[R] Mixed effects model with binomial errors - problem

RFTW l.temarvelde at nioo.knaw.nl
Thu Sep 11 16:27:35 CEST 2008

```ok... the model now runs properly (say, without errors). Now about the
result.
These are the averages per treatments

tapply(VecesArbolCo.VecesCo.C1,T2,mean)
a     b      c     d
0.49 0.56 0.45 0.58

I run this very simple model

> summary(model1<-lmer(cbind(VisitsExpTree,TotalVisits-VisitsExpTree)~
> treatment +(1|Individual), family=binomial, data=r))

Generalized linear mixed model fit by the Laplace approximation
Formula: cbind(VisitsExpTree,TotalVisits-VisitsExpTree)~ treatment
+(1|Individual)
Data: r
AIC   BIC logLik deviance
242.3 255.9 -116.2    232.3
Random effects:
Groups    Name        Variance Std.Dev.
Individuo (Intercept) 0.14075  0.37517
Number of obs: 112, groups: Individuo, 37

Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept)          0.37228    0.19031  1.9562  0.05044 .
treatmentb          0.03367    0.24520  0.1373  0.89079
treatmentc         -0.60606    0.23330 -2.5978  0.00938 **
treatmentd         -0.25504    0.22790 -1.1191  0.26311
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Correlation of Fixed Effects:
(Intr) T2b    T2c
T2b -0.675
T2c -0.697  0.543
T2d -0.720  0.544  0.581

wouldnt we expect the intercept to be roughtly the mean of treatment a? and
thus the estimate of treatmentb to be +0.07, c: -0.04 and d: +0.09 roughly?

Is this model just completely not estimating well, or are the estimates not
the 'real values'.

I tried to get teh predict function to give me the 4 predicted values based
on the model, but i havent succeeded in doing so. maybe someone can help me
on that one too (predict(model1,type="response") doesnt work)

thnx
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