[R-sig-ME] modeling question
Joaquín Aldabe
joaquin.aldabe at gmail.com
Thu Jan 26 15:38:10 CET 2017
Dear Ben, it's me again 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?
(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?
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
<https://sites.google.com/site/perfilprofesionaljoaquinaldabe>
[[alternative HTML version deleted]]
More information about the R-sig-mixed-models
mailing list