rwty: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

Share:

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.

Author
Dan Warren <dan.l.warren@gmail.com>, Anthony Geneva <anthony.geneva@gmail.com>, Rob Lanfear <rob.lanfear@gmail.com>
Date of publication
2016-06-22 05:42:18
Maintainer
Dan Warren <dan.l.warren@gmail.com>
License
GPL-2
Version
1.0.1

View on CRAN

Man pages

analyze.rwty
analyze.rwty, the main interface for rwty analyses and plots.
check.chains
Function for checking suitability of chains for rwty...
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...
fungus
MrBayes output from analysis of Hibbett et al. data
load.multi
Load all matching files from a directory into a list of...
load.trees
Custom functions to load tree lists so that rwty can do basic...
makeplot.acsf.cumulative
Plot the Change in Split Frequencies (CSF) in sliding windows...
makeplot.acsf.sliding
Plot the Chaing in Split Frequencies (CSF) in sliding windows...
makeplot.all.params
Plotting all parameters
makeplot.asdsf
Plot the Standard Deviation of Split Frequencies over the...
makeplot.autocorr
Make autocorrelation plots of tree topologies from MCMC...
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...
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...
makeplot.topology
Plotting parameters
makeplot.treespace
Plot chains in treespace.
parse.clades
Rename clades for easy recall
print.rwty.trees
Function for printing rwty.trees 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...
topological.autocorr
Calculate data for autocorrelation plots of tree topologies...
topological.pseudo.ess
Calculate the pseudo Effective Sample Size (ESS) of tree...
tree.dist.matrix
Tree distance matrix calculation
treespace
MDS scaling of treespace for a single tree list.

Files in this package

rwty
rwty/NAMESPACE
rwty/data
rwty/data/fungus.RData
rwty/data/salamanders.RData
rwty/data/datalist
rwty/R
rwty/R/check.chains.R
rwty/R/cumulative.freq.R
rwty/R/analyze.rwty.R
rwty/R/makeplot.asdsf.R
rwty/R/topological.pseudo.ess.R
rwty/R/parse.clades.R
rwty/R/makeplot.splitfreqs.cumulative.R
rwty/R/makeplot.autocorr.R
rwty/R/makeplot.acsf.cumulative.R
rwty/R/treespace.R
rwty/R/fungus.R
rwty/R/makeplot.pseudo.ess.R
rwty/R/makeplot.splitfreq.matrix.R
rwty/R/makeplot.topology.R
rwty/R/print.rwty.trees.R
rwty/R/topological.autocorr.R
rwty/R/makeplot.treespace.R
rwty/R/load.trees.R
rwty/R/estimate.autocorr.m.R
rwty/R/makeplot.all.params.R
rwty/R/salamanders.R
rwty/R/makeplot.pairs.R
rwty/R/makeplot.acsf.sliding.R
rwty/R/topological.approx.ess.R
rwty/R/slide.freq.R
rwty/R/clade.freq.R
rwty/R/tree.dist.matrix.R
rwty/R/makeplot.param.R
rwty/R/makeplot.splitfreqs.sliding.R
rwty/R/combine.ptables.R
rwty/R/load.multi.R
rwty/MD5
rwty/DESCRIPTION
rwty/man
rwty/man/check.chains.Rd
rwty/man/makeplot.topology.Rd
rwty/man/load.multi.Rd
rwty/man/topological.approx.ess.Rd
rwty/man/makeplot.pairs.Rd
rwty/man/combine.ptables.Rd
rwty/man/salamanders.Rd
rwty/man/topological.pseudo.ess.Rd
rwty/man/makeplot.treespace.Rd
rwty/man/parse.clades.Rd
rwty/man/makeplot.splitfreqs.cumulative.Rd
rwty/man/treespace.Rd
rwty/man/makeplot.splitfreqs.sliding.Rd
rwty/man/analyze.rwty.Rd
rwty/man/topological.autocorr.Rd
rwty/man/print.rwty.trees.Rd
rwty/man/estimate.autocorr.m.Rd
rwty/man/makeplot.param.Rd
rwty/man/makeplot.splitfreq.matrix.Rd
rwty/man/makeplot.acsf.cumulative.Rd
rwty/man/load.trees.Rd
rwty/man/clade.freq.Rd
rwty/man/tree.dist.matrix.Rd
rwty/man/makeplot.acsf.sliding.Rd
rwty/man/makeplot.asdsf.Rd
rwty/man/slide.freq.Rd
rwty/man/makeplot.autocorr.Rd
rwty/man/makeplot.all.params.Rd
rwty/man/fungus.Rd
rwty/man/cumulative.freq.Rd
rwty/man/makeplot.pseudo.ess.Rd