Plot random effects from lmer (lme4 package) using qqmath or dotplot: How to make it look fancy?

Question

The qqmath function makes great caterpillar plots of random effects using the output from the lmer package. That is, qqmath is great at plotting the intercepts from a hiera

Answer 1

Didzis' answer is great! Just to wrap it up a little bit, I put it into its own function that behaves a lot like qqmath.ranef.mer() and dotplot.ranef.mer(). In addition to Didzis' answer, it also handles models with multiple correlated random effects (like qqmath() and dotplot() do). Comparison to qqmath():

require(lme4)                            ## for lmer(), sleepstudy
require(lattice)                         ## for dotplot()
fit <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
ggCaterpillar(ranef(fit, condVar=TRUE))  ## using ggplot2
qqmath(ranef(fit, condVar=TRUE))         ## for comparison

Comparison to dotplot():

ggCaterpillar(ranef(fit, condVar=TRUE), QQ=FALSE)
dotplot(ranef(fit, condVar=TRUE))

Sometimes, it might be useful to have different scales for the random effects - something which dotplot() enforces. When I tried to relax this, I had to change the facetting (see this answer).

ggCaterpillar(ranef(fit, condVar=TRUE), QQ=FALSE, likeDotplot=FALSE)

## re = object of class ranef.mer
ggCaterpillar <- function(re, QQ=TRUE, likeDotplot=TRUE) {
    require(ggplot2)
    f <- function(x) {
        pv   <- attr(x, "postVar")
        cols <- 1:(dim(pv)[1])
        se   <- unlist(lapply(cols, function(i) sqrt(pv[i, i, ])))
        ord  <- unlist(lapply(x, order)) + rep((0:(ncol(x) - 1)) * nrow(x), each=nrow(x))
        pDf  <- data.frame(y=unlist(x)[ord],
                           ci=1.96*se[ord],
                           nQQ=rep(qnorm(ppoints(nrow(x))), ncol(x)),
                           ID=factor(rep(rownames(x), ncol(x))[ord], levels=rownames(x)[ord]),
                           ind=gl(ncol(x), nrow(x), labels=names(x)))

        if(QQ) {  ## normal QQ-plot
            p <- ggplot(pDf, aes(nQQ, y))
            p <- p + facet_wrap(~ ind, scales="free")
            p <- p + xlab("Standard normal quantiles") + ylab("Random effect quantiles")
        } else {  ## caterpillar dotplot
            p <- ggplot(pDf, aes(ID, y)) + coord_flip()
            if(likeDotplot) {  ## imitate dotplot() -> same scales for random effects
                p <- p + facet_wrap(~ ind)
            } else {           ## different scales for random effects
                p <- p + facet_grid(ind ~ ., scales="free_y")
            }
            p <- p + xlab("Levels") + ylab("Random effects")
        }

        p <- p + theme(legend.position="none")
        p <- p + geom_hline(yintercept=0)
        p <- p + geom_errorbar(aes(ymin=y-ci, ymax=y+ci), width=0, colour="black")
        p <- p + geom_point(aes(size=1.2), colour="blue") 
        return(p)
    }

    lapply(re, f)
}