Going full Bayesian with mixed effects regression models

Interesting new statistics tools

HLP/Jaeger lab blog

Thanks to some recently developed tools, it’s becoming very convenient to do full Bayesian inference for generalized linear mixed-effects models. First, Andrew Gelman et al. have developed Stan, a general-purpose sampler (like BUGS/JAGS) with a nice R interface which samples from models with correlated parameters much more efficiently than BUGS/JAGS. Second, Richard McElreath has written glmer2stan, an R package that essentially provides a drop-in replacement for the lmer command that runs Stan on a generalized linear mixed-effects model specified with a lme4-style model formula.

This means that, in many cases, you simply simply replace calls to (g)lmer() with calls to glmer2stan():

lmer.fit <- glmer(accuracy ~ (1|item) + (1+condition|subject) + condition, 
                  data=data, family='binomial')
stan.fit <- glmer2stan(accuracy ~ (1|item) + (1+condition|subject) + condition, 
                       data=data, family='binomial')

There’s the added benefit that you get a sample from the full, joint posterior distribution of the model…

View original post 482 more words