Dear Mike,



Thanks for your help. To answer your questions, I need to explain a little
bit about my study.

My question is about the determining factors on the local ant species. I
want to know if the local species richness is influenced by local factors
or factors that act at an immediately superior/lager scale. I am also
considering the interaction between local and larger factors.

Thus, I am considering the local species richness the number of ant species
sample in pitfall traps. I have the following sampling design: I sample the
ants in three large areas that are the parks. In each park, I established
four transects. In each transect, 10 pitfall traps were set 10 m apart from
each other.

Thus I did this model:

sepi~lhet+ldth+transect+leht:transect+(1/park/transect),family=”poisson”

where:

sepi = number of ant species in each pitfall trap (count data);

lhet = litter heterogeneity. This is a continue variable measured for each
trap. I consider it as a local factor

ldth = litter depth. Like lhet. It is also a local factor

transect = the site where the traps were set. I have in total 12 transects.
This is a categorical variable. I considered the transect as way to see the
influence of factors that act at large scale on the local species richness.

Then, in the model, transect is a fixed and random effect, because it is
part of my question and because the sampled transect represent a subset of
the possible site to be sampled within each park. In the same way park was
considered a random effect, because the three parks means a subset of the
possible parks within the same region/biome.

In a second model a changed the interaction, I used ldth:transect. In both
I have had the “possible bug” with the dredge function from the MuMIn
package. The delta and weight of the models are missing.

I ran similar models (with the same structure) with other data set that is
different, but with the same nested design and I got the full result.  I
hope this could help you understand my study and my doubts.

Thanks again for your attention.

Best wishes,

Fernando


2011/12/13 Dunbar, Michael J. <mdu@ceh.ac.uk>

> Fernando
>
> You have transect in both the fixed and random part of the model. Will the
> model fit when transect is not in the fixed part? Will it fit when you just
> call lmer with the full model without dredge? Can you explain a bit more
> about you data and in particular how the transect variable is coded?
>
> regards
> Mike
>
>
> ________________________________________
> From: r-sig-ecology-bounces@r-project.org [
> r-sig-ecology-bounces@r-project.org] On Behalf Of Pedro Lima Pequeno [
> pacolipe@gmail.com]
> Sent: 13 December 2011 19:01
> To: Fernando Schmidt
> Cc: r-sig-ecology@r-project.org
> Subject: Re: [R-sig-eco] Possible bug with dredge function
>
>  Hi, Fernando.
>
> The warning message "In mer_finalize(ans) : gr cannot be computed at
> initial par (65)" points to problems during the iterative process of
> model fitting. This may be caused by the complexity of the global
> model you're implying. Have you tried using dredge() with a simpler
> global model (e.g. without interactions)?
>
> 2011/12/14, Fernando Schmidt <schmidt.fa@gmail.com>:
> > Dear colleagues,
> >
> > I am working with information-theoretic based on the second-order
> AKaike’s
> > Information criterion corrected for small samples sizes AICc.  I have run
> > the mixed-effect models with “glmer” function in the lme4 package. Then,
> I
> > used the dredge function from the MuMIn package to test models defined by
> > all possible variables combinations and rank them by AICc-based model
> > weight.
> >
> > Usually, the main results from dredge function are AICc, delta and
> weight.
> > However, for one model seems to have some “bug” I just could get AICc.
> > Delta and weight were missing:
> >
> >>
> >
> mfullepi1<-glmer(sepi~lhet+ldth+transect+lhet:transect+(1|park/transect),family="poisson")
> >
> >> dredge(mfullepi1)
> >
> > Global model: glmer(formula = sepi ~ lhet + ldth + transect +
> lhet:transect
> > +
> >
> >     (1 | park/transect), family = "poisson")
> >
> > ---
> >
> > Model selection table
> >
> >    (Int)  ldt      lht     trn lht:trn k      Dev.            AICc
> >
> > 5  1.1630                  +                   14     97.79        129.8
> >
> > 7  1.0000           0.5228 +            15     95. 62       130.2
> >
> > 6  0.9803 0.002208         +          15    96.32        130.9
> >
> > 8  0.8236 0.002160  0.5188 +    16   94.17       131.5
> >
> > 3  1.4120           0.5538                    4   124.30      132.7
> >
> > 4  1.2810 0.002287  0.5153           5   122.40     132.9
> >
> > 2  1.3920 0.002544                          4   125.00     133.3
> >
> > 1  1.5480                                             3   127.20
> 133.4
> >
> > 15 1.4660          -1.0140 +   +       26
> >
> > 16 1.2560 0.002198 -0.9244 +   +       27
> >
> > Random terms: 1 | park/transect
> >
> > Mensagens de aviso perdidas:
> >
> > 1: In mer_finalize(ans) : gr cannot be computed at initial par (65)
> >
> > 2: In mer_finalize(ans) : gr cannot be computed at initial par (65)
> >
> >
> >
> > Please, someone could explain me what is going on?
> >
> >
> >
> > Thanks a lot!
> >
> > All the best,
> >
> > Fernando
> >
> >
> > --
> > Fernando Augusto Schmidt
> > Lab. de Ecologia de Comunidades
> > PPG - Entomologia. Universidade Federal de Viçosa
> > Viçosa, MG - Brazil 36570-000
> > www.labecol.ufv.br
> > +55 3182388810
> >
> >       [[alternative HTML version deleted]]
> >
> >
>
>
> --
> Pedro A. C. Lima Pequeno
> Programa de Pós-graduação em Ecologia
> Instituto Nacional de Pesquisas da Amazônia
> Manaus, AM, Brasil
>
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