[R-sig-ME] modeling question
Joaquín Aldabe
joaquin.aldabe at gmail.com
Thu Jan 26 20:11:45 CET 2017
Thanks Ben, I sent all emails to the whole list. See below (in caps lock
for differentiating from the other text). Regards, Joaquin
2017-01-26 15:59 GMT-03:00 Ben Bolker <bbolker at gmail.com>:
> On Thu, Jan 26, 2017 at 9:38 AM, Joaquín Aldabe
> <joaquin.aldabe at gmail.com> wrote:
> > Dear Ben, it's me again
>
>
> (I don't mind if you cc: me, but this is really a question to the
> list. Probably better to frame it as "I sent this to the list and Ben
> Bolker said ...")
>
> > with this subject about invertebrate biomass and its
> > possible effect on shorebird density. I have a couple of extra doubts
> about
> > your recommendations:
>
>
> >
> > You suggested this:
> >
> > (1) The relationship between bird density and invert biomass, as well
> > as the intercept (i.e., expected bird density at invert_biomass=0, or
> > better invert_biomass=<some sensible reference quantity>).
> >
> > I tried a quantity considering the lowest value of the invertebrate
> biomass
> > variable, but the model did not converge. So I wonder if I should pick
> this
> > value or a different one?
>
> Hmm, is this with lme or lmer? Can you give more detail? If it's
> lmer, it's quite likely a false positive. I USED LME. I DON'T REALLY KNOW
> WHAT DO YOU EXACTLY MEAN WITH SENSIBLE REFERENCE QUANTITY. I THOUGHT IT WAS
> THE MINIMUM VALUE OF MY X VARIABLE (AS CERO IS NOT A POSSIBILITY).
>
> >
> > (2) The relationship might be changing over time?
> >
> > lme(Bird.density~Invertebrate biomass+sample_time,
> > random=~invert_biomass|Plot_identity, data=)
> >
> > How should I treat sample time? Is it a ordered categorical variable?
>
> Depends on a number of things. Your original message suggested
> that you sampled over the course of 30 days (maybe at different times
> in different plots?) If this is the case (e.g. you sampled plot 1 on
> days 1, 5, 9, ... and plot 2 on days 2, 6, 10 ...) then it is probably
> most sensible to treat time as a numeric variable (i.e., assume a
> linear trend over days) and possibly a random effect with days as a
> grouping variable (in which case you might have to switch from lme to
> lmer). If you have a small number of distinct sample days then a
> categorical variable makes sense. Whether you specify it as ordered or
> (default) unordered doesn't affect the overall fit of the model, just
> the particular contrasts that get tested with respect to the time
> variable.
>
>
> >
> > Thankyou very much.
> >
> > Joaquin
> >
> >
> > 2017-01-16 19:49 GMT-03:00 Ben Bolker <bbolker at gmail.com>:
> >>
> >>
> >> Center your biomass variable on this value: either create a
> >>
> >> mydata$invert_biomass_c <- mydata$invert_biomass-ref_value
> >>
> >> or include it directly in your formula:
> >>
> >> bird_dens ~ I(invert_biomass-ref_value), ...
> >>
> >> On 17-01-16 05:44 PM, Joaquín Aldabe wrote:
> >> > Thankyou very much Ben. Can you please suggest a way of fixing some
> >> > sensible reference quantity for Invertebrate biomass?
> >> > All the best,
> >> > Joaquín
> >> >
> >> > 2017-01-16 18:59 GMT-03:00 Ben Bolker <bbolker at gmail.com
> >> > <mailto:bbolker at gmail.com>>:
> >> >
> >> > That seems perfectly reasonable. There are a couple of things to
> >> > consider, although you may or may not find that your data supports
> >> > that much complexity.
> >> >
> >> > (1) The relationship between bird density and invert biomass, as
> >> > well
> >> > as the intercept (i.e., expected bird density at invert_biomass=0,
> >> > or
> >> > better invert_biomass=<some sensible reference quantity>)
> >> >
> >> > lme(Bird.density~Invertebrate biomass,
> >> > random=~invert_biomass|Plot_identity, data=)
> >> >
> >> >
> >> > (2) The relationship might be changing over time?
