Fig. 1
From: VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces
Graphical trace visualization. The figure depicts the “Graph” tab of VMCMC from analysis of a typical MCMC trace obtained from JPrIME by using tetrapod dataset “DS1” collected by Hedges et al. [25]. The trace of the “DLRModelDensity” parameter is shown, which appears to be converged (the difference between values of initial few samples and later samples) and also shows good mixing (fuzzy caterpillar-like trace). The left panel shows the selected burnin, the parameter statistics after removing the burn-in, and convergence diagnostics from three standard methods. The panel also provides the option to zoom in to the trace by selecting a portion of the trace and then pressing the “Extract interval” button to see the behaviour of a chain in the selected interval