[R-sig-ME] Comparing mixed models
Carlos Barboza
c@r|o@@mb@rboz@ @end|ng |rom gm@||@com
Wed Jun 19 17:42:34 CEST 2024
Thank you,
yes I know that, it's the same interpretation when using the summary
function when we have f*x
thank you
Carlos
Em qua., 19 de jun. de 2024 às 12:20, John Fox <jfox using mcmaster.ca> escreveu:
> Dear Carlos,
>
> On 2024-06-19 11:13 a.m., Carlos Barboza wrote:
> >
> > You don't often get email from carlosambarboza using gmail.com. Learn why
> this
> > is important <https://aka.ms/LearnAboutSenderIdentification>
> >
> >
> >
> > Caution: External email.
> >
> >
> > Thank you Jonh for you answer
> > I indeed used contr.sum, contr.poly before to model definition
> > after that I get the same results using any names for the same factors
> > but, what do you exactly mean when testing for factors for differences
> > over the origin?
>
> The context here is models with both numeric and factor predictors.
> Consider a model of the form y ~ x*f, where x is numeric and f is a
> factor. A type-III test for the "main effect" of f tests for differences
> among factor levels where x = 0 (the origin).
>
> More generally, the issues concerning "types" of tests in models with
> linear predictors are sufficiently complicated that discussing them in a
> help file or by email is likely to prove unsatisfactory. See the first
> two references in ?Anova for more details.
>
> I hope this helps,
> John
>
> > best regards
> > Carlos
> >
> >
> > Em qua., 19 de jun. de 2024 às 10:14, John Fox <jfox using mcmaster.ca
> > <mailto:jfox using mcmaster.ca>> escreveu:
> >
> > Dear Carlos,
> >
> > From ?Anova:
> >
> > "Warning
> >
> > Be careful of type-III tests: For a traditional multifactor ANOVA
> model
> > with interactions, for example, these tests will normally only be
> > sensible when using contrasts that, for different terms, are
> orthogonal
> > in the row-basis of the model, such as those produced by contr.sum,
> > contr.poly, or contr.helmert, but not by the default
> > contr.treatment. In
> > a model that contains factors, numeric covariates, and interactions,
> > main-effect tests for factors will be for differences over the
> origin.
> > In contrast (pun intended), type-II tests are invariant with respect
> to
> > (full-rank) contrast coding. If you don't understand this issue, then
> > you probably shouldn't use Anova for type-III tests."
> >
> > I hope this helps,
> > John
> >
> > --
> > John Fox, Professor Emeritus
> > McMaster University
> > Hamilton, Ontario, Canada
> > web: https://www.john-fox.ca/ <https://www.john-fox.ca/>
> > --
> > On 2024-06-18 5:59 a.m., Carlos Barboza wrote:
> > > [You don't often get email from carlosambarboza using gmail.com
> > <mailto:carlosambarboza using gmail.com>. Learn why this is important at
> > https://aka.ms/LearnAboutSenderIdentification
> > <https://aka.ms/LearnAboutSenderIdentification> ]
> > >
> > > Caution: External email.
> > >
> > >
> > > sorry, Anova type III function form car package in R
> > >
> > > Em ter., 18 de jun. de 2024 às 06:59, Carlos Barboza <
> > > carlosambarboza using gmail.com <mailto:carlosambarboza using gmail.com>>
> > escreveu:
> > >
> > >> Dear all,
> > >> why Anova type III function gives different results if I change
> > the names
> > >> of a categorical factor? I suspect that is because contrast type
> > but it's
> > >> something strange get different results using the same data.
> > >> thank you
> > >>
> > >> Em sáb., 7 de mai. de 2016 às 12:26, Carlos Barboza <
> > >> carlosambarboza using gmail.com <mailto:carlosambarboza using gmail.com>>
> > escreveu:
> > >>
> > >>> Dear Dr. Ben Bolker
> > >>>
> > >>> My name is Carlos Barboza and I am a Marine Biologist from the
> > Rio de
> > >>> Janeiro University, Brazil. First it's a pleasure to again have
> the
> > >>> opportunity to send you a message.The reason for it is a simple
> > doubt:
> > >>> Can I compare AIC from:
> > >>>
> > >>> 1. glmmADMB: Density ~ 1 + 1|Site
> > >>>
> > >>> 2. glmmADMB: Density ~ Sector + 1|Site + Cage
> > >>>
> > >>> Note that they have different random and fixed structures. I
> > know that
> > >>> this is not the best choice to model selection but, I think
> > that the AIC
> > >>> values can be compared.
