[R-sig-ME] modeling question

[Joaquín Aldabe]

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>

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