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

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.

AuthorDan Warren <dan.l.warren@gmail.com>, Anthony Geneva <anthony.geneva@gmail.com>, Rob Lanfear <rob.lanfear@gmail.com>
Date of publication2016-06-22 05:42:18
MaintainerDan Warren <dan.l.warren@gmail.com>
LicenseGPL-2
Version1.0.1

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.

Functions

analyze.rwty Man page
check.chains Man page
clade.freq Man page
combine.ptables Man page
cumulative.freq Man page
estimate.autocorr.m Man page
fungus Man page
load.multi Man page
load.trees Man page
makeplot.acsf.cumulative Man page
makeplot.acsf.sliding Man page
makeplot.all.params Man page
makeplot.asdsf Man page
makeplot.autocorr Man page
makeplot.pairs Man page
makeplot.param Man page
makeplot.pseudo.ess Man page
makeplot.splitfreq.matrix Man page
makeplot.splitfreqs.cumulative Man page
makeplot.splitfreqs.sliding Man page
makeplot.topology Man page
makeplot.treespace Man page
parse.clades Man page
print.rwty.trees Man page
salamanders Man page
slide.freq Man page
topological.approx.ess Man page
topological.autocorr Man page
topological.pseudo.ess Man page
tree.dist.matrix Man page
treespace Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.