Random effects are usualy modelled as normally distributed with zero mean. Thus I would expect that the mean of the estimated random intercepts is close to zero. However, in my example this mean is far from 0, which leads to an extremely high (fixed) intercept. If I fit an ordinary logistic regression model, the intercept is much smaller. Does this mean that the mixed model is not appropriate?
Here is a reproducible example:
library(lme4)
outcome <- c(0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1,
0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1,
0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1,
0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1,
1, 0, 0, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 1,
1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1,
1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 0,
1, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1,
1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1,
1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1,
0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 0,
0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1,
1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 1, 0,
1, 1, 0, 1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1,
1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1,
1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1,
0, 1, 0, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0,
1, 1, 1, 0)
cluster <- as.factor(rep(1:90, 4))
glm(outcome ~ 1 , family = "binomial")
(fit2 <- glmer(outcome ~ 1 + (1|cluster), family = "binomial"))
mean(ranef(fit2)$cluster$"(Intercept)")
lattice::dotplot(ranef(fit2,condVar=TRUE))