unary class union of an S3 class
On Sat, Mar 19, 2016 at 12:10 AM, Herv? Pag?s <hpages at fredhutch.org> wrote:
On 03/18/2016 03:28 PM, Michael Lawrence wrote:
On Fri, Mar 18, 2016 at 2:53 PM, Herv? Pag?s <hpages at fredhutch.org
<mailto:hpages at fredhutch.org>> wrote:
Hi,
Short story
-----------
setClassUnion("ArrayLike", "array")
showClass("ArrayLike") # no slot
setClass("MyArrayLikeConcreteSubclass",
contains="ArrayLike",
representation(stuff="ANY")
)
showClass("MyArrayLikeConcreteSubclass") # 2 slots!!
That doesn't seem right.
Long story
----------
S4 provides at least 3 ways to create a little class hierarchy
like this:
FooLike ............. virtual class with no slot
^ ^
| |
foo anotherfoo ..... 2 concrete subclasses
(1) The "standard" way: define FooLike first, then foo and anotherfoo
as subclasses of FooLike:
setClass("FooLike")
setClass("foo",
contains="FooLike",
representation(stuff="ANY")
)
setClass("anotherfoo",
contains="FooLike",
representation(stuff="ANY")
)
showClass("FooLike") # displays foo and anotherfoo as
# known subclasses
x1 <- new("foo")
is(x1, "foo") # TRUE
is(x1, "FooLike") # TRUE
is(x1, "anotherfoo") # FALSE
x2 <- new("anotherfoo")
is(x2, "anotherfoo") # TRUE
is(x2, "FooLike") # TRUE
is(x2, "foo") # FALSE
Everything works as expected.
(2) Using a class union: define foo and anotherfoo first, then FooLike
as the union of foo and anotherfoo:
setClass("foo", representation(stuff="ANY"))
setClass("anotherfoo", representation(stuff="ANY"))
setClassUnion("FooLike", c("foo", "anotherfoo"))
showClass("FooLike") # displays foo and anotherfoo as
# known subclasses
(3) Using a *unary* class union: define foo first, then FooLike as the
(unary) union of foo, then anotherfoo as a subclass of FooLike:
setClass("foo", representation(stuff="ANY"))
setClassUnion("FooLike", "foo")
showClass("FooLike") # displays foo as the only known subclass
setClass("anotherfoo",
contains="FooLike",
representation(stuff="ANY")
)
showClass("FooLike") # now displays foo and anotherfoo as
# known subclasses
The 3 ways lead to the same hierarchy. However the 3rd way is
interesting because it allows one to define the FooLike virtual
class as the parent of an existing foo class that s/he doesn't
control.
Why not use setIs() for this?
> setClass("ArrayLike")
> setIs("array", "ArrayLike")
Error in setIs("array", "ArrayLike") :
class ?array? is sealed; new superclasses can not be defined, except
by 'setClassUnion'
How do you define a virtual class as the parent of an existing class
with setIs?
You can only do that with setClassUnion(). But the new classes should use
setIs() to inherit from the union. So it's:
setClassUnion("ArrayLike", "array")
setClass("MyArrayLike")
setIs("MyArrayLike", "ArrayLike")
Everything then behaves as expected. I
don't think it makes much sense to "contain" a class union.
Why is that? A class union is just a virtual class with no slot that is the parent of the classes that are in the union. All the classes in the union contain their parent. What's interesting is that this union is actually open to new members: when I later define a new class that contains the class union, I'm just adding a new member to the union. Rather, you
just want to establish the inheritance relationship.
Isn't what I'm doing when I define a new class that contains the class union?
Containing does two things: establishes the is() relationship and adds slots to the class. These slots are comprised of the slots of the contained class, and as a special case the "array" class and other native types confer a data part that comes from the prototype of the class. The "array" class has a double vector with a dim attribute as its prototype. That is all well understood. What is surprising is that "ArrayLike" has the same prototype as "array". That happens via setIs(doComplete=TRUE), called by setClassUnion(). When a class gains its first non-virtual child, the parent assumes the prototype of its child. I'm not sure why, but the logic is very explicit and I've come to just accept it as a "feature". I ran into this some months ago when defining my own ArrayLike when working on a very similar package to the one you are developing ;)
For example, to define an ArrayLike class:
setClassUnion("ArrayLike", "array")
showClass("ArrayLike") # displays array as a known subclass
Note that ArrayLike is virtual with no slots (analog to a Java
Interface), which is what is expected.
setClass("MyArrayLikeConcreteSubclass",
contains="ArrayLike",
representation(stuff="ANY")
)
showClass("MyArrayLikeConcreteSubclass") # shows 2 slots!!
What is the .Data slot doing here? I would expect to see that slot
if MyArrayLikeConcreteSubclass was extending array but this is not
the case here.
a <- new("MyArrayLikeConcreteSubclass")
is(a, "MyArrayLikeConcreteSubclass") # TRUE --> ok
is(a, "ArrayLike") # TRUE --> ok
is(a, "array") # FALSE --> ok
But:
is.array(a) # TRUE --> not ok!
Is is.array() confused by the presence of the .Data slot?
It looks like the unary union somehow equates ArrayLike and array
Clearly the unary union makes ArrayLike a parent of array, as it should be. This can be confirmed by extends():
> extends("array", "ArrayLike")
[1] TRUE
> extends("ArrayLike", "array")
[1] FALSE
The results for is(a, "ArrayLike") (TRUE) and is(a, "array") (FALSE)
on a MyArrayLikeConcreteSubclass instance are consistent with this.
So the little 3-class hierarchy I end up with in the above example
is exactly how expected:
ArrayLike
^ ^
| |
array MyArrayLikeConcreteSubclass
What is not expected is that MyArrayLikeConcreteSubclass has a .Data
slot and that is.array(a) returns TRUE on a MyArrayLikeConcreteSubclass
object.
H.
and
thus makes ArrayLike confer a dim attribute (and thus is.array(a)
returns TRUE). Since S4 objects cannot have attributes that are not
slots, it must do this via a data part, thus the .Data slot.
I can fix it by defining an "is.array" method for
MyArrayLikeConcreteSubclass objects:
setMethod("is.array", "MyArrayLikeConcreteSubclass",
function(x) FALSE
)
However, it feels that I shouldn't have to do this.
Is the presence of the .Data slot in MyArrayLikeConcreteSubclass
objects an unintended feature?
Thanks,
H.
> sessionInfo()
R Under development (unstable) (2016-01-07 r69884)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
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-- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319