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Variance components in a binomial mixed model
2 messages · Nicholas Lewin-Koh, Ben Bolker
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On 02/15/2011 12:42 PM, Nicholas Lewin-Koh wrote:
Howdy,
I have a question sort of related to Ben's "differing variances within
different random effects levels".
I have a data set consisting of 23 mice, 11 Treated and 12 controls. The
mice are bred to have
a neurodengerative disease, and their neuromuscular connections degrade over
time. So the animals were sacrificed and
a left and right leg muscle were removed and sectioned, fixed on slides and
stained appropriately. There were 12 slides
per a muscle, and 6 sections per slide. Two slides per side were chosen, and
in all sections on the slide the total number of neuro-muscular
junctions, and the number innervated was counted. Oh and within each muscle,
there were 5 compartments, so counts are by muscle compartment.
So I have a binomial response, and for fixed effects I have Sex +
Treatment*Musclecompartment
and random (1|Animal/Side/Slide/Section) So the model is
gm1 <- glmer(cbind(Innervated.count,Total.count-Innervated.count) ~ Sex +
Treatment*Muscle.Compartment+(1|animal.ID/Side/Slide/Section), data=dat,
family = binomial)
So my questions are about interpretation of the variance components in a
binomial model.
1) the variance component for slide is 0, is that because there are only 2
slides
or is something else going on, there is an estimated variance for side,
and when I last
counted there were only 2 of those as well :)
It basically means that you have so little power to detect variance among slides within side that your best estimate is zero; the total observed variation among slides is not much bigger than that expected from the variation at lower levels (sections within slides).
2) do the variances/covariances have a similar interpretation to the
Gaussian case
for which in an lmm everything is easier to understand? Meaning that
the error term is
binomal, glm part, but the random effects are gaussian, so i am looking
at the variances
from a mixture model, or is that just the integrated variance over all
levels.
Since you are using a random effects on the intercept only, the
variances are variances of (assumed) Gaussian random variation in the
logit probability (since you are using the default logit link) across
groups at particular grouping levels.
This is a small data set, be very careful with the p-values (Wald or
LRT)! If you are happy on the bleeding edge, you can try the parametric
bootstrapping examples that I committed to the r-forge repository. (It
looks like the Linux builds might be a bit out of date -- if you install
the package and don't get a result for help("simulate-mer"), let me know
...)
cheers
Ben Bolker
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