glmer.nb(): Residual term ??
Hi Christine, Others more knowledgeable than I may chime in, but as far as I know the GLMM parameterization that lme4 uses doesn't have a residual error term. Other R software does have residuals, such as MCMCglmm. HTH, Dan.
Christine Adrion wrote:
Hello,
I fit a negative binomial GLMM using the lme4 package (version
lme4_1.1-7), R-function glmer.nb(). It seems that this is still an
experimental feature. The help function does not explain the residual term
in the resulting R output.
#---------------
# Reproducible example:
tmpf<- function() {
x<- runif(400) - 0.5
z<- gl(n=40, k=10)
m<- model.matrix(~x + z)
u<- rnorm(40, sd=0.5)
eta<- m %*% c(0, 3, u[-1] - u[1])
y<- rnbinom(n=length(eta), size=3, mu=exp(eta))
data.frame(y, x, z)
}
set.seed(2011)
simdf<- tmpf()
m<- glmer.nb(y ~ x + (1|z), data=simdf)
m
##------------ output --------------------
Generalized linear mixed model fit by maximum likelihood (Laplace
Approximation) ['glmerMod']
Family: Negative Binomial(6.7839) ( log )
Formula: y ~ x + (1 | z)
Data: ..2
AIC BIC logLik deviance df.resid
890.5451 906.5109 -441.2725 882.5451 396
Random effects:
Groups Name Std.Dev.
z (Intercept) 0.3923
Residual 0.9665
Number of obs: 400, groups: z, 40
Fixed Effects:
(Intercept) x
-0.5511 2.5969
#-----------------------------------------
Unfortunately, it's not clear to me what the measure "Residual" exactly
expresses and thus why it is used by glmer.nb.
[BTW, the fitted dispersion parameter 'size' is not very close to the true
one (which was 3).]
Thanks for any help/explanation.
Kind regards
Christine
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Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2220 Life Sciences Addition, One Shields Ave. Davis, CA 95616