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