[Rd] package methods different behaviour R1.9.1 patched and R2.0.0

[Wolski]

Hello!

A simple example.

setClass("myclass"
,representation(info="character")
,contains="matrix"
)

setAs("myclass","vector"
,def=function(from)
{
	print("enters?")
	to<-summary(from[,1])
	to<-as.vector(to)
	to
}
)

#init
dd<-matrix(1:6,nrow=2)
rownames(dd)<-c("a","b")
tt<-new("myclass",dd)

class(tt)
as(tt,"vector")
summary(dd[,1])

What I expect.
R : Copyright 2004, The R Foundation for Statistical Computing
Version 1.9.1 Patched (2004-08-30), ISBN 3-900051-00-3

> class(tt)
[1] "myclass"
attr(,"package")
[1] ".GlobalEnv"
> as(tt,"vector")
[1] "enters?"
[1] 1.00 1.25 1.50 1.50 1.75 2.00
> summary(dd[,1])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.25    1.50    1.50    1.75    2.00 


R : Copyright 2004, The R Foundation for Statistical Computing
Version 2.0.0 Under development (unstable) (2004-09-06), ISBN 3-900051-07-0

> class(tt)
[1] "myclass"
attr(,"package")
[1] ".GlobalEnv"
> as(tt,"vector")
[1] 1 2 3 4 5 6
> summary(dd[,1])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.25    1.50    1.50    1.75    2.00 

Yours
Eryk




*********** REPLY SEPARATOR  ***********

On 9/7/2004 at 10:34 AM John Chambers wrote:

>>>It's not possible to tell what you're expecting or actually seeing
>>>from
>>>this mail.   We need to see your code and the results, not your
>>>interpretation of how as() is implemented.
>>>
>>>Meanwhile, here's how a simple class that extends "matrix" works in
>>>2.0.0
>>>
>>>With the code:
>>>
>>> setClass("mat1", representation(id="character"), contains = "matrix")
>>>
>>> mm <- matrix(1:12,3,4)
>>>
>>> mmm <- new("mat1", mm, id = "numeric")
>>>
>>>The result is:
>>>
>>>R> as(mmm, "vector")
>>> [1]  1  2  3  4  5  6  7  8  9 10 11 12
>>>
>>>Class "vector" is one of the basic R classes;  as explained in ?as, the
>>>methods for these use the exisiting as.<class> functions, as.vector in
>>>this case.  
>>>
>>>The result is indeed the same as coercing mmm to "matrix" first and then
>>>to vector
>>>
>>>R> as(as(mmm, "matrix"), "vector")
>>> [1]  1  2  3  4  5  6  7  8  9 10 11 12
>>>
>>>as one would expect, but the method for coercing class "mat1" does not
>>>go through "matrix":
>>>
>>>R> selectMethod("coerce", c("mat1", "vector"))
>>>function (from, to, strict = TRUE) 
>>>{
>>>    value <- as.vector(from)
>>>    if (strict) 
>>>        attributes(value) <- NULL
>>>    value
>>>}
>>><environment: namespace:methods>
>>>
>>>
>>>
>>>Wolski wrote:
>>>> 
>>>> Hi!
>>>> 
>>>> Concerning different behaviour between 1.9.1 patched and:
>>>> R : Copyright 2004, The R Foundation for Statistical Computing
>>>> Version 2.0.0 Under development (unstable) (2004-09-06), ISBN
>>>3-900051-07-0
>>>> 
>>>> Subtitle:
>>>> as(x,"vector"); x is of class "Massvector"; never enters
>>>setAs("Massvector","vector"...
>>>> 
>>>> The same code:
>>>> 
>>>> as(mvl[[1]],"vector")
>>>> causes under R1.9.1 to enter the function
>>>> setAs("Massvector","vector"
>>>>       ,function(from)
>>>> ...
>>>> 
>>>> This never happens under R2.0.0.
>>>> 
>>>> The class "Massvector" contains class "Matrix"
>>>> 
>>>> A phenomenological description of what happens instead with R2.0.0 is
>>>> 
>>>> as(as(mvl[[1]],"Matrix"),"vector")
>>>> 
>>>> and its not what I would expect.
>>>> 
>>>> Is this an intended behaviour in R2.0.0?
>>>> 
>>>> /E
>>>> 
>>>> ______________________________________________
>>>> R-devel at stat.math.ethz.ch mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>-- 
>>>John M. Chambers                  
>>>Bell Labs, Lucent Technologies    office: (908)582-2681
>>>700 Mountain Avenue, Room 2C-282  fax:    (908)582-3340
>>>Murray Hill, NJ  07974



Dipl. bio-chem. Witold Eryk Wolski             @         MPI-Moleculare Genetic   
Ihnestrasse 63-73 14195 Berlin                'v'    
tel: 0049-30-83875219                        /   \       
mail: witek96 at users.sourceforge.net        ---W-W----    http://www.molgen.mpg.de/~wolski 
      wolski at molgen.mpg.de