R We There Yet? Visualizing MCMC Convergence in Phylogenetics

---

Documentation for package ‘rwty’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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
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.