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Exercise

Markov chain density plots

Whereas a trace plot captures a Markov chain's longitudinal behavior, a density plot illustrates the final distribution of the chain values. In turn, the density plot provides an approximation of the posterior model. You will construct and examine density plots of the \(m\) Markov chain below. The mcmc.list object sleep_sim and sleep_chains data frame are in your workspace:

sleep_sim <- coda.samples(model = sleep_jags, variable.names = c("m", "s"), n.iter = 10000)
sleep_chains <- data.frame(sleep_sim[[1]], iter = 1:10000)

Instructions

100 XP

  • Apply plot() to sleep_sim with trace = FALSE to construct density plots for the \(m\) and \(s\) chains.

  • Apply ggplot() to sleep_chains to re-construct a density plot of the \(m\) chain.