> >> >
> >> > lme(Bird.density~Invertebrate biomass+sample_time,
> >> > random=~invert_biomass|Plot_identity, data=)
> >> >
> >> > (3) In principle you could consider random effects of both time
> and
> >> > invert biomass, but that will almost certainly overwhelm your
> data.
> >> >
> >> > Don't forget to do the standard post-fitting checks: are your
> >> > residuals *approximately* equal-variance and (even more
> >> > approximately)
> >> > Normally distributed? Is the relationship between bird density
> and
> >> > invert biomass *approximately* linear? (See ?plot.lme)
> >> >
> >> >
> >> > On Mon, Jan 16, 2017 at 2:06 PM, Joaquín Aldabe
> >> > <joaquin.aldabe at gmail.com <mailto:joaquin.aldabe at gmail.com>>
> wrote:
> >> > > Dear all, I'm interested in modeling the effect of invertebrate
> >> > biomass on
> >> > > the density of a grassland shorebird (they eat invertebrates).
> For
> >> > this, I
> >> > > picked 8 plots and sampled invertebrates and birds 6 times in
> each
> >> > plot for
> >> > > about 30 days. This is, I went to each plot and did repeated
> >> > measures of
> >> > > invertebrates biomass and shorebird density separated in time by
> >> > four or
> >> > > five days, as invertebrates biomass may change over time and it
> is
> >> > expected
> >> > > that birds density change accordingly.
> >> > >
> >> > > So, I'm trying to see a general pattern of the effect of changes
> >> > in biomass
> >> > > on the density of this shorebird species at a plot scale. Plot
> >> > identity is
> >> > > not important; I consider them as particular events of a random
> >> > process.
> >> > >
> >> > > Is this model correct:
> >> > >
> >> > > lme(Bird.density~Invertebrate biomass, random=~1|Plot_identity,
> >> > data=)
> >> > >
> >> > > Thank you very much,
> >> > >
> >> > > Joaquin.
> >> > >
> >> > >
> >> > > --
> >> > > *Joaquín Aldabe*
> >> > >
> >> > > *Grupo Biodiversidad, Ambiente y Sociedad*
> >> > > Centro Universitario de la Región Este, Universidad de la
> >> > República
> >> > > Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> >> > >
> >> > > *Departamento de Conservación*
> >> > > Aves Uruguay
> >> > > BirdLife International
> >> > > Canelones 1164, Montevideo
> >> > >
> >> > > https://sites.google.com/site/joaquin.aldabe
> >> > <https://sites.google.com/site/joaquin.aldabe>
> >> > > <https://sites.google.com/site/perfilprofesionaljoaquinaldabe
> >> > <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>>
> >> > >
> >> > > [[alternative HTML version deleted]]
> >> > >
> >> > > _______________________________________________
> >> > > R-sig-mixed-models at r-project.org
> >> > <mailto:R-sig-mixed-models at r-project.org> mailing list
> >> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >> > <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > *Joaquín Aldabe*
> >> >
> >> > /Grupo Biodiversidad, Ambiente y Sociedad/
> >> > Centro Universitario de la Región Este, Universidad de la República
> >> > Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> >> >
> >> > /Departamento de Conservación/
> >> > Aves Uruguay
> >> > BirdLife International
> >> > Canelones 1164, Montevideo
> >> >
> >> > https://sites.google.com/site/joaquin.aldabe
> >> > <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>
> >> >
> >> >
> >> >
> >
> >
> >
> >
> > --
> > Joaquín Aldabe
> >
> > Grupo Biodiversidad, Ambiente y Sociedad
> > Centro Universitario de la Región Este, Universidad de la República
> > Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> >
> > Departamento de Conservación
> > Aves Uruguay
> > BirdLife International
> > Canelones 1164, Montevideo
> >
> > https://sites.google.com/site/joaquin.aldabe
> >
> >
> >
>
--
*Joaquín Aldabe*
*Grupo Biodiversidad, Ambiente y Sociedad*
Centro Universitario de la Región Este, Universidad de la República
Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
*Departamento de Conservación*
Aves Uruguay
BirdLife International
Canelones 1164, Montevideo
https://sites.google.com/site/joaquin.aldabe
<https://sites.google.com/site/perfilprofesionaljoaquinaldabe>
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