[R-sig-ME] Mixed model parameterization

Tue May 21 21:35:53 CEST 2019

I agree that using the mean you miss a lot of information. The simplest
case would be no interaction between random effects. Say,
(1|month)+(1|day)+(1|hour)+(1|plot). As far as I understand, if you think
that, for example, hour effect depends on the day, then you should consider
a nested structure of randoms effects.

Let us know your progress!

joaquin

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El mar., 21 may. 2019 a las 14:01, Manuel Spínola (<mspinola10 using gmail.com>)
escribió:

> Thank you very much Thierry.
>
> Manuel
>
> El lun., 20 may. 2019 a las 8:59, Thierry Onkelinx (<
> thierry.onkelinx using inbo.be>) escribió:
>
> > Aggregating the data will remove al lot of information. And might
> > introduce bias in case of an unbalanced design.
> >
> > You need to think about the (combination of) variables which have a
> common
> > effect. (1|plot) + (1|plot:hour) assumes a plot effect and an effect of
> > each combination of plot and hour, but no common hour effect.
> >
> > Days are nested in months. The corresponding random effect is (1|month) +
> > (1|month:day). You have (1|day) + (1|day:month) which is nonsense.
> >
> > You really need to do some reading on mixed models. I recommend Zuur et
> al
> > (2009) Mixed Effects Models and Extensions in Ecology with R
> >
> > ir. Thierry Onkelinx
> > Statisticus / Statistician
> >
> > Vlaamse Overheid / Government of Flanders
> > INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> AND
> > FOREST
> > Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> > thierry.onkelinx using inbo.be
> > Havenlaan 88 bus 73, 1000 Brussel
> > www.inbo.be
> >
> >
> >
> ///////////////////////////////////////////////////////////////////////////////////////////
> > To call in the statistician after the experiment is done may be no more
> > than asking him to perform a post-mortem examination: he may be able to
> say
> > what the experiment died of. ~ Sir Ronald Aylmer Fisher
> > The plural of anecdote is not data. ~ Roger Brinner
> > The combination of some data and an aching desire for an answer does not
> > ensure that a reasonable answer can be extracted from a given body of
> data.
> > ~ John Tukey
> >
> >
> ///////////////////////////////////////////////////////////////////////////////////////////
> >
> > <https://www.inbo.be>
> >
> >
> > Op ma 20 mei 2019 om 16:07 schreef Salvador Sánchez-Colón <
> > salvadorsanchezcolon using prodigy.net.mx>:
> >
> >> Hola Manuel:
> >>
> >> If you are not interested in examining the between-hours or between-days
> >> variability, then you might consider analyzing the average of your
> hourly
> >> values and thus simplify the model.
> >>
> >> Best regards,
> >>
> >> Salvador
> >>
> >> Salvador SÁNCHEZ-COLÓN
> >>
> >>
> >> > On May 20, 2019, at 8:54 AM, Manuel Spínola <mspinola10 using gmail.com>
> >> wrote:
> >> >
> >> > Thank you very much Thierry.
> >> >
> >> > I just only want to accomodate the nested repeated measure of my
> >> sampling.
> >> >
> >> > I measure the index at the same plot, several times in an hour,
> several
> >> > days and during several month.
> >> >
> >> > 3 "habitats", within each habitat 12 plots, and on each plot I
> measured
> >> the
> >> > index several times, within hours, several days and several months.
> >> >
> >> > I am not interested in the evolution of the index in time, just to
> >> account
> >> > for the repeated measure of my design (I measured the index hundreds
> of
> >> > time on each plot).
> >> >
> >> > Maybe I don't need to worry about hour, day and month?
> >> >
> >> > Manuel
> >> >
> >> > El lun., 20 may. 2019 a las 2:00, Thierry Onkelinx (<
> >> > thierry.onkelinx using inbo.be>) escribió:
> >> >
> >> >> Dear Manuel,
> >> >>
> >> >> You'll need to think about the structure of your random effects. Your
> >> >> current random effect structure is (1|plot) + (1|plot:hour) +
> >> >> (1|plot:hour:day) + (1|plot:hour:day:month). Which might not be what
> >> you
