R devel - Mar 2011 - Problem with defining new method for residuals()

Dear all,

I'm writing a package and I would like to reuse the residuals() function.
When I use a function which calls the redefined residuals (for my custom class)
I get an error (see below). It looks like the wrong method is used. The strange
this is, that when it execute the code manually it get no error.

Any suggestions?

Best regards,

Thierry

The entire source code is at svn://scm.r-forge.r-project.org/svnroot/aflp

The code with the error.
> normalise(dummy)
Error in object$na.action : $ operator not defined for this S4
class
> traceback()
5: naresid(object$na.action, object$residuals) at normalise.R#30
4: residuals.default(outliers(data)) at normalise.R#30
3: residuals(outliers(data)) at normalise.R#30
2: nrow(residuals(outliers(data))) at normalise.R#30
1: normalise(dummy)
#This works fine
> data <- dummy
> nrow(residuals(outliers(data)))
[1] 0

NAMESPACE
importFrom(stats, residuals, resid, hclust, princomp)
exportPattern(".")

METHODS
setMethod("residuals", signature(object = "AFLP.outlier"), 
	function(object, ...){
		object at Residual
	}
)

setMethod("resid", signature(object = "AFLP.outlier"), 
	function(object, ...){
		object at Residual
	}
)

----------------------------------------------------------------------------
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium

Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium

tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey

On 03/10/2011 08:21 AM, ONKELINX, Thierry wrote:
> Dear all,
> 
> I'm writing a package and I would like to reuse the residuals()
> function. When I use a function which calls the redefined residuals
> (for my custom class) I get an error (see below). It looks like the
> wrong method is used. The strange this is, that when it execute the
> code manually it get no error.
Hi Thierry --

I think this is a bug in the methods package.

Your package promotes stats::residuals to an S4 generic. Normally this
should work.

However, your package Depends: on lme4, which also promotes
stats::residuals to an S4 generic. Apparently, this interferes with your
own attempt to make a generic, even though you do not import lme4 into
your name space. As a consequence of the (putative) bug, your package
sees the original stats::residuals.

A work-around seems to be to importFrom(lme4, residuals) and do NOT
import residuals from stats, so that your own method is associated with
the generic defined in lme4.

Martin
> 
> Any suggestions?
> 
> Best regards,
> 
> Thierry
> 
> The entire source code is at
> svn://scm.r-forge.r-project.org/svnroot/aflp
> 
> The code with the error.
> 
>> normalise(dummy)
> Error in object$na.action : $ operator not defined for this S4 class
>> traceback()
> 5: naresid(object$na.action, object$residuals) at normalise.R#30 4:
> residuals.default(outliers(data)) at normalise.R#30 3:
> residuals(outliers(data)) at normalise.R#30 2:
> nrow(residuals(outliers(data))) at normalise.R#30 1:
> normalise(dummy) #This works fine
>> data <- dummy nrow(residuals(outliers(data)))
> [1] 0
> 
> NAMESPACE importFrom(stats, residuals, resid, hclust, princomp) 
> exportPattern(".")
> 
> METHODS setMethod("residuals", signature(object =
"AFLP.outlier"),
> function(object, ...){ object at Residual } )
> 
> setMethod("resid", signature(object = "AFLP.outlier"), 
> function(object, ...){ object at Residual } )
> 
>
----------------------------------------------------------------------------
>
> 
ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek team Biometrie &
> Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium
> 
> Research Institute for Nature and Forest team Biometrics & Quality
> Assurance Gaverstraat 4 9500 Geraardsbergen Belgium
> 
> tel. + 32 54/436 185 Thierry.Onkelinx at inbo.be www.inbo.be
> 
> To call in the statistician after the experiment is done may be no
> more than asking him to perform a post-mortem examination: he may be
> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> 
> The plural of anecdote is not data. ~ Roger Brinner
> 
> The combination of some data and an aching desire for an answer does
> not ensure that a reasonable answer can be extracted from a given
> body of data. ~ John Tukey
> 
> ______________________________________________ R-devel at r-project.org
> mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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