[ADMB Users] Nested random effects syntax in glmmADMB 0.6.2 alpha
Shawn McCracken
frocga at gmail.com
Thu Aug 4 21:52:57 PDT 2011
Today I managed to get the alpha version of glmmADMB 0.6.2 loaded and
running. I am running negative binomial model with nested random effects.
I decided to start with a reduced model of my data, so I began with the
following syntax and R would just hang and I get the pinwheel of death (Mac
OS 10.6.8):
> m1=glmmadmb(Y~X+(1|A/B),data=ecpad5,family="nbinom")
I can't find the exact mailing list message, but somewhere I believe I read
that +(1|A)+(1|B) is the same as the above syntax in lme4 as long as factor
B is coded with unique individual labels.
I then tried the following model syntax and it worked just fine:
> m2=glmmadmb(Y~X+(1|A)+(1|B),data=ecpad,family="nbinom")
> summary(m2)
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.841 0.234 -3.59 0.00034 ***
treaty -0.702 0.311 -2.26 0.02413 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Number of observations: total=160, =32, =160
Random effect variance(s):
$tree
(Intercept)
(Intercept) 2.9858e-09
$trbr
(Intercept)
(Intercept) 1.2847
Negative binomial dispersion parameter: 403.43 (std. err.: 2.1584)
Log-likelihood: -162.773
My data structure:
A =(randomly selected plot) B =(randomly selected sub-plot within A)
X =(disturbed=Y or N) Y =(total count of individuals present)
T01 B001
N 2
T01 B002
N 0
T01 B003
N 0
T01 B004
N 1
T01 B005
N 0
T02 B006
N 0
T02 B007
N 4
T02 B008
N 1
T02 B009
N 0
T02 B010
N 0
. .
. .
. .
. .
. .
. .
T32 B156
Y 3
T32 B157
Y 0
T32 B158
Y 0
T32 B159
Y 1
T32 B160
Y 0
Is glmmADMB treating B as being nested in A like it does in lme4? To the
best of your knowledge do the results look like they should?
I'll have more questions later but gotta get this sorted first.
Thanks for the help,
Shawn
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