From bolker at ufl.edu  Sat Dec 15 22:39:44 2007
From: bolker at ufl.edu (Ben Bolker)
Date: Sat, 15 Dec 2007 13:39:44 -0800 (PST)
Subject: [Rd] S4 class extending data.frame?
In-Reply-To: <6ph7ijir640.fsf@gopher4.fhcrc.org>
References: <4760BD69.2020807@ufl.edu>
	<1197542502.7435.4.camel@maitai.windows.ebi.ac.uk>
	<6ph7ijir640.fsf@gopher4.fhcrc.org>
Message-ID: <14355388.post@talk.nabble.com>



  Thanks, Martin.  In the short term (a) seems best.  In the long
run we may try (c), because there are other things that data.frame
doesn't do that we want it to do (i.e., allow arbitrary objects with
[ methods, print methods, and the same length to be bound together,
rather than being restricted to atomic vectors + Date/factor).

  cheers
    Ben




Martin Morgan wrote:
> 
> Ben, Oleg --
> 
> Some solutions, which you've probably already thought of, are (a) move
> the data.frame into its own slot, instead of extending it, (b) manage
> the data.frame attributes yourself, or (c) reinvent the data.frame
> from scratch as a proper S4 class (e.g., extending 'list' with
> validity constraints on element length and homogeneity of element
> content).
> 
> (b) places a lot of dependence on understanding the data.frame
> implementation, and is probably too tricky (for me) to get right,(c)
> is probably also tricky, and probably caries significant performance
> overhead (e.g., object duplication during validity checking).
> 
> (a) means that you don't get automatic method inheritance. On the plus
> side, you still get the structure. It is trivial to implement methods
> like [, [[, etc to dispatch on your object and act on the appropriate
> slot. And in some sense you now know what methods i.e., those you've
> implemented, are supported on your object.
> 
> Oleg, here's my cautionary tale for extending list, where manually
> subsetting the .Data slot mixes up the names (callNextMethod would
> have done the right thing, but was not appropriate). This was quite a
> subtle bug for me, because I hadn't been expecting named lists in my
> object; the problem surfaced when sapply used the (incorrectly subset)
> names attribute of the list. My solution in this case was to make sure
> 'names' were removed from lists used to construct objects. As a
> consequence I lose a nice little bit of sapply magic.
> 
>> setClass('A', 'list')
> [1] "A"
>> setMethod('[', 'A', function(x, i, j, ..., drop=TRUE) {
> +     x at .Data <- x at .Data[i]
> +     x
> + })
> [1] "["
>> names(new('A', list(x=1, y=2))[2])
> [1] "x"
> 
> Martin
> 
> Oleg Sklyar <osklyar at ebi.ac.uk> writes:
> 
>> I had the same problem. Generally data.frame's behave like lists, but
>> while you can extend list, there are problems extending a data.frame
>> class. This comes down to the internal representation of the object I
>> guess. Vectors, including list, contain their information in a (hidden)
>> slot .Data (see the example below). data.frame's do not seem to follow
>> this convention.
>>
>> Any idea how to go around?
>>
>> The following example is exactly the same as Ben's for a data.frame, but
>> using a list. It works fine and one can see that the list structure is
>> stored in .Data
>>
>> * ~: R
>> R version 2.6.1 (2007-11-26) 
>>> setClass("c3",representation(comment="character"),contains="list")
>> [1] "c3"
>>> l = list(1:3,2:4)
>>> z3 = new("c3",l,comment="hello")
>>> z3
>> An object of class ?c3?
>> [[1]]
>> [1] 1 2 3
>>
>> [[2]]
>> [1] 2 3 4
>>
>> Slot "comment":
>> [1] "hello"
>>
>>> z3 at .Data
>> [[1]]
>> [1] 1 2 3
>>
>> [[2]]
>> [1] 2 3 4
>>
>> Regards,
>> Oleg
>>
>> On Thu, 2007-12-13 at 00:04 -0500, Ben Bolker wrote:
>>> -----BEGIN PGP SIGNED MESSAGE-----
>>> Hash: SHA1
>>> 
>>> I would like to build an S4 class that extends
>>> a data frame, but includes several more slots.
>>> 
>>> Here's an example using integer as the base
>>> class instead:
>>> 
>>> setClass("c1",representation(comment="character"),contains="integer")
>>> z1 = new("c1",55,comment="hello")
>>> z1
>>> z1+10
>>> z1[1]
>>> z1 at comment
>>> 
>>>  -- in other words, it behaves exactly as an integer
>>> for access and operations but happens to have another slot.
>>> 
>>>  If I do this with a data frame instead, it doesn't seem to work
>>> at all.
>>> 
>>> setClass("c2",representation(comment="character"),contains="data.frame")
>>> d = data.frame(1:3,2:4)
>>> z2 = new("c2",d,comment="goodbye")
>>> z2  ## data all gone!!
>>> z2[,1]  ## Error ... object is not subsettable
>>> z2 at comment  ## still there
>>> 
>>>   I can achieve approximately the same effect by
>>> adding attributes, but I was hoping for the structure
>>> of S4 classes ...
>>> 
>>>   Programming with Data and the R Language Definition
>>> contain 2 references each to data frames, and neither of
>>> them has allowed me to figure out this behavior.
>>> 
>>>  (While I'm at it: it would be wonderful to have
>>> a "rich data frame" that could include as a column
>>> any object that had an appropriate length and
>>> [ method ... has anyone done anything in this direction?
>>> ?data.frame says the allowable types are
>>>  "(numeric, logical, factor and character and so on)",
>>>  but I'm having trouble sorting out what the limitations
>>> are ...)
>>> 
>>>   hoping for enlightenment (it would be lovely to be
>>> shown how to make this work, but a definitive statement
>>> that it is impossible would be useful too).
>>> 
>>>   cheers
>>>     Ben Bolker
>>> 
>>> -----BEGIN PGP SIGNATURE-----
>>> Version: GnuPG v1.4.6 (GNU/Linux)
>>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>>> 
>>> iD8DBQFHYL1pc5UpGjwzenMRAqErAJ9jj1KgVVSGIf+DtK7Km/+JBaDu2QCaAkl/
>>> eMi+WCEWK6FPpVMpUbo+RBQ=
>>> =huvz
>>> -----END PGP SIGNATURE-----
>>> 
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> -- 
>> Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> 
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 

-- 
View this message in context: http://www.nabble.com/S4-class-extending-data.frame--tp14310126p14355388.html
Sent from the R devel mailing list archive at Nabble.com.



[Rd] S4 class extending data.frame?
Ben Bolker