[R] Extracting overdispersion estimates from lmer amd glm objects
mothsailor at googlemail.com
Tue Sep 12 09:55:43 CEST 2006
You can extract it from a summary.lmer object, which has a slot names
"sigma" that contains this scale parameter. For example,
> sum.modeltest <- summary(modeltest)
> sum.modeltest at sigma
On 11/09/06, Toby Gardner <t.gardner at uea.ac.uk> wrote:
> Dear list,
> I am needing to extract the estimate of overdispersion (deviance / residual degrees of freedom or c-hat) from multiple model objects - so they can then be used to compare the extent of overdispersion among alternative models as well as calculate qausi-AIC values. I have been unable to do this, despite consulting a number of manuals and searching the R-help. I am imaging that in theory it should be possible with some call to attr(), but i have so far had no success.
> An example model output would be:
> > modeltest<-lmer(Coleodactylus_amazonicus_N~USD + (1|site),data=SFArray,family=poisson,method="Laplace",control=list(usePQL=FALSE, msVerbose=TRUE))
> > summary(modeltest)
> Generalized linear mixed model fit using Laplace
> Formula: Coleodactylus_amazonicus_N ~ USD + (1 | site)
> Data: SFArray
> Family: poisson(log link)
> AIC BIC logLik deviance
> 75.94996 81.68603 -34.97498 69.94996
> Random effects:
> Groups Name Variance Std.Dev.
> site (Intercept) 2.6076 1.6148
> number of obs: 50, groups: site, 5
> Estimated scale (compare to 1) 1.080798
> What I need is to extract this value (1.080798) from multiple lmer objects. Has anyone any recommendations? I also need to do this for glm objects although I suspect if someone was able to kindly point me in the right direction then the solution is likely to be similar.
> Very many thanks,
> Toby Gardner
> > sessionInfo()
> Version 2.3.1 (2006-06-01)
> attached base packages:
>  "datasets" "graphics" "grDevices" "methods" "stats" "utils" "base"
> other attached packages:
> JGR iplots JavaGD lme4 Matrix lattice MASS rJava
> "1.4-7" "1.0-3" "0.3-4" "0.995-2" "0.995-15" "0.13-8" "7.2-27.1" "0.4-6"
> School of Environmental Sciences
> University of East Anglia
> Norwich, NR4 7TJ
> United Kingdom
> Email: t.gardner at uea.ac.uk
> Website: www.uea.ac.uk/~e387495
> [[alternative HTML version deleted]]
> R-help at stat.math.ethz.ch mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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