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lme vs. lmer

Chris,
Thanks for that - I should probably have mentioned that I'm using
family=quasipoisson  in glmer since my data has Poisson distribution
as well as being overdispersed. I'm unsure how one decides which term
to drop without being informed by p-values, and so don't quite
understand how the "Likelihood ratio test using anova()" , or the AIC
or BIC model comparison will work in this case (I thought one's
supposed to remove the term with the highest p-value from the model,
and compare it with the model with the term included to see if there's
a difference, not so?).

Douglas,
Yes I have data (see attached). The response variable ('Counts'
column) is the number of seedlings per plot. There are four sites that
are not the same (since these are previously mined sites and it's
impossible to get even two sites that are exactly the same, in terms
of age, soil properties etc). Each site has 20 reps of each treatment
- Control, G, N and NG, and the data was collected over three
consecutive years. Each set of treatments were grouped together in a
'Patch' (sort of a split plot design, although I've ignored this thus
far).

So the model using glmer looks like this (I'm not sure if the 'random'
factors are correct, or if it should just be '(1|Site)', and i've
ignore the split plot design...):
Generalized linear mixed model fit by the Laplace approximation
Formula: Counts~ N + G + Year + N:Year + G:Year + N:G:Year + (Year |      Site)
   Data: ex4o
  AIC  BIC logLik deviance
 5731 5823  -2846     5693
Random effects:
 Groups   Name        Variance Std.Dev. Corr
 Site     (Intercept) 1.35594  1.1644
          Yearthree   3.53069  1.8790   0.752
          Yeartwo     0.88908  0.9429   0.169 0.777
 Residual             6.76955  2.6018
Number of obs: 936, groups: Site, 4

Fixed effects:
              Estimate Std. Error t value
(Intercept)    2.93093    0.58598   5.002
N              0.03767    0.09071   0.415
G              0.14927    0.08833   1.690
Yearthree     -3.22170    0.98325  -3.277
Yeartwo       -1.96111    0.50636  -3.873
N:Yearthree    0.15713    0.37544   0.419
N:Yeartwo      0.14736    0.24210   0.609
G:Yearthree   -0.25103    0.40152  -0.625
G:Yeartwo      0.07549    0.23937   0.315
N:G:Yearone   -0.31633    0.12888  -2.455
N:G:Yearthree  0.04722    0.52594   0.090
N:G:Yeartwo   -0.32787    0.31260  -1.049

Correlation of Fixed Effects:
            (Intr) N      G      Yerthr Yeartw N:Yrth N:Yrtw G:Yrth
G:Yrtw N:G:Yrn N:G:Yrth
N           -0.079
G           -0.081  0.523
Yearthree    0.706  0.047  0.048
Yeartwo      0.141  0.091  0.094  0.707
N:Yearthree  0.019 -0.242 -0.126 -0.209 -0.022
N:Yeartwo    0.030 -0.375 -0.196 -0.018 -0.259  0.091
G:Yearthree  0.018 -0.115 -0.220 -0.195 -0.021  0.511  0.043
G:Yeartwo    0.030 -0.193 -0.369 -0.018 -0.262  0.047  0.547  0.081
N:G:Yearone  0.056 -0.704 -0.685 -0.033 -0.064  0.170  0.264  0.151
0.253
N:G:Yearthr  0.000  0.000  0.000  0.141  0.000 -0.672  0.000 -0.726
0.000  0.000
N:G:Yeartwo  0.000  0.000  0.000  0.000  0.174  0.000 -0.666  0.000
-0.661  0.000   0.000

Hope you can work with that?
Thanks,
Raldo
On Wed, Sep 30, 2009 at 6:20 PM, Douglas Bates <bates at stat.wisc.edu> wrote: