RWTY produces a number of different plots and statistics for evaluating the performance of MCMC chains. These plots can help to illustrate problems with convergence in idividual chains as well as explore differences between chains built from different sequence data. Here we're going to explore some of these plots in detail, comparing well-behaved to poorly-behaved chains when appropriate. | Running RWTY | Parameter plots | Topology trace plots and histograms | Split frequency plots | Pairs plots | Average Change in Split Frequency (ACSF) plots | Treespace plots | Autocorrelation plots | Pseudo-ESS plots | Split frequency matrix plots | ASDSF plots | Citations

RWTY: R We There Yet? | Plot comparisons - what does it all mean? | Installation | Installing from GitHub using devtools | Install from zip file | Setting the number of cores | Interacting with RWTY | load.trees() | load.multi() | analyze.rwty() | makeplot.x() | topological.approx.ess() | RWTY outputs | Parameter trace plots | Parameter correlation plots | Tree topology trace plot | Autocorrelation plots | Treespace plots | Sliding window and cumulative split frequency plots | Sliding window and cumulative average change in split frequency (ACSF) plots | Multiple chains only | Average Standard Deviation of Split Frequency (ASDSF) plot | Split frequency scatterplot matrix | ASDSF tree