[R-sig-ME] Mixed model parameterization

Tue May 21 22:48:55 CEST 2019

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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