[R-sig-ME] Comparing mixed models
John Fox
j|ox @end|ng |rom mcm@@ter@c@
Wed Jun 19 17:20:07 CEST 2024
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
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>
>
>
> 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
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>
>
>
> --
> 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>
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