[R-sig-ME] about graphical checking on glmm and contradiction between parsimony and AIC values
glenda mendieta
glendamendieta at gmail.com
Tue Dec 13 15:40:07 CET 2011
Dear list members,
I am running GLMMs with count data, Laplace approximation, poisson
family, using glmer {lme4}, the last version of R and R studio in
windows platform.
When fitting my final models, I run an anova to look at the
"significance" of a term inclusion (random effect term), of course, this
does not apply for random effects, but at least it gives me differences
in DFs and whether the models are significantly different or not.
It basically tells me that the least parsimonious model is the one with
the lowest AIC value. As you can see below the difference in AIC values
is pretty big.
> anova(g,gwi)
Data: db.e
Models:
gwi: abundance ~ census * avail.surface + (1 | tree) + (1 | spp)
g: abundance ~ census * avail.surface + (1 | tree) + (1 | spp) + (1 |
spp:tree)
Df AIC BIC logLik Chisq Chi Df Pr(>Chisq)
gwi 12 22342.0 22442.9 -11159.0
g 13 9702.5 9811.8 -4838.3 12641 1 < 2.2e-16 ***
Then I run a qqplot on residuals vs. fitted values for each model and I
can see that the more parsimonious model (*gwi*) is the one with the
better fit (the points are pretty well alined across a straight line);
whereas in the other model (*g*) the points are in a curved line.
Would this be because random crossed effects should not be included as
an interaction term (like in the last model [g]) (Johnson & Omland,
2004)? or I am overfiting?
My intuition tells me I should go for the most parsimonious model, since
the graphical checking works. But, I wonder if there any advise you can
give me to improve the fit of this model?. There is still a lot of
variance unexplained there, the model with the random effect interaction
term "spp:tree" has a variance of 59.87 sd. 7.73, in comparison to the
model with only tree and spp (2.45 sd. 1.55 & 3.5 sd. 1.90).
Greetings and thanks in advance for your time,
Glenda Mendieta-Leiva
PhD candidate
University of Oldenburg
PS. Johnson, J. B. and Omland, K. S. 2004. Model selection in ecology
and evolution. Trends Ecol. Evol. 19: 101-108.
More information about the R-sig-mixed-models
mailing list