Corina
2015-Jul-18 05:30 UTC
[R] Why does dredge() rank models differently for lmer() and MCMCglmm()?
Hello, I am running my full model (fm) through lmer() and MCMCglmm() using the default settings: model.lmer <- lmer(fm) model.MCMCglmm <- MCMCglmm(fm) And the summary outputs are almost exactly the same: summary(model.lmer) summary(model.MCMCglmm) However, when I run the models through dredge(): dredge(model.lmer) dredge(model.MCMCglmm) It ranks the models very differently for lmer() and MCMCglmm() in the model selection tables, even though I used the default settings for dredge() as well (ranked by AICc). I would assume the difference is because lmer() uses REML and MCMCglmm() uses Bayes Rule, however if this is the case then why weren?t the summary outputs different as well? I have checked through the documentation for all of the associated R packages and searched the R forums and Google for the answer, but I haven?t seen this question addressed. I would be grateful if someone could let me know why this happens. Thanks in advance! Corina -- View this message in context: http://r.789695.n4.nabble.com/Why-does-dredge-rank-models-differently-for-lmer-and-MCMCglmm-tp4710020.html Sent from the R help mailing list archive at Nabble.com.
Ben Bolker
2015-Jul-18 17:03 UTC
[R] Why does dredge() rank models differently for lmer() and MCMCglmm()?
Corina <itsme <at> CorinaLogan.com> writes:> > Hello, > I am running my full model (fm) through lmer() and MCMCglmm() using the > default settings: > > model.lmer <- lmer(fm) > model.MCMCglmm <- MCMCglmm(fm) >[snip]> However, when I run the models through dredge(): > > dredge(model.lmer) > dredge(model.MCMCglmm)> It ranks the models very differently for lmer() and MCMCglmm() in > the model selection tables, even though I used the default settings > for dredge() as well (ranked by AICc). I would assume the difference > is because lmer() uses REML and MCMCglmm() uses Bayes Rule, however > if this is the case then why weren?t the summary outputs different > as well?[snip] This question *might* be better on r-sig-mixed-models at r-project.org ... You shouldn't be comparing models with fixed effects that are fitted with REML -- try refitting with REML=FALSE. The model comparison functions in the lme4 package (e.g. anova()) try to stop you from making this mistake, but I'm not sure the MuMIn::dredge does.
Bert Gunter
2015-Jul-18 20:23 UTC
[R] Why does dredge() rank models differently for lmer() and MCMCglmm()?
(slightly off topic) One might also add that different model fitting criteria might produce rankings that are quite different, but with model predictions that are very similar. This reflects the inconvenient reality that empirical models are merely data interpolators and not representations of "truth." Ergo quite different looking models might fit essentially equally well, the differences in fits and therefore rankings being nothing more than noise. Cheers, Bert Bert Gunter "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." -- Clifford Stoll On Sat, Jul 18, 2015 at 10:03 AM, Ben Bolker <bbolker at gmail.com> wrote:> Corina <itsme <at> CorinaLogan.com> writes: > >> >> Hello, >> I am running my full model (fm) through lmer() and MCMCglmm() using the >> default settings: >> >> model.lmer <- lmer(fm) >> model.MCMCglmm <- MCMCglmm(fm) >> > > [snip] > >> However, when I run the models through dredge(): >> >> dredge(model.lmer) >> dredge(model.MCMCglmm) > >> It ranks the models very differently for lmer() and MCMCglmm() in >> the model selection tables, even though I used the default settings >> for dredge() as well (ranked by AICc). I would assume the difference >> is because lmer() uses REML and MCMCglmm() uses Bayes Rule, however >> if this is the case then why weren?t the summary outputs different >> as well? > > [snip] > > This question *might* be better on r-sig-mixed-models at r-project.org ... > You shouldn't be comparing models with fixed effects that are fitted > with REML -- try refitting with REML=FALSE. The model comparison > functions in the lme4 package (e.g. anova()) try to stop you from > making this mistake, but I'm not sure the MuMIn::dredge does. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.
Corina
2015-Jul-21 09:20 UTC
[R] Why does dredge() rank models differently for lmer() and MCMCglmm()?
Hi Ben, Thank you so much for your helpful advice! I changed the lmer model to REML=FALSE and the best-fitting model in dredge is MUCH more similar to what I found with MCMCglmm. My best, Corina -- Dr. Corina Logan Leverhulme Early Career Research Fellow Department of Zoology University of Cambridge itsme at CorinaLogan.com www.CorinaLogan.com On Jul 18, 2015, at 18:06, bbolker [via R] <ml-node+s789695n4710029h10 at n4.nabble.com> wrote: Corina <itsme <at> CorinaLogan.com> writes:> > Hello, > I am running my full model (fm) through lmer() and MCMCglmm() using the > default settings: > > model.lmer <- lmer(fm) > model.MCMCglmm <- MCMCglmm(fm) >[snip]> However, when I run the models through dredge(): > > dredge(model.lmer) > dredge(model.MCMCglmm)> It ranks the models very differently for lmer() and MCMCglmm() in > the model selection tables, even though I used the default settings > for dredge() as well (ranked by AICc). I would assume the difference > is because lmer() uses REML and MCMCglmm() uses Bayes Rule, however > if this is the case then why weren?t the summary outputs different > as well?[snip] This question *might* be better on [hidden email] <x-msg://2/user/SendEmail.jtp?type=node&node=4710029&i=0> ... You shouldn't be comparing models with fixed effects that are fitted with REML -- try refitting with REML=FALSE. The model comparison functions in the lme4 package (e.g. anova()) try to stop you from making this mistake, but I'm not sure the MuMIn::dredge does. ______________________________________________ [hidden email] <x-msg://2/user/SendEmail.jtp?type=node&node=4710029&i=1> mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help <https://stat.ethz.ch/mailman/listinfo/r-help> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html <http://www.r-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code. If you reply to this email, your message will be added to the discussion below: http://r.789695.n4.nabble.com/Why-does-dredge-rank-models-differently-for-lmer-and-MCMCglmm-tp4710020p4710029.html <http://r.789695.n4.nabble.com/Why-does-dredge-rank-models-differently-for-lmer-and-MCMCglmm-tp4710020p4710029.html> To unsubscribe from Why does dredge() rank models differently for lmer() and MCMCglmm()?, click here <http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4710020&code=aXRzbWVAQ29yaW5hTG9nYW4uY29tfDQ3MTAwMjB8LTIwNjUwNjEyMzQ=>. NAML <http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> -- View this message in context: http://r.789695.n4.nabble.com/Why-does-dredge-rank-models-differently-for-lmer-and-MCMCglmm-tp4710020p4710129.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]]