From hpages at fredhutch.org  Sat Mar 19 21:03:44 2016
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Date: Sat, 19 Mar 2016 13:03:44 -0700
Subject: [Rd] unary class union of an S3 class
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On 03/19/2016 06:35 AM, Michael Lawrence wrote:
>
>
> On Sat, Mar 19, 2016 at 4:29 AM, Herv? Pag?s <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
>     On 03/19/2016 01:22 AM, Michael Lawrence wrote:
>
>
>
>         On Sat, Mar 19, 2016 at 12:10 AM, Herv? Pag?s
>         <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>         <mailto:hpages at fredhutch.org <mailto: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>
>         <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>
>                  <mailto:hpages at fredhutch.org
>         <mailto:hpages at fredhutch.org> <mailto: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.
>
>
>     I understand that. But in that case, since a class union has no slots,
>     one would expect that using setIs() is equivalent to containing.
>
>         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".
>
>
>     Never noticed that. Thanks for clarifying. So with this "feature":
>
>        - setClassUnion("A", c("B", "C")) is not the same as
>          setClassUnion("A", c("C", "B"))
>
>        - if 2 packages define concrete subclasses of a virtual
>          class defined in a 3rd package, the prototype of the virtual
>          class will depend on the order the packages are loaded
>
>        - using setIs("MyArrayLike", "ArrayLike") is not equivalent
>          to containing (even though ArrayLike has no slots)
>
>        - containing adds an undesirable .Data slot
>
>        - containing breaks is.array() but not is( , "array")
>
>     Seems pretty harmful to me. Would be good to understand the
>     rationale behind this feature. In particular it's not clear to me
>     why a virtual
>     class with no slot would need to have a prototype at all (i.e. other
>     than NULL).
>
>         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 ;)
>
>
>     After giving it more thoughts I realized that I can do without the
>     ArrayLike class. That will keep the class hierarchy in HDF5Array to the
>     strict minimum.
>
>
> Yea I've come to realize that declaring virtual classes that indicate
> whether an object behaves like a base type is overkill.

If it was just to indicate this, it would definitely be overkill.
But it's convenient to be able to define methods at the level of
ArrayLike. A typical use case is when a method for a subclass
coerces to "array" and delegates to the method for "array":

     x <- as.array(x)
     callGeneric()

If you don't have the ArrayLike class, you have to define the same
method over and over for each ArrayLike subclass.

It's also useful to be able to use ArrayLike as slots in other
classes.

Anyway, it turns out that I don't need any of these features in
HDF5Array, at least for now.

> It usually
> suffices to say that the object satisfies the basic contract of an
> array, list, vector, etc. It would be nice to have something like a Java
> interface for specifying such contracts.

I'd rather fix what we already have ;-)

H.

>
>     Thanks for the feedback,
>     H.
>
>
>
>
>                       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> <mailto:hpages at fredhutch.org
>         <mailto:hpages at fredhutch.org>>
>                  <mailto:hpages at fredhutch.org
>         <mailto:hpages at fredhutch.org> <mailto:hpages at fredhutch.org
>         <mailto:hpages at fredhutch.org>>>
>                       Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>         <tel:%28206%29%20667-5791>
>                  <tel:%28206%29%20667-5791>
>                       Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>         <tel:%28206%29%20667-1319>
>                  <tel:%28206%29%20667-1319>
>
>                       ______________________________________________
>         R-devel at r-project.org <mailto:R-devel at r-project.org>
>         <mailto:R-devel at r-project.org <mailto:R-devel at r-project.org>>
>                  <mailto:R-devel at r-project.org
>         <mailto:R-devel at r-project.org> <mailto:R-devel at r-project.org
>         <mailto:R-devel at r-project.org>>>
>                  mailing list
>         https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
>              --
>              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>
>         <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>
>              Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>         <tel:%28206%29%20667-5791>
>              Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>         <tel:%28206%29%20667-1319>
>
>
>
>     --
>     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>
>
>

-- 
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



[Rd] unary class union of an S3 class
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