Thank you very much ! Renaud
2008/8/20 Peter Dalgaard <[EMAIL PROTECTED]> > 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 <[EMAIL PROTECTED]> > > > > > >>>>>>> <[EMAIL PROTECTED]> > >>>>>>> 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 > ~~~~~~~~~~ - ([EMAIL PROTECTED]) 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 [[alternative HTML version deleted]]
______________________________________________ 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.