[R-sig-ME] Mixed model parameterization

[Manuel Spínola]

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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