phytools: markChanges – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

markChanges

Add marked changes to a plotted tree with mapped discrete character

This function adds the reconstructed changes to a plotted tree with a stochastically mapped discrete character.

markChanges(tree, colors=NULL, cex=1, lwd=2, plot=TRUE)

`tree`	an object of class `"simmap"`.
`colors`	a named vector of colors used to plot the stochastically mapped character on the tree.
`cex`	expansion factor for line height.
`lwd`	line width.
`plot`	logical value indicating whether the changes should be plotted or not.

This function returns (invisibly) a matrix containing the x & y coordinates of the marked changes on the plotted tree.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.