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. |