[R-sig-ME] Mixed model parameterization

[Thierry Onkelinx]

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
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<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
>
>

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