> >> >> had in mind.
> >> >>
> >> >> Best regards,
> >> >>
> >> >> ir. Thierry Onkelinx
> >> >> Statisticus / Statistician
> >> >>
> >> >> Vlaamse Overheid / Government of Flanders
> >> >> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR
> NATURE
> >> AND
> >> >> FOREST
> >> >> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> >> >> thierry.onkelinx using inbo.be
> >> >> Havenlaan 88 bus 73, 1000 Brussel
> >> >> www.inbo.be
> >> >>
> >> >>
> >> >>
> >>
> ///////////////////////////////////////////////////////////////////////////////////////////
> >> >> To call in the statistician after the experiment is done may be no
> more
> >> >> than asking him to perform a post-mortem examination: he may be able
> >> to say
> >> >> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> >> >> The plural of anecdote is not data. ~ Roger Brinner
> >> >> The combination of some data and an aching desire for an answer does
> >> not
> >> >> ensure that a reasonable answer can be extracted from a given body of
> >> data.
> >> >> ~ John Tukey
> >> >>
> >> >>
> >>
> ///////////////////////////////////////////////////////////////////////////////////////////
> >> >>
> >> >> <https://www.inbo.be>
> >> >>
> >> >>
> >> >> Op za 18 mei 2019 om 01:56 schreef Manuel Spínola <
> >> mspinola10 using gmail.com>:
> >> >>
> >> >>> Dear list members,
> >> >>>
> >> >>> I am measuring an index in plots, in different hours, different
> days,
> >> and
> >> >>> different months in 3 different "habitats".
> >> >>>
> >> >>> 12 plots by "habitats".
> >> >>>
> >> >>> I would like to estimate the mean index in the 3 environments.
> >> >>>
> >> >>> Is this model appropriate to achieve my goal?
> >> >>>
> >> >>> model <- lmer(index ~  habitat + (1 | plot/hour/day/month), data =
> >> mydata,
> >> >>> REML = FALSE)
> >> >>>
> >> >>> Best,
> >> >>>
> >> >>> Manuel
> >> >>>
> >> >>> --
> >> >>> *Manuel Spínola, Ph.D.*
> >> >>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> >> >>> Universidad Nacional
> >> >>> Apartado 1350-3000
> >> >>> Heredia
> >> >>> COSTA RICA
> >> >>> mspinola using una.cr <mspinola using una.ac.cr>
> >> >>> mspinola10 using gmail.com
> >> >>> Teléfono: (506) 8706 - 4662
> >> >>> Personal website: Lobito de río <
> >> >>> https://sites.google.com/site/lobitoderio/>
> >> >>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
> >> >>>
> >> >>>        [[alternative HTML version deleted]]
> >> >>>
> >> >>> _______________________________________________
> >> >>> R-sig-mixed-models using r-project.org mailing list
> >> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >> >>>
> >> >>
> >> >
> >> > --
> >> > *Manuel Spínola, Ph.D.*
> >> > Instituto Internacional en Conservación y Manejo de Vida Silvestre
> >> > Universidad Nacional
> >> > Apartado 1350-3000
> >> > Heredia
> >> > COSTA RICA
> >> > mspinola using una.cr <mspinola using una.ac.cr>
> >> > mspinola10 using gmail.com
> >> > Teléfono: (506) 8706 - 4662
> >> > Personal website: Lobito de río <
> >> https://sites.google.com/site/lobitoderio/>
> >> > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
> >> >
> >> >    [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
> >> > R-sig-mixed-models using r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >>
> >>
>
> --
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> mspinola using una.cr <mspinola using una.ac.cr>
> mspinola10 using gmail.com
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río <
> https://sites.google.com/site/lobitoderio/>
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>
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>
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>

-- 
*Joaquín Aldabe*

Departamento de Sistemas Agrarios y Paisajes Culturales
Centro Universitario de la Región Este, Universidad de la República, Uruguay
Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha

*https://sites.google.com/view/joaquin-aldabe
<https://sites.google.com/view/joaquin-aldabe>*

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