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rwty (version 1.0.2)

R We There Yet? Visualizing MCMC Convergence in Phylogenetics

Description

Implements various tests, visualizations, and metrics for diagnosing convergence of MCMC chains in phylogenetics. It implements and automates many of the functions of the AWTY package in the R environment.

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Version

Install

install.packages('rwty')

Monthly Downloads

216

Version

1.0.2

License

GPL-2

Maintainer

Dan Warren

Last Published

February 15th, 2019

Functions in rwty (1.0.2)

combine.ptables

Function for merging p tables for multiple MCMC chains
topological.pseudo.ess

Calculate the pseudo Effective Sample Size (ESS) of tree topologies
topological.approx.ess

Calculate the approximate Effective Sample Size (ESS) of tree topologies
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.
topological.autocorr

Calculate data for autocorrelation plots of tree topologies from MCMC analyses
tree.dist.matrix

Tree distance matrix calculation
treespace

MDS scaling of treespace for a single tree list.
makeplot.acsf.cumulative

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
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
load.multi

Load all matching files from a directory into a list of rwty.chain objects
salamanders

MrBayes output from analysis of Williams et al. data
slide.freq

Sliding window measurements of clade split frequencies.
makeplot.topology

Plotting 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
parse.clades

Rename clades for easy recall
print.rwty.chain

Function for printing rwty.chain objects
makeplot.param

Plotting parameters
makeplot.treespace

Plot chains in treespace.
analyze.rwty

analyze.rwty, the main interface for rwty analyses and plots.
cumulative.freq

Cumulative means of clade split frequencies.
clade.freq

Returns clade names and frequencies
load.trees

Custom functions to load tree lists so that rwty can do basic processing on the way in.
fungus

MrBayes output from analysis of Hibbett et al. data
estimate.autocorr.m

Calculate sampling interval based on exponential semivariogram model.
check.chains

Function for checking suitability of chains for rwty analyses, auto-generating labels, etc
makeplot.pairs

Plotting parameters against each other