[R] bug in lme4?

[Peter Dalgaard]

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/ )
>>
>> ______________________________________________
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>> 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.
>>
>>     
>
>
>
>   
> ------------------------------------------------------------------------
>
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>   


-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
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