Plot Metropolis coupling acceptance rates between all adjacent rungs. It is important that acceptance rates are greater than zero between all pairs of rungs in order to give confidence that the MCMC has thoroughly explored the full posterior distribution. If there are any points in this plot where acceptance rates drop close to zero then consider changing the number of rungs or their distribution (see rungs and GTI_pow arguments in run_mcmc(), respectively).

plot_mc_acceptance(proj, K = NULL, x_axis_type = 1)

Arguments

proj

an rmaverick project, as produced by the function mavproject()

K

which value of K to produce the plot for

x_axis_type

how to format the x-axis. 1 = integer rungs, 2 = values of the thermodynamic power.