dotplot of random effects

Question

I have an generalized mixed effects model such as the following:

d <- data.frame(
    g = sample(c("A","B","C","D","E"), 250, replace=TRUE),
    x = runif(250, max=100),
    y = sample(c(0,1), 250, replace=TRUE)
)

require(lme4)

fm <- lmer(y ~ x + (1 + x | g), data=d, family=binomial)

I'd like to plot the random effect of the intercepts using dotplot but without plotting the random slope component of x. My problem is that I can't seem to figure out how to access just the intercept component and not the random slopes.

For example, what I want is the left hand side of this plot:

dotplot(ranef(fm, postVar=TRUE))

Using dotplot(ranef(fm, postVar=TRUE)$g[,2]) doesn't give me what I want even though I think it should! I've looked at str(fm), but didn't see anything that helped me get any closer.

Any help and hints would be much appreciated!

Answer 1

You were almost there in your original code:

dotplot(ranef(fm, postVar=TRUE))$g[1]

An additional tip to free the scales for each plot:

dotplot(ranef(fm, postVar=TRUE),
        scales = list(x =list(relation = 'free')))

Answer 2

This should get you pretty close. I've been meaning to add support for lme4 objects to coefplot so maybe this be my catalyst.

theRan <- ranef(fm, postVar=TRUE)
pv <- attr(theRan$g, "postVar")
se <- pv[1, 1, ]
theIntercepts <- theRan$g[, 1, drop=F]
theFrame <- cbind(theIntercepts, se)
names(theFrame)[1] <- "Intercept"
theFrame$Low <- with(theFrame, Intercept - 2 * se)
theFrame$High <- with(theFrame, Intercept + 2 * se)
theFrame$Variable <- rownames(theFrame)
ggplot(theFrame, aes(y=Intercept, x=reorder(Variable, Intercept))) + geom_linerange(aes(ymin=Low, ymax=High), colour="black") + geom_point(, colour="blue") + coord_flip() + labs(y="Intercept", x=NULL)