[R-sig-ME] Mixed model parameterization

Tue May 21 23:10:43 CEST 2019

Hi, pseudoreplication is what random effects model by inducing correlation
among observations grouped by a categortical variable.
Chévere, Joaquín

El mar., 21 de may. de 2019 5:45 PM, Salvador SANCHEZ COLON <
salvadorsanchezcolon using prodigy.net.mx> escribió:

> Apologies for my insistence:
>
>
> "...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). ..."
>
>
> ...and that also assumes that the only effect of random factors is on the
> intercept, but not on the slope of the relationship between the fixed
> factor(s) and the response. Overall, if you want to consider (isolate) all
> the possible random effects that might be involved in your design, you
> would need a very complex model. But you previously suggested that some of
> those factors might not be that important and perhaps may be dismissed; in
> my view, I wonder if some of your dat are actually pseudoreplicates (e.g.,
> measurements at different times of the same day) and, if so, a parsimonious
> way to handle them is by averaging across them and analyzing the average
> values.
>
>
> Best regards,
>
>
> Salvador SÁNCHEZ-COLÓN
>
>
> En Mar, 21 Mayo, 2019 en 14:37, Joaquín Aldabe <joaquin.aldabe using gmail.com>
> escribió:
>
> Para: Manuel Spínola; r-sig-mixed-models using r-project.org
> 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/>
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > 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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