John Fox wrote:
Dear r-devel list members,
I'm moving this question to r-devel because it seems thornier than I originally thought.
Yes, it's certainly not for r-help.
I've already mentioned (on r-help) that the approach that John Chambers suggested (below) fails for objects of class "by":
x <- rnorm(100) y <- sample(2, 100, replace=TRUE) res <- by(x, y, mean) res
INDICES: 1
[1] -0.03429679
------------------------------------------------------------ INDICES: 2
[1] -0.1273790
class(res)
[1] "by"
isS4object <- function(object)(length(attr(object, "class"))==1 &&
+ !is.null(getClass(class(object))))
isS4object(res)
Error in getClass(class(object)) : "by" is not a defined class
I tried to fix that, but I've now discovered more general problems; e.g.:
Let's not revert to slotNames(). For the reasons I mentioned it's inevitably going to produce a confusing definition.
There are a couple of problems (aside from my having used getClass() where I meant to use getClassDef() :-{):
- we need to handle S3 classes that have been registered with S4 dispatch by calling setOldClass(). Doing this is strongly recommended, but the effect is to create an S4 definition. That's one reason why lm() objects might appear to be S4 objects. Presumably, we don't want that.
- eventually, if this is a serious thing that people need, we need to worry about objects defined in namespaces, with private class definitions.
Here's a more careful version of the previous idea, which I believe handles the first of these problems, by using the fact that an object generated by new("foo",...) cannot come from a VIRTUAL class. That gets actually to "What do we really mean by an S4 object?" I'm essentially saying that an object that could not have been created by a new() call is not an S4 object. People could cheat, of course, and it's not clear what we should do with such objects. Both the case of no definition and the case of S3 classes registered with setOldClass() should produce a VIRTUAL class.
(By the way, I was wondering what the actual intent of this function was. Usually, one would try to have generic functions deal sensibly with objects for which they had no method--either some default calculation or an error message. The notion of "S4 object" is pretty general or vague, as we're demonstrating. On the whole, it would be better not to get tangled up in it.)
I'm weakly confident that the current version also handles the namespace issue, by using the actual class() call, which should include a "package" attribute to get to the right namespace.
But no assertions that extensive testing has been done. Nevertheless, here is a second approximation.
isS4Object <- function(object) {
if(length(attr(object, "class"))!= 1)
return(FALSE)
!isVirtualClass(getClass(class(object), TRUE))
}
mod <- lm(y ~ x) class(mod)
[1] "lm"
isS4object(mod)
[1] TRUE
class(summary(mod))
[1] "summary.lm"
isS4object(summary(mod))
Error in getClass(class(object)) : "summary.lm" is not a defined class
I've reverted to a modified version of my original proposal:
isS4object <- function(object) {
+ !(length(object) == 1 && class(object) == "character") && length(slotNames(object)) != 0 + }
isS4object(res)
[1] FALSE
isS4object(mod)
[1] FALSE
isS4object(summary(mod))
[1] FALSE
# example from ?mle x <- 0:10 y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8) ll <- function(ymax=15, xhalf=6)
+ -sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE))
fit <- mle(ll)
Warning message: NaNs produced in: dpois(x, lambda, log)
isS4object(fit)
[1] TRUE
isS4object("mle")
[1] FALSE
All this is with R 2.0.1 under Windows NT.
Comments would be appreciated.
John
--------------------------------
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox --------------------------------
-----Original Message-----
From: John Chambers [mailto:[EMAIL PROTECTED] Sent: Tuesday, November 30, 2004 9:40 AM
To: John Fox
Cc: Martin Maechler; [EMAIL PROTECTED]
Subject: Re: [R] Testing for S4 objects
Let me suggest a different test, because slotNames was written to work differently when given a string or a class definition. With your definition,
R> x <- "classRepresentation" R> isS4object(x) [1] TRUE
which I assume is not what you wanted. (Given a single string, slotNames() tries to look up the class definition of that name.)
How about the following? The logic is that an S4 object must have an actual class attribute of length 1 (that rules out basic data types, where class(x) is a string but there is no actual attribute, and also rules out some S3 objects). Then if that's true, try to look up the class definition. If it is non-null, seems like an S4 object.
R> isS4object <- function(object)(length(attr(object, "class"))==1 && + !is.null(getClass(class(object)))) R> isS4object(x) [1] FALSE R> isS4object(getClass(class(x))) [1] TRUE
This definition seems to work, at least on the examples I could think of right away. Notice though, that some classes, such as "ts", that have been around for a long while are nevertheless legitimate S4 classes, so:
R> t1 = ts(1:12) R> isS4object(t1) [1] TRUE
(this applies to either version of isS4object).
There are a couple of details, more appropriate for the r-devel list. Seems a good candidate for a function to add to R.
On Sat, 27 Nov 2004 17:48:30 -0500, John Fox <[EMAIL PROTECTED]> wrote:
Dear Martin,
As it turns out, the test that I proposed (i.e., testing for NULL slotNames) sometimes fails. For example:
library(car) data(Prestige) sum <- summary(lm(prestige ~ income + education, data=Prestige)) slotNames(sum)
character(0)
The following, however, seems to work (at least as far as I've been able to
ascertain):
isS4object <- function(object) length(slotNames(object)) != 0
I hope that this is a more robust test.
John
-------------------------------- John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox --------------------------------
-----Original Message----- From: Martin Maechler [mailto:[EMAIL PROTECTED] Sent: Friday, November 26, 2004 3:18 AM To: John Fox Cc: [EMAIL PROTECTED] Subject: Re: [R] Testing for S4 objects
"JohnF" == John Fox <[EMAIL PROTECTED]> on Thu, 25 Nov 2004 22:28:50 -0500 writes:
JohnF> Dear r-help list members, Is there a way to test JohnF> whether an object is an S4 object? The best that I've JohnF> been able to come up with is
JohnF> isS4object <- function(object) !(is.null(slotNames(object)))
you can drop one pair of "(..)" to give
isS4object <- function(object) !is.null(slotNames(object))
JohnF> which assumes that an S4 object has at least one JohnF> slot. I think this is safe, but perhaps I'm missing JohnF> something.
The question is a very good one -- that I have posed to R-core a while ago myself.
Inside utils:::str.default {which doesn't show the many
commments
in the *source* of str.default()}, I have wanted a way that even works when the 'methods' package is not attached and use the more obscure
#NOT yet:if(has.class <- !is.null(cl <- class(object))) if(has.class <- !is.null(cl <- attr(object, "class")))# S3 or S4 class S4 <- !is.null(attr(cl, "package"))## <<<'kludge' FIXME! ##or length(methods::getSlots(cl)) > 0
For the time being, I'd keep your function, but I don't
think we'd
guarantee that it will remain the appropriate test in all
future.
But till then many things will have happened (if not all of them ;-).
Martin Maechler, ETH Zurich
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