Re: [Rd] factor S4 class is NA when as.character method exists

[Prof Brian Ripley]

On 24/01/2012 17:17, William Dunlap wrote:
Here is code that does make factor() work on a new
class like yours.  It uses Sv3 methods.

Which is necessary as unique() is an S3 generic in the base namespace, 
and creating some other function named 'unique' elsewhere (which is what 
setGeneric does) is ineffective.

   >  setClass("foo", contains="numeric")
   [1] "foo"
   >  as.character.foo<- function(x) paste("x=",x@.Data,sep="")
   >  unique.foo<- function(x, ...) structure(NextMethod("unique"), 
class=class(x))
   >  someFoo<- new("foo", c(11, 13, 11, 13, 12))
   >  str(factor(someFoo))
    Factor w/ 3 levels "x=11","x=12",..: 1 3 1 3 2

It would be nice to have a list of methods that one
needs to define for a new class in order to make it
do the "basic" things you expect.

It would be nice to have a list of such things ... I suspect they depend 
more heavily on the value of 'you' than the class.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com

-----Original Message-----
From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On 
Behalf Of Dan Murphy
Sent: Monday, January 23, 2012 10:31 PM
To: peter dalgaard
Cc: r-devel@r-project.org
Subject: Re: [Rd] factor S4 class is NA when as.character method exists

Thank you for your reply, Peter. But that didn't work either. Continuing
the example:

setGeneric("unique")
setMethod("unique", "foo",  function(x,  incomparables = FALSE, ...){
     y<- callNextMethod(x = getDataPart(x),  incomparables = incomparables,
...)
     new("foo", y)
     })

unique(bar)
An object of class "foo"
[1] 12
factor(bar)
[1]<NA>
Levels: 12

Indeed I had tried stepping through the 'factor' call, but perhaps in an
unsophisticated manner -- I had copied the body of 'factor' to a local
version of the function:

myfactor<- function (x = character(), levels, labels = levels, exclude =
NA,
     ordered = is.ordered(x))
{
     if (is.null(x)) ...
etc.

And 'myfactor' worked as desired:

myfactor(bar)
[1] x= 12
Levels: x= 12

I hypothesized that there might be a deeper interaction of an S4
'as.character' method with base::factor, but, having exhausted my woeful
lack of expertise, I decided to write my original email.

Thanks for your consideration.

Dan

On Mon, Jan 23, 2012 at 8:25 AM, peter dalgaard<pda...@gmail.com>  wrote:


On Jan 23, 2012, at 16:07 , Dan Murphy wrote:

Hello,

'factor' returns<NA>  for my S4 object when the class is given an
"as.character" method. Here is a minimal example:

setClass("foo", contains="numeric")
bar<- new("foo", 12)
factor(bar)
[1] 12
Levels: 12
setMethod("as.character", "foo", function(x) paste("x=", x@.Data))
[1] "as.character"
as.character(bar)
[1] "x= 12"
factor(bar)
[1]<NA>
Levels: 12

I would like to 'aggregate' by my S4 objects, but 'factor' seems to be
getting in the way. Is there an 'as.character' implementation that works
better for S4 classes? I searched help.search("factor S4 class") and
help.search("factor S4 as.character") without success.

Single-stepping the factor call would have shown you that the real problem
is that you don't have a unique() method for your class:

unique(bar)
[1] 12

i.e., you are getting the default numeric method, which returns a numeric
vector, so the levels become as.character(unique(bar)) which is c("12") and
doesn't match any of the values of as.character(bar).

So, either provide a unique() method, or use factor(as.character(bar)).


Thank you.

Dan Murphy

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Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd....@cbs.dk  Priv: pda...@gmail.com



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--
Brian D. Ripley,                  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
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