treespace: MDS scaling of treespace for a single tree list.
In rwty: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

Description Usage Arguments Value Examples

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.

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

`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.

Returns a list containing the points and a plot.

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

## End(Not run)

Loading required package: ape
Loading required package: ggplot2
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