analyze.rwty            analyze.rwty, the main interface for rwty
                        analyses and plots.
check.chains            Function for checking suitability of chains for
                        rwty analyses, auto-generating labels, etc
clade.freq              Returns clade names and frequencies
combine.ptables         Function for merging p tables for multiple MCMC
                        chains
cumulative.freq         Cumulative means of clade split frequencies.
estimate.autocorr.m     Calculate sampling interval based on
                        exponential semivariogram model.
fungus                  MrBayes output from analysis of Hibbett et al.
                        data
load.multi              Load all matching files from a directory into a
                        list of rwty.chain objects
load.trees              Custom functions to load tree lists so that
                        rwty can do basic processing on the way in.
makeplot.acsf.cumulative
                        Plot the Change in Split Frequencies (CSF) in
                        sliding windows over the course of an MCMC.
makeplot.acsf.sliding   Plot the Chaing in Split Frequencies (CSF) in
                        sliding windows over the course of an MCMC.
makeplot.all.params     Plotting all parameters
makeplot.asdsf          Plot the Standard Deviation of Split
                        Frequencies over the course of an MCMC.
makeplot.autocorr       Make autocorrelation plots of tree topologies
                        from MCMC analyses
makeplot.pairs          Plotting parameters against each other
makeplot.param          Plotting parameters
makeplot.pseudo.ess     Plot the pseudo ESS of tree topologies from
                        MCMC chains.
makeplot.splitfreq.matrix
                        Plots a matrix of split frequency comparisons
                        between multiple MCMC chains.
makeplot.splitfreqs.cumulative
                        Plot cumulative split frequencies over the
                        course of an MCMC
makeplot.splitfreqs.sliding
                        Plot split frequencies in sliding windows over
                        the course of an MCMC
makeplot.topology       Plotting parameters
makeplot.treespace      Plot chains in treespace.
parse.clades            Rename clades for easy recall
parse.slide.clades      Rename clades for easy recall
print.rwty.chain        Function for printing rwty.chain objects
salamanders             MrBayes output from analysis of Williams et al.
                        data
slide.freq              Sliding window measurements of clade split
                        frequencies.
topological.approx.ess
                        Calculate the approximate Effective Sample Size
                        (ESS) of tree topologies
topological.autocorr    Calculate data for autocorrelation plots of
                        tree topologies from MCMC analyses
topological.pseudo.ess
                        Calculate the pseudo Effective Sample Size
                        (ESS) of tree topologies
tree.dist.matrix        Tree distance matrix calculation
treespace               MDS scaling of treespace for a single tree
                        list.
