods for table and array objects
from my current (non-representative) session.
> methods(class="table")
[1] as.data.frame.table barchart.table* cloud.table*
contourplot.table* dotplot.table*
[6] head.table* levelplot.table* pairs.table*
plot.table* print.table
[11] summary.table tail.table*
Non-visible functions are asterisked
>
> methods(class="array")
[1] anyDuplicated.array as.data.frame.array as.raster.array*
barchart.array* contourplot.array* dotplot.array*
[7] duplicated.array levelplot.array* unique.array
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street Web:http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA