Models with different fixed effects estimated by REML cannot be compared by anova.
In future, please post questions on mixed effects models on the r-sig-mixed-effects mailing lists. You're likely to receive more informative replies there, too. -- Bert On Wed, Aug 22, 2012 at 7:23 AM, Rainer M Krug <r.m.k...@gmail.com> wrote: > Hi > > I am comparing four different linear mixed effect models, derived from > updating the original one. To compare these, I want to use anova(). I > therefore do the following (not reproducible - just to illustration > purpose!): > > dat <- loadSPECIES(SPECIES) > subs <- expression(dead==FALSE & recTreat==FALSE) > feff <- noBefore~pHarv*year # fixed effect in the model > reff <- ~year|plant # random effect in the model, where year is > the > corr <- corAR1(form=~year|plant) # describing the within-group correlation > structure > # > dat.lme <- lme( > fixed = feff, # fixed effect in the > model > data = dat, > subset = eval(subs), > method = "ML", > random = reff, # random effect in the > model > correlation = corr, > na.action = na.omit > ) > dat.lme.r1 <- update(dat.lme, random=~1|plant) > dat.lme.f1 <- update(dat.lme, fixed=noBefore~year) > dat.lme.r1.f1 <- update(dat.lme.r1, fixed=noBefore~year) > > > The anova is as follow: > >> anova(dat.lme, dat.lme.r1, dat.lme.f1, dat.lme.r1.f1) > Model df AIC BIC logLik Test L.Ratio > p-value > dat.lme 1 9 1703.218 1733.719 -842.6089 > dat.lme.r1 2 7 1699.218 1722.941 -842.6089 1 vs 2 1.019230e-07 > 1 > dat.lme.f1 3 7 1705.556 1729.279 -845.7779 > dat.lme.r1.f1 4 5 1701.556 1718.501 -845.7779 3 vs 4 8.498318e-08 > 1 > > I have two questions: > 1) I am wondering why the "2 vs 3" does not give the Test values? > Is this because the two models are considered as "identical", which would be > strange, due to the different logLik values. > > 2) If I want to compare all models among each other - is there a "best" way? > I would be reluctant to do several ANOVA's, due to necessary corrections for > multple tests (although this should not be a problem here?) > > I can obviously select the best model based on the AIC. > > Thanks in advance, > > Rainer > > -- > Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, > UCT), Dipl. Phys. (Germany) > > Centre of Excellence for Invasion Biology > Stellenbosch University > South Africa > > Tel : +33 - (0)9 53 10 27 44 > Cell: +33 - (0)6 85 62 59 98 > Fax : +33 - (0)9 58 10 27 44 > > Fax (D): +49 - (0)3 21 21 25 22 44 > > email: rai...@krugs.de > > Skype: RMkrug > > ______________________________________________ > 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm ______________________________________________ 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.
