[R-sig-ME] modeling question

[Ben Bolker]

  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]]
>     >
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> 
> 
> 
> 
> -- 
> *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>
> 
> 
>