From ripley at stats.ox.ac.uk  Tue May  1 15:33:20 2007
From: ripley at stats.ox.ac.uk (ripley at stats.ox.ac.uk)
Date: Tue,  1 May 2007 15:33:20 +0200 (CEST)
Subject: [Rd] [Fwd: Re: [R-downunder] Beware unclass(factor)] (PR#9641)
Message-ID: <20070501133320.38A0A5DE55@slim.kubism.ku.dk>

It really is unclear what is claimed to be a bug here.  But see

https://stat.ethz.ch/pipermail/r-devel/2007-May/045592.html

for why the bug is not in R: your old and new data do not match.
Your fit is to a category.


[The problem with the web interface to R-bugs was reported last week: it 
is being worked on.]


On Mon, 30 Apr 2007, r.darnell at uq.edu.au wrote:

> This is a multi-part message in MIME format.
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> The following "issue" was found using
>
> > version
>               _
> platform       i386-pc-mingw32
> arch           i386
> os             mingw32
> system         i386, mingw32
> status
> major          2
> minor          4.1
> year           2006
> month          12
> day            18
> svn rev        40228
> language       R
> version.string R version 2.4.1 (2006-12-18)
> >
>
>
> and discussed on the R-downunder mailing list.
>
> I hope I have provided enough info.  I tried to look at the Bugs
> Tracking page but got---
>
>
> The system encountered a fatal error
>
> *
>
> cannot open config file /home/sfe/r-bugs/jitterbug/R : No such file or directory
>
> *
>
> The last error code was: No such file or directory
>
> uid/gid=30/8
>
>
> Regards
>
> Ross Darnell
>
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> Date: Mon, 30 Apr 2007 19:25:09 +1000
> From: John Maindonald <john.maindonald at anu.edu.au>
> Subject: Re: [R-downunder] Beware unclass(factor)
> In-reply-to: <46359373.50504 at uq.edu.au>
> To: Ross Darnell <r.darnell at uq.edu.au>
> Cc: r-downunder at stat.auckland.ac.nz
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>
> Observe the following
>
> > z <- model.frame(cbind(moths,(20-moths)) ~sex+ doselin,data=worms)
> > class(z$doselin)
> [1] "other"
> > levels(z$doselin)
> [1] "1"  "2"  "4"  "8"  "16" "32"
> > attributes(z$doselin)
> $levels
> [1] "1"  "2"  "4"  "8"  "16" "32"
>
> $class
> [1] "other"
>
> The problem surfaces in the call for model.frame() from predict.lm()
> when it is called by predict.glm().  This call is jumping to conclusions
> when it uses the presence of a levels attribute as an indication that
> doselin is a factor, ironic as it was the call that was initiated by glm
> that seems to have given the column doselin of the object returned
> by model.frame() the class "other".
>
> This seems to me to be a bug. The call to unclass() does not
> strip the levels attribute from doselin.  (This is not, I think, the
> bug; rather the problem is in the model matrix that is created.)
> The column worms$doselin does though have class "integer",
> at least as far as the function class() is concerned.
>
> You can fix the problem by setting:
>
>   worms$doselin <- as.vector(unclass(worms$Dose))
>
> This strips off the levels attribute.
>
> In my view model.frame ought to have stripped the levels
> attribute from the column doselin in the object that it
> returned.
>
> I consider that this should be reported as a bug, or at least
> as an undesirable feature.
>
> John Maindonald             email: john.maindonald at anu.edu.au
> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
> Centre for Mathematics & Its Applications, Room 1194,
> John Dedman Mathematical Sciences Building (Building 27)
> Australian National University, Canberra ACT 0200.
>
>
> On 30 Apr 2007, at 4:57 PM, Ross Darnell wrote:
>
>> Just an observation about the use of unclass() to generate codes
>> for factors.
>>
>> As an example take the  dataset from the MASS4 book
>>
>>> worms <- data.frame(sex=gl(2,6),Dose=factor(rep(2^(0:5),
>> 2)),moths=c(1,4,9,13,18,20,0,2,6,10,12,16))
>>
>>> worms$doselin <- unclass(worms$Dose)
>>
>>> worms.glm <- glm(cbind(moths,(20-moths)) ~sex+
>> doselin,data=worms,family=binomial)
>>
>>> predict(worms.glm,new=data.frame(sex="1",doselin=6))
>> Error: variable 'doselin' was fitted with class "other" but class
>> "numeric" was supplied
>> In addition: Warning message:
>> variable 'doselin' is not a factor in: model.frame.default(Terms,
>> newdata, na.action = na.action, xlev = object$xlevels)
>>>
>>
>>
>> The /doselin/ vector is "atomic" --- good enough for the glm()
>> function but not acceptable by predict()
>>
>>> str(worms$doselin)
>> atomic [1:12] 1 2 3 4 5 6 1 2 3 4 ...
>> - attr(*, "levels")= chr [1:6] "1" "2" "4" "8" ...
>>>
>>
>> Cheers
>>
>> Ross Darnell
>>
>> --
>> R-downunder at stat.auckland.ac.nz
>> http://www.stat.auckland.ac.nz/r-downunder
>>
>> To unsubscribe send an email to R-downunder-
>> unsubscribe at stat.auckland.ac.nz
>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] [Fwd: Re: [R-downunder] Beware unclass(factor)] (PR#9641)
ripley at stats.ox.ac.uk