[R] bug in lme4?
Peter Dalgaard
P.Dalgaard at biostat.ku.dk
Wed Aug 20 11:59:35 CEST 2008
Renaud Lancelot wrote:
> Dear all,
>
> As the maintener of package aod, I thank you for bringing my attention on
> this problem. I will try to alter the code in aod. However, I am not sure to
> be able to do it right now.
>
Looks like it should be fairly easy:
Get rid of
setMethod(f = "AIC", signature = "logLik", ...etc...
Instead, define a (local) function, say AIC1(), and use that inside
setMethod(f = "AIC", signature = "glimML", ....
Redefining methods from stats is just a bad idea. Packages might protect
themselves from it, but command-line behaviour of AIC(ll) is also affected.
> Best regards,
>
> Renaud
>
> 2008/8/20 Martin Maechler <maechler at stat.math.ethz.ch>
>
>
>>>>>>> <Antonio.Gasparrini at lshtm.ac.uk>
>>>>>>> on Wed, 20 Aug 2008 03:03:29 +0100 writes:
>>>>>>>
>> > Dear all,
>> > I found a problem with 'lme4'. Basically, once you load the package
>> 'aod' (Analysis of Overdispersed Data), the functions 'lmer' and 'glmer'
>> don't work anymore:
>>
>> > library(lme4)
>> > (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
>> > (gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 |
>> herd),
>> > family = binomial, data = cbpp))
>> > install.packages("aod")
>> > library(aod)
>> > (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
>> > (gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 |
>> herd),
>> > family = binomial, data = cbpp))
>>
>> > Taking into account that this package is used to perform
>> > similar analyses, this could be a problem.
>>
>> It is a problem, and it *is* a bug;
>> thank you for reporting it, Antonio.
>>
>> Since lme4 uses a NAMESPACE, it could and probably should make
>> sure to protect itself from incompatible function redefinitions
>> such as the one the 'aod' package "provides" :
>>
>> Arguably, the bug is really in package 'aod' rather than 'lme4':
>> 'aod' redefines the AIC() method for 'logLik' objects in a not quite
>> backward-compatible way:
>>
>> The standard method (S3 alas, in package 'stats') is
>>
>> > stats:::AIC.logLik
>> function (object, ..., k = 2)
>> -2 * c(object) + k * attr(object, "df")
>> <environment: namespace:stats>
>>
>> The redefinition from package 'aod' is
>>
>> > selectMethod(AIC, "logLik")
>> Method Definition:
>>
>> function (object, ..., k = 2)
>> {
>> npar <- attr(object, "df")
>> nobs <- attr(object, "nobs")
>> c(AIC = -2 * c(object) + k * npar, AICc = -2 * c(object) +
>> k * npar + 2 * npar * (npar + 1)/(nobs - npar - 1))
>> }
>> <environment: 0x1cd22b80>
>>
>> Signatures:
>> object
>> target "logLik"
>> defined "logLik"
>>
>> which returns a (named) numeric vector of length 2,
>> and the code in lme4 was expecting length 1.
>>
>> As a matter of fact, I even like the idea to extend AIC() to
>> also compute newer versions of AIC; but probably 'aod' should
>> have done so in a different way {maybe with an additional
>> 'kind' argument to the method}.
>>
>> Martin
>>
>> > All the best
>>
>> > Antonio Gasparrini
>> > Public and Environmental Health Research Unit (PEHRU)
>> > London School of Hygiene & Tropical Medicine
>> > Keppel Street, London WC1E 7HT, UK
>> > Office: 0044 (0)20 79272406 - Mobile: 0044 (0)79 64925523
>> > http://www.lshtm.ac.uk/people/gasparrini.antonio (
>> http://www.lshtm.ac.uk/pehru/ )
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
>
>
>
> ------------------------------------------------------------------------
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
More information about the R-help
mailing list