From lecoutre at stat.ucl.ac.be  Thu Sep 30 15:06:53 2004
From: lecoutre at stat.ucl.ac.be (Eric Lecoutre)
Date: Thu Sep 30 15:12:00 2004
Subject: [Rd] Problem with _new_ if class "lm" in object representatio n.
In-Reply-To: <415BFD9F.2080101@molgen.mpg.de>
References: <18D602BD42B7E24EB810D6454A58DB900A29BB79@ibfftce505.de.ad.drkw.net>
	<415BFD9F.2080101@molgen.mpg.de>
Message-ID: <6.0.1.1.2.20040930145247.01faaec0@stat4ux.stat.ucl.ac.be>


Hi,

For your lm problem, you could begin to create a virtual class that accepts 
either NULL or a lm object:

 > setClassUnion("mylm", c("NULL","lm"))
 > setClass("foo", representation(x="numeric", y="mylm"))
 > new("foo",x=1,y=NULL)

Then, you have to check the content of slot y in any function that will 
manipulate objects of class "foo":


         setMethod("show","foo",function(object)
         {
         cat("\n object of class foo")
         if (!is.null(object@y)) cat(" does have a lm object in slot y!")
         })


Eric


At 14:35 30/09/2004, Witold Eryk Wolski wrote:
>Hi,
>
>But "any" rises some other problems well known from S3. One has "any" for 
>"free" in S3. You don't need S4. . But I know how "if" polluted 
>functions  look like in S3. They are hard to understand and  to maintain. 
>Hence I am quite happy to use S4.
>Type-checking is usefull if you program with data. Also if you are on the 
>"C side" of the object. A further problem which I have with "any" is, that 
>lm="any" in setClass tells you exactly ANYthing (and you are back in S3). 
>And thats not what I like.*
>Hence, I do not want to use any in this case.
>
>I think that allowing to assing NULL to a slot will solve some problems 
>which I have with S4 so far.
>
>a) How to express that an a slot content was not assigned so far? J.C. 
>suggest to use character(0), lm(1~1) etc. The problem I have with 
>insterting lm(1~1) in slot mod in my class Ctest are that I have 100000 
>instances of object Ctest. At initialization everyone contains an object 
>lm(1~1). But please  note the following.
>
> > x<-lm(1~1)
> > object.size(x)
>[1] 6388
> > object.size(NULL)
>[1] 0
>
>Unfortunately S4 do not have references. Hence, I can not store a 
>reference to a single instance of lm(1~1) .
>
>Exactly the same problems I have if I want to "delete" an object. For 
>example you like to have a slot  which stores some data which is important 
>if the object is in one state. But if the state of the object changes you 
>do not need that data anymore. Hence, you would like to delete it to get 
>storage.  You can only do it if you have like you suggest "any", but the 
>consequence is "if" polluted code, or using slot(obj,"mod",check=FALSE)<- NULL.
>
>But the documentation for slot states.
>check: " You should never set this to 'FALSE' in normal
>          use, since the result can create invalid objects. "
>
>
>b) The Problem which I have writing intitialization functions like 
>suggested by J.C  is:  Imagine you have an object with twenty slots. You 
>have to write and initialize function with approximately 20 "if"'s. One of 
>the contribution of S4, as mentioned above, is to help you to avoid 
>writing such "if" polluted functions. But as I sometimes forget any role 
>has it's exceptions. So I can live with one function looking ugly in S4 
>instead of having all functions "if" polluted like in case of S3.  The 
>only consequence so far is that I try to avoid to write initialize 
>functions. I do it only in some rare very special cases.
>
>The NULL exception in slot assignement will allow me object initialization 
>using just "new" without providing a "if" polluted function initialize.
>
> > setClass("bar")
>[1] "bar"
> > setClass("foo", representation(x="numeric", y="bar"))
>[1] "foo"
> > new("foo", x=1)
>Error in validObject(.Object) : Invalid "foo" object: Invalid object for 
>slot "y" in class "foo": got class "NULL", should be or extend class "bar"
> >
>
>
>Are there S4 inherent solutions to this questions?
>
>
>Yours.
>/E
>
>*(I would rather compare "any" to the Object class then to null in java. 
>It has a different function.)
>
>Pfaff, Bernhard wrote:
>
>>>Hi,
>>>
>>>Thanks a lot for pointing me to setOldClass().
>>>
>>>What is exactly the point against it, to allow NULL to be a special case 
>>>which can be assigned to any slot? I think in java one can assing null 
>>>to any slot (I do not like java but not because of that).
>>>I am asking because for some objects it may be hard to define something 
>>>equivalent to numeric(0). And even lm(1~1) is not that what I am looking 
>>>for. I would like to have the case
>>>of an unassigned slot (Just think about storage?) even to the expense 
>>>checking every time if the slot is not null.
>>>
>>
>>
>>Hello Eryk,
>>
>>how about "ANY" and checking where suitable/needed if the passed object for
>>"mod" is of class "lm" at a later stage in your code, like in:
>>
>>setClass("Ctest"
>>         ,representation(
>>                 test="character"
>>                 ,bla="character"
>>                 ,mod="ANY"              )
>>         )
>>
>>test1 <- new("Ctest",mod=lm(1~1))
>>is(test1@mod, "lm")
>>
>>test2 <- new("Ctest",test="bla")
>>is(test2@mod, "lm")
>>
>>test3 <- new("Ctest",bla="brum")
>>is(test3@mod, "lm")
>>
>>test4 <- new("Ctest",test="bla",bla="brum")
>>is(test4@mod, "lm")
>>
>> From there on you could use stop() or warning() or whatever you want to
>>return to the user as information which class mod should belong to.
>>
>>HTH,
>>Bernhard
>>
>
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>https://stat.ethz.ch/mailman/listinfo/r-devel

Eric Lecoutre
UCL /  Institut de Statistique
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tel: (+32)(0)10473050
lecoutre@stat.ucl.ac.be
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If the statistics are boring, then you've got the wrong numbers. -Edward 
Tufte


[Rd] Problem with _new_ if class "lm" in object representatio n.
Eric Lecoutre