Man pages for danlwarren/RWTY
R We There Yet? Visualizing MCMC Convergence in Phylogenetics

analyze.rwtyanalyze.rwty, the main interface for rwty analyses and plots.
check.chainsFunction for checking suitability of chains for rwty...
clade.freqReturns clade names and frequencies
combine.ptablesFunction for merging p tables for multiple MCMC chains
cumulative.freqCumulative means of clade split frequencies.
estimate.autocorr.mCalculate sampling interval based on exponential...
fungusMrBayes output from analysis of Hibbett et al. data
load.multiLoad all matching files from a directory into a list of...
load.treesCustom functions to load tree lists so that rwty can do basic...
makeplot.acsf.cumulativePlot the Change in Split Frequencies (CSF) in sliding windows...
makeplot.acsf.slidingPlot the Chaing in Split Frequencies (CSF) in sliding windows...
makeplot.all.paramsPlotting all parameters
makeplot.asdsfPlot the Standard Deviation of Split Frequencies over the...
makeplot.autocorrMake autocorrelation plots of tree topologies from MCMC...
makeplot.pairsPlotting parameters against each other
makeplot.paramPlotting parameters
makeplot.pseudo.essPlot the pseudo ESS of tree topologies from MCMC chains.
makeplot.splitfreq.matrixPlots a matrix of split frequency comparisons between...
makeplot.splitfreqs.cumulativePlot cumulative split frequencies over the course of an MCMC
makeplot.splitfreqs.slidingPlot split frequencies in sliding windows over the course of...
makeplot.topologyPlotting parameters
makeplot.treespacePlot chains in treespace.
parse.cladesRename clades for easy recall
print.rwty.chainFunction for printing rwty.chain objects
salamandersMrBayes output from analysis of Williams et al. data
slide.freqSliding window measurements of clade split frequencies.
topological.approx.essCalculate the approximate Effective Sample Size (ESS) of tree...
topological.autocorrCalculate data for autocorrelation plots of tree topologies...
topological.pseudo.essCalculate the pseudo Effective Sample Size (ESS) of tree...
tree.dist.matrixTree distance matrix calculation
treespaceMDS scaling of treespace for a single tree list.
danlwarren/RWTY documentation built on Nov. 7, 2019, 5:30 p.m.