Thank you very much !

Renaud

2008/8/20 Peter Dalgaard <P.Dalgaard@biostat.ku.dk>

> 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@stat.math.ethz.ch>
> >
> >
> >>>>>>>   <Antonio.Gasparrini@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@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@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@biostat.ku.dk)              FAX: (+45) 35327907
>
>
>


-- 
Renaud LANCELOT
Département Systèmes Biologiques du CIRAD
CIRAD, Biological Systems Department

Campus International de Baillarguet
TA 30 / B
F34398 Montpellier
Tel +33 (0)4 67 59 37 17
Secr. +33 (0)4 67 59 37 37
Fax +33 (0)4 67 59 37 95

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