In the past week, colleagues of mine and me started using the lme4-package to compute multi level models. This inspired me doing two new functions for visualizing random effects (as retrieved by
ranef()) and fixed effects (as retrieved by
fixef()) of (generalized) linear mixed effect models.
The upcoming version of my sjPlot package will contain two new functions to plot fitted lmer and glmer models from the lme4 package:
sjp.glmer (not that surprising function names). Since I’m new to mixed effects models, I would appreciate any suggestions on how to improve the functions, which results are important to report (plot) and so on. Furthermore, I’m not sure whether my approach of computing confident intervals for random effects is the best?
I have used following code to compute confident intervals for the estimates returned by the
lme4::ranef() function (bases on this stackoverflow answer):
coev <- as.matrix(lme4::vcov.merMod(fit)) tmp <- as.data.frame(cbind(OR = exp(mydf.ef[,i]), lower.CI = exp(mydf.ef[,i] - (1.96 * sqrt(diag(coev))[i])), upper.CI = exp(mydf.ef[,i] + (1.96 * sqrt(diag(coev))[i]))))
The update to version 1.6 of sjPlot is still in development (feature-freeze, mostly fixes now), however, you can download the latest snapshot from GitHub (see also this post for further information). Now to some examples. First, an example model is fitted and the random effects (default) for each predictor are plotted as „forest plot“:
# fit model library(lme4) fit <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) # simple plot sjp.lmer(fit)
Sorting a predictor (i.e. estimates of a facet) is done by specifying the predictor’s name as
sjp.lmer(fit, sort = "Days")
Each facet plot can also be plotted as single plot, when
facet.grid is set to
FALSE. In this case, it is possible to sort the estimates for each plots. See following example from the
library(lme4) # create binary response sleepstudy$Reaction.dicho <- sju.dicho(sleepstudy$Reaction, dichBy = "md") # fit model fit <- glmer(Reaction.dicho ~ Days + (Days | Subject), sleepstudy, family = binomial("logit")) sjp.setTheme(theme = "forest") sjp.glmer(fit, facet.grid = FALSE, sort = "sort.all")
Plotting the fixed effects is not much spectacular, because we only have one estimate beside intercept here.
sjp.glmer(fit, type = "fe", sort = TRUE)
To summarize, you can plot random and fixed effects in the way as shown above. Are there any other or better plot options for visualizing mixed effects models?
Any suggestions are welcome…
Disclaimer: all misspellings belong to Safari’s autocorrect feature!