# 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.