makeplot.splitfreq.matrix: Plots a matrix of split frequency comparisons between...

In danlwarren/RWTY: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

Description

This function takes list of rwty.chain objects, and returns a scatterplot matrix in which each plot shows the split frequencies of all clades that appear in one or both MCMC chains at least once. In the upper diagonal, we show the correlation between the split frequencies (Pearson's R), and the Average Standard Deviation of the split frequencies.

Usage

makeplot.splitfreq.matrix(chains, burnin = 0)

Arguments

chains	A list of rwty.chain objects.
burnin	The number of trees to eliminate as burnin

Value

output A list of two plots: the first is a matrix of scatterplots, where each point is a clade, and the values are the split frequencies of that clade in the post-burnin trees of each chain. The second plot is a tree of the chains clustered by their ASDSFs.

Examples

## Not run: 
data(salamanders)
makeplot.splitfreq.matrix(salamanders[1:4], burnin = 20)

## End(Not run)

danlwarren/RWTY documentation built on Sept. 5, 2021, 8:35 p.m.