[R-sig-ME] mixed model?
Evan Palmer-Young
ecp52 at cornell.edu
Tue May 2 21:11:13 CEST 2017
Ah, I saw in another thread the link to the updated version, now in github:
http://bbolker.github.io/mixedmodels-misc/glmmFAQ.html#nested-or-crossed
On Tue, May 2, 2017 at 3:03 PM, Evan Palmer-Young <ecp52 at cornell.edu> wrote:
> There is a thorough but readable discussion of the fixed-or-random
> consideration at the glmm wiki.
> http://glmm.wikidot.com/faq, administrated by Prof. Bolker.
> See the heading:
> Should I treat factor xxx as fixed or random?
> You'll also find plenty of useful tips for model coding and
> troubleshooting, consideration of p-values, and a separate page for package
> comparison.
> http://glmm.wikidot.com/pkg-comparison
>
> On Tue, May 2, 2017 at 1:56 PM, Joaquín Aldabe <joaquin.aldabe at gmail.com>
> 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>:
>>
>>> 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>
>>> 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>:
>>> >
>>> >> 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>
>>> >> 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/perfilprofesionaljoaquinaldabe>
>>> >>>
>>> >>> [[alternative HTML version deleted]]
>>> >>>
>>> >>> _______________________________________________
>>> >>> R-sig-mixed-models at r-project.org mailing list
>>> >>> 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://sites.google.com/a/cornell.edu/evan-palmer-young/
>>> >> epalmery at cns.umass.edu
>>> >> 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/perfilprofesionaljoaquinaldabe>
>>> >
>>> > [[alternative HTML version deleted]]
>>> >
>>> > _______________________________________________
>>> > R-sig-mixed-models at r-project.org mailing list
>>> > 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>
>>
>>
>>
>>
>
>
> --
> 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://sites.google.com/a/cornell.edu/evan-palmer-young/
> epalmery at cns.umass.edu
> ecp52 at cornell.edu
>
--
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://sites.google.com/a/cornell.edu/evan-palmer-young/
epalmery at cns.umass.edu
ecp52 at cornell.edu
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