[R-sig-ME] mixed model?
Joaquín Aldabe
joaquin.aldabe at gmail.com
Wed May 3 14:34:54 CEST 2017
Thanks Ben. I'll work on those options.
Cheers,
Joaquin
2017-05-02 19:19 GMT-03:00 Ben Bolker <bbolker at gmail.com>:
>
> It's a little difficult.
> Unless you have very large sample sizes per year or very small noise
> levels, it's quite likely that lme4 and friends will collapse the
> among-year variance to zero in this case, which may be anticonservative.
> You have a variety of choices, none of them super-easy or universally
> appropriate:
>
> - collect more data (hah!)
> - fit year as a fixed effect
> - fit year as a random effect and accept the risk of getting a
> completely pooled model
> - use some form of regularization to push the variance away from zero
> (e.g., blmer)
> - go completely Bayesian/MCMC, e.g. brms/MCMCglmm (you'll probably
> still need an informative prior to get the model to converge)
>
> Someone has also pointed to the GLMM FAQ.
>
> On 17-05-02 01:56 PM, Joaquín Aldabe wrote:
> > Thanks Ben. In this case I considered grass height as continuous. Is it
> > fine to consider year as random effect with only 4 years?
> > Best,
> > Joaquín
> >
> > 2017-05-02 14:49 GMT-03:00 Ben Bolker <bbolker at gmail.com
> > <mailto:bbolker at gmail.com>>:
> >
> > Minor correction: if GrassHeight is a continuous variable then you
> > need (GrassHeight|Field) to model the among-Field variation in the
> > effect of grass height. If GrassHeight is categorical, then
> > (GrassHeight|Field) will also work, but it will fit an unstructured
> > variance-covariance model (n*(n+1)/2 parameters for an n-level
> > categorical predictor), whereas (1|Field/GrassHeight) would fit a
> > (positive) compound-symmetric model for the variation in grass height
> > effects among fields (2 parameters instead of n*(n+1)/2)
> >
> > On Tue, May 2, 2017 at 1:36 PM, Joaquín Aldabe
> > <joaquin.aldabe at gmail.com <mailto:joaquin.aldabe at gmail.com>> wrote:
> > > Thankyou very much Evan. I´ll try that!
> > > Cheers,
> > > Joaquín.
> > >
> > > 2017-05-02 14:17 GMT-03:00 Evan Palmer-Young <ecp52 at cornell.edu
> > <mailto:ecp52 at cornell.edu>>:
> > >
> > >> Joaquin,
> > >> It looks like you could use Year and Field as random effects,
> > since there
> > >> might be variation in bird abundance across years, and similarly,
> > variation
> > >> across fields.
> > >>
> > >> So in this case your model is
> > >> Birdmodel<- glmer(Presence~ GrassHeight * ForestCover + (1|Year) +
> > >> (1|Field), data=BirdData, family = "binomial")
> > >>
> > >> Alternatively you could use Year as a fixed effect, if you are
> > interested
> > >> in particular years.
> > >> Another option is to include interaction terms as random effects,
> eg
> > >> (1|Field:GrassHeight), to allow the effect of GrassHeight to vary
> > across
> > >> fields.
> > >>
> > >>
> > >> On Fri, Apr 28, 2017 at 9:32 AM, Joaquín Aldabe
> > <joaquin.aldabe at gmail.com <mailto:joaquin.aldabe at gmail.com>>
> > >> wrote:
> > >>
> > >>> Dear all, I'm analysing bird presence/absence in 16 grassland
> > fields over
> > >>> 4
> > >>> seasons (different years) and want to know the effect of grass
> > height and
> > >>> forest cover on presence/absence of the species. Grass height
> > varied among
> > >>> season but not forest cover in each field. So we have a spatial
> > dimension
> > >>> and a time dimension. I tried a binomial glm but wonder if I
> > should use
> > >>> generalized linear mixed models with field identity as the
> > random as I
> > >>> have
> > >>> repeated measures (bird counts) in each field.
> > >>>
> > >>> I appreciate your opinion.
> > >>>
> > >>> Thanks in advanced,
> > >>>
> > >>> Joaquin Aldabe.
> > >>>
> > >>> --
> > >>> *Joaquín Aldabe*
> > >>>
> > >>> *Grupo Biodiversidad, Ambiente y Sociedad*
> > >>> Centro Universitario de la Región Este, Universidad de la
> República
> > >>> Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> > >>>
> > >>> *Departamento de Conservación*
> > >>> Aves Uruguay
> > >>> BirdLife International
> > >>> Canelones 1164, Montevideo
> > >>>
> > >>> https://sites.google.com/site/joaquin.aldabe
> > <https://sites.google.com/site/joaquin.aldabe>
> > >>> <https://sites.google.com/site/perfilprofesionaljoaquinaldabe
> > <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>>
> > >>>
> > >>> [[alternative HTML version deleted]]
> > >>>
> > >>> _______________________________________________
> > >>> R-sig-mixed-models at r-project.org
> > <mailto:R-sig-mixed-models at r-project.org> mailing list
> > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> > <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
> > >>
> > >>
> > >>
> > >>
> > >> --
> > >> Evan Palmer-Young
> > >> PhD candidate
> > >> Department of Biology
> > >> 221 Morrill Science Center
> > >> 611 North Pleasant St
> > >> Amherst MA 01003
> > >> https://scholar.google.com/citations?user=VGvOypoAAAAJ&hl=en
> > <https://scholar.google.com/citations?user=VGvOypoAAAAJ&hl=en>
> > >> https://sites.google.com/a/cornell.edu/evan-palmer-young/
> > <https://sites.google.com/a/cornell.edu/evan-palmer-young/>
> > >> epalmery at cns.umass.edu <mailto:epalmery at cns.umass.edu>
> > >> ecp52 at cornell.edu <mailto:ecp52 at cornell.edu>
> > >>
> > >
> > >
> > >
> > > --
> > > *Joaquín Aldabe*
> > >
> > > *Grupo Biodiversidad, Ambiente y Sociedad*
> > > Centro Universitario de la Región Este, Universidad de la República
> > > Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> > >
> > > *Departamento de Conservación*
> > > Aves Uruguay
> > > BirdLife International
> > > Canelones 1164, Montevideo
> > >
> > > https://sites.google.com/site/joaquin.aldabe
> > <https://sites.google.com/site/joaquin.aldabe>
> > > <https://sites.google.com/site/perfilprofesionaljoaquinaldabe
> > <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>>
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > R-sig-mixed-models at r-project.org
> > <mailto:R-sig-mixed-models at r-project.org> mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> > <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
> >
> >
> >
> >
> > --
> > *Joaquín Aldabe*
> >
> > /Grupo Biodiversidad, Ambiente y Sociedad/
> > Centro Universitario de la Región Este, Universidad de la República
> > Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> >
> > /Departamento de Conservación/
> > Aves Uruguay
> > BirdLife International
> > Canelones 1164, Montevideo
> >
> > https://sites.google.com/site/joaquin.aldabe
> > <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>
> >
> >
> >
>
--
*Joaquín Aldabe*
*Grupo Biodiversidad, Ambiente y Sociedad*
Centro Universitario de la Región Este, Universidad de la República
Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
*Departamento de Conservación*
Aves Uruguay
BirdLife International
Canelones 1164, Montevideo
https://sites.google.com/site/joaquin.aldabe
<https://sites.google.com/site/perfilprofesionaljoaquinaldabe>
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