Message-ID: <CAMM93=JOiZwshHyve-vRFXqhBtNXOM1c+vvTXiC078rT=48JUg@mail.gmail.com>
Date: 2019-05-21T22:43:52Z
From: Joaquín Aldabe
Subject: Mixed model parameterization
In-Reply-To: <CABkCotQAfAwWxNDG99PWc=e_eSQU3pSr-AJJDMGXgDpVyfLvgw@mail.gmail.com>
You can also try the function corr and assess the effect of diferent
correlation structures. And consider AIC or BIC for model selection.
El mar., 21 de may. de 2019 7:15 PM, Manuel Sp?nola <mspinola10 at gmail.com>
escribi?:
> Thank you very much Salvador.
>
> Yes, I think most of my data are pseudoreplicates, the sampling unit was
> the plot and there was several measurements through time at the plot. This
> is why I was thinking in the mixed model to take into account the structure
> of my data.
>
> Maybe I don?t need to think in hour, day and month and use:
>
> model <- lmer(index ~ habitat + (1 | plot), data = mydata, REML = FALSE)
>
>
> Manuel
>
> El mar., 21 may. 2019 a las 14:45, Salvador SANCHEZ COLON (<
> salvadorsanchezcolon at prodigy.net.mx>) escribi?:
>
>> 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 S?NCHEZ-COL?N
>>
>>
>> En Mar, 21 Mayo, 2019 en 14:37, Joaqu?n Aldabe <joaquin.aldabe at gmail.com>
>> escribi?:
>>
>> Para: Manuel Sp?nola; r-sig-mixed-models at 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
>>
>> <
>> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> >
>> Libre
>> de virus. www.avast.com
>> <
>> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> >
>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>> El mar., 21 may. 2019 a las 14:01, Manuel Sp?nola (<mspinola10 at gmail.com
>> >)
>> escribi?:
>>
>> > Thank you very much Thierry.
>> >
>> > Manuel
>> >
>> > El lun., 20 may. 2019 a las 8:59, Thierry Onkelinx (<
>> > thierry.onkelinx at inbo.be>) escribi?:
>> >
>> > > 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 at 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 S?nchez-Col?n <
>> > > salvadorsanchezcolon at 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 S?NCHEZ-COL?N
>> > >>
>> > >>
>> > >> > On May 20, 2019, at 8:54 AM, Manuel Sp?nola <mspinola10 at 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 at inbo.be>) escribi?:
>> > >> >
>> > >> >> 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 at 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 Sp?nola <
>> > >> mspinola10 at 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 Sp?nola, Ph.D.*
>> > >> >>> Instituto Internacional en Conservaci?n y Manejo de Vida
>> Silvestre
>> > >> >>> Universidad Nacional
>> > >> >>> Apartado 1350-3000
>> > >> >>> Heredia
>> > >> >>> COSTA RICA
>> > >> >>> mspinola at una.cr <mspinola at una.ac.cr>
>> > >> >>> mspinola10 at gmail.com
>> > >> >>> Tel?fono: (506) 8706 - 4662
>> > >> >>> Personal website: Lobito de r?o <
>> > >> >>> https://sites.google.com/site/lobitoderio/>
>> > >> >>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>> > >> >>>
>> > >> >>> [[alternative HTML version deleted]]
>> > >> >>>
>> > >> >>> _______________________________________________
>> > >> >>> R-sig-mixed-models at r-project.org mailing list
>> > >> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> > >> >>>
>> > >> >>
>> > >> >
>> > >> > --
>> > >> > *Manuel Sp?nola, Ph.D.*
>> > >> > Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
>> > >> > Universidad Nacional
>> > >> > Apartado 1350-3000
>> > >> > Heredia
>> > >> > COSTA RICA
>> > >> > mspinola at una.cr <mspinola at una.ac.cr>
>> > >> > mspinola10 at gmail.com
>> > >> > Tel?fono: (506) 8706 - 4662
>> > >> > Personal website: Lobito de r?o <
>> > >> https://sites.google.com/site/lobitoderio/>
>> > >> > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>> > >> >
>> > >> > [[alternative HTML version deleted]]
>> > >> >
>> > >> > _______________________________________________
>> > >> > R-sig-mixed-models at r-project.org mailing list
>> > >> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> > >>
>> > >>
>> >
>> > --
>> > *Manuel Sp?nola, Ph.D.*
>> > Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
>> > Universidad Nacional
>> > Apartado 1350-3000
>> > Heredia
>> > COSTA RICA
>> > mspinola at una.cr <mspinola at una.ac.cr>
>> > mspinola10 at gmail.com
>> > Tel?fono: (506) 8706 - 4662
>> > Personal website: Lobito de r?o <
>> > https://sites.google.com/site/lobitoderio/>
>> > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > R-sig-mixed-models at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> >
>>
>>
>> --
>> *Joaqu?n Aldabe*
>>
>> Departamento de Sistemas Agrarios y Paisajes Culturales
>> Centro Universitario de la Regi?n Este, Universidad de la Rep?blica,
>> 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>*
>>
>>
>> <
>> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> >
>> Libre
>> de virus. www.avast.com
>> <
>> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> >
>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> .
>>
>
>
> --
> *Manuel Sp?nola, Ph.D.*
> Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> mspinola at una.cr <mspinola at una.ac.cr>
> mspinola10 at gmail.com
> Tel?fono: (506) 8706 - 4662
> Personal website: Lobito de r?o
> <https://sites.google.com/site/lobitoderio/>
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>
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