S3 objects in S4 slots

On 16/09/2009 12:50 PM, John Chambers wrote:
<snip>

2. Restricting the revision to setOldClass() leads to a clean 
concept, and makes the S3 class more compatible with S4 classes.   
The proposal at the moment is to interpret the setOldClass call much 
like the corresponding setClass() call above.  The included "list" 
would be examined to see if it was a valid "data part" in S4 terms. 
That's a little more general than just giving an object type.  The 
implementation and interpretation are then simple, and the result 
should be consistent with the treatment of similar S4 classes.

At least in this specific case, the idea is that corpus objects can be
used as a list of character vectors and code does not need to know
anything about the object structure as long as only the contents of
the list are needed. So (again, in this specific case), I would
consider "defaulting" to the underlying data type optimal.

 

Martin Morgan's code is indeed a workaround.  And as Martin Maechler
commented, the intention is to make S3 and S4 classes play together 
as much
as possible.

I didn't comment on this before, because I think that's a good 
intention, and I think users appreciate all the work you're doing to 
bring it about:  but I'd still stick by my advice not to mix S3 and 
S4.  As a general principle it's better to keep your programming life 
simple.  Don't take advantage of every feature the language offers, 
work within a subset, where you're sure you understand how everything 
works.  Someone like you or either Martin M. has a deep enough 
knowledge of S3 and S4 and how they interact to get away with mixing 
them, but most users don't.

The original question came up because Martin K., working with S4 
objects, wanted to make use of an object from a package that used S3.  
I still think he would have been better off to spend a little bit of 
time writing the function to convert the S3 object into an S4 object, 
and then never having to worry again about the intricacies of how S4 
inheritance interacts with S3 inheritance.

Duncan Murdoch

Thanks to Martin Morgan for the workaround, it works very well.

 

Morgan wrote:

Hi Martin Kober --
Martin Kober wrote:


Hello,
I am the maintainer of the stringkernels package and have come across
a problem with using S3 objects in my S4 classes.
Specifically, I have an S4 class with a slot that takes a text corpus
as a list of character vectors. tm (version 0.5) saves corpora as
lists with a class attribute of c("VCorpus", "Corpus", "list"). I
don't actually need the class-specific attributes, I only care about
the list itself.
Here's a simplified example of my problem:


setClass("testclass", representation(slot="list"))


[1] "testclass"


a = list(a="1", b="2")
class(a) = c("VCorpus", "Corpus", "list") # same as corpora in tm v0.5


This has the feel of a workaround, but
setOldClass(class(a)[1:2]); setIs("Corpus", "list")
helps here, first registering c('vCorpus', 'Corpus') as an S3 
hierarchy
and then defining the relationship between the root of the 
hierarchy and
(the S4 class) 'list'.
Martin (Morgan)


x = new("testclass", slot=a)


Error in validObject(.Object) :
  invalid class "testclass" object: 1: invalid object for slot "slot"
in class "testclass": got class "VCorpus", should be or extend class
"list"
invalid class "testclass" object: 2: invalid object for slot "slot" in
class "testclass": got class "Corpus", should be or extend class
"list"
invalid class "testclass" object: 3: invalid object for slot "slot" in
class "testclass": got class "list", should be or extend class "list"
The last line is a bit confusing here (``got class "list", should be
or extend class "list"''). There's an even more confusing error
message when I try to assign the slot later on:


y = new("testclass")
y at slot = a


Error in checkSlotAssignment(object, name, value) :
  c("assignment of an object of class \"VCorpus\" is not valid for
slot \"slot\" in an object of class \"testclass\"; is(value, \"list\")
is not TRUE", "assignment of an object of class \"Corpus\" is not
valid for slot \"slot\" in an object of class \"testclass\"; is(value,
\"list\") is not TRUE", "assignment of an object of class \"list\" is
not valid for slot \"slot\" in an object of class \"testclass\";
is(value, \"list\") is not TRUE")
The last part of the message claims that ``is(value, "list") is not
TRUE'', but is(a, "list") is certainly TRUE. (??)
On a side note, it does work when "list" is the first entry in 
class().
I tried to use setOldClass, but seemingly using list is not possible
because it does not extend oldClass, or I didn't find out how to do
it:


setOldClass(c("VCorpus", "Corpus", "list"))


Error in setOldClass(c("VCorpus", "Corpus", "list")) :
  inconsistent old-style class information for "list"; the class is
defined but does not extend "oldClass"
Intuitively I would have thought that, because the underlying data is
of type list, it would "fit" into an object slot requiring a list,
irrespective of S3 class attributes. The only thing I can think of is
a manual solution removing the class attribute.
Is there a way to define lists with S3 class attributes such that they
are accepted as lists in S4 object slots? Or any other ways to solve
this?
Thanks in advance
Best Regards
Martin

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