treespace: MDS scaling of treespace for a single tree list.

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

Description

This function constructs a distance matrix from a list of trees and uses multi-dimensional scaling to collapse it to a two- dimensional tree space for plotting.

Usage

treespace(chains, n.points = 100, burnin = 0, fill.color = NA)

Arguments

chains	A list of 1 or more rwty.chain objects.
n.points	The minimum number of points you want in your plot.
burnin	The number of trees to eliminate as burnin. Default is zero.
fill.color	The name of the column from the log table that that you would like to use to colour the points in the plot.

Value

Returns a list containing the points and a plot.

Examples

## Not run: 
data(fungus)
treespace(fungus, n.points=50, burnin=20, fill.color="LnL")

## End(Not run)

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