> > >>>
> > >>> thank you very much for your attention
> > >>>
> > >>>
> > >>> is Cage a random effect? Are you intentionally leaving out
> the
> > >>> intercept in the second case (it will be included anyway unless
> you
> > >>> use -1)? In any case, I don't see any obvious reason you can't
> > >>> compare AIC values; see
> > >>>
> > >>>
> >
> https://rawgit.com/bbolker/mixedmodels-misc/master/glmmFAQ.html#can-i-use-aic-for-mixed-models-how-do-i-count-the-number-of-degrees-of-freedom-for-a-random-effect
> <
> https://rawgit.com/bbolker/mixedmodels-misc/master/glmmFAQ.html#can-i-use-aic-for-mixed-models-how-do-i-count-the-number-of-degrees-of-freedom-for-a-random-effect
> >
> > >>>
> > >>> Follow-ups to r-sig-mixed-models using r-project.org
> > <mailto:r-sig-mixed-models using r-project.org>, please ...
> > >>>
> > >>> sorry, yes, cage was included only to examplify a different
> random
> > >>> structure in the second case...it should be coded (1|Site) +
> > (1|Cage)
> > >>> yes, I know that the intercept will be included in the second
> model
> > >>>
> > >>> it's an example of comparing AIC values from mixed models with
> > different
> > >>> fixed and random structures:
> > >>>
> > >>> 1. Density ~ 1 + 1|Site
> > >>>
> > >>> 2. Density ~ Sector + 1|Site + 1|Cage
> > >>>
> > >>> comparing AIC...I beleive that both values can be compared
> > >>>
> > >>> again, thank you very much for your very fast message
> > >>>
> > >>>
> > >>>
> > >>>
> > >>
> > >> --
> > >> Universidade Federal do Rio de Janeiro (UFRJ)
> > >> Instituto de Biodiversidade e Sustentabilidade - NUPEM
> > >> Caixa Postal 119331, CEP 27910-970
> > >> Macaé, RJ, Brazil
> > >> https://www.macae.ufrj.br/nupem/ <
> https://www.macae.ufrj.br/nupem/>
> > >> http://lattes.cnpq.br/3629226944950076
> > <http://lattes.cnpq.br/3629226944950076>
> > >>
> > https://scholar.google.com.br/citations?user=p-PRvd4AAAAJ&hl=pt-BR
> > <https://scholar.google.com.br/citations?user=p-PRvd4AAAAJ&hl=pt-BR>
> > >> https://www.researchgate.net/profile/Carlos_Barboza3
> > <https://www.researchgate.net/profile/Carlos_Barboza3>
> > >>
> > >
> > >
> > > --
> > > Universidade Federal do Rio de Janeiro (UFRJ)
> > > Instituto de Biodiversidade e Sustentabilidade - NUPEM
> > > Caixa Postal 119331, CEP 27910-970
> > > Macaé, RJ, Brazil
> > > https://www.macae.ufrj.br/nupem/ <
> https://www.macae.ufrj.br/nupem/>
> > > http://lattes.cnpq.br/3629226944950076
> > <http://lattes.cnpq.br/3629226944950076>
> > >
> > https://scholar.google.com.br/citations?user=p-PRvd4AAAAJ&hl=pt-BR
> > <https://scholar.google.com.br/citations?user=p-PRvd4AAAAJ&hl=pt-BR>
> > > https://www.researchgate.net/profile/Carlos_Barboza3
> > <https://www.researchgate.net/profile/Carlos_Barboza3>
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > R-sig-mixed-models using r-project.org
> > <mailto:R-sig-mixed-models using r-project.org> mailing list
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> > <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
> >
> >
> >
> > --
> > Universidade Federal do Rio de Janeiro (UFRJ)
> > Instituto de Biodiversidade e Sustentabilidade - NUPEM
> > Caixa Postal 119331, CEP 27910-970
> > Macaé, RJ, Brazil
> > https://www.macae.ufrj.br/nupem/ <https://www.macae.ufrj.br/nupem/>
> > http://lattes.cnpq.br/3629226944950076
> > <http://lattes.cnpq.br/3629226944950076>
> > https://scholar.google.com.br/citations?user=p-PRvd4AAAAJ&hl=pt-BR
> > <https://scholar.google.com.br/citations?user=p-PRvd4AAAAJ&hl=pt-BR>
> > https://www.researchgate.net/profile/Carlos_Barboza3
> > <https://www.researchgate.net/profile/Carlos_Barboza3>
>
>
--
Universidade Federal do Rio de Janeiro (UFRJ)
Instituto de Biodiversidade e Sustentabilidade - NUPEM
Caixa Postal 119331, CEP 27910-970
Macaé, RJ, Brazil
https://www.macae.ufrj.br/nupem/
http://lattes.cnpq.br/3629226944950076
https://scholar.google.com.br/citations?user=p-PRvd4AAAAJ&hl=pt-BR
https://www.researchgate.net/profile/Carlos_Barboza3
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