Plot MCMC diagnostics

Calculates posterior parameter summaries, effective sample sizes, and R-hat values when more than one chain is available. It also returns the parameter and infection-history diagnostic plots.

plot_mcmc_diagnostics(
  location,
  par_tab,
  burnin,
  inf_hist_mcmc_summaries = TRUE
)

Arguments

location

character string giving the directory containing the saved MCMC chain files

par_tab

the model control table used to identify estimated parameters

burnin

number of initial MCMC samples to discard when loading the chains

inf_hist_mcmc_summaries

if TRUE, calculates infection-history summaries and plots as well as parameter diagnostics

Value

A list containing `theta_estimates`, `p_thetas`, `inf_hist_estimates`, and `p_inf_hists`.

See also

Other theta_plots: plot_2d_density(), plot_posteriors_theta(), plot_samples_distances()