Creates phylomorphospace plot (Sidlauskas 2008).
phylomorphospace(): This function takes a "phylo" tree object along with one or two matrices, X and (optionally) A, containing the character states for two traits for tips (in X) and internal nodes (A); it can also take vectors for the colors of plotted edges and nodes. It then creates a phylomorphospace plot following Sidlauskas (2008). If A is not specified it will be estimated using the "ape" function ace() (ancestral character estimation).
Input
phylomorphospace(tree,X,A=NULL,label=TRUE,control=list())
"tree" is a phylogenetic tree in "phylo" format;
"X" is an n x 2 matrix of tip values for two characters in n species;
"A" is an optional m x 2 matrix (for m nodes) of values for two traits at internal nodes of the tree;
"label" if TRUE will print the tip labels next to the terminal nodes of the tree;
"control" is a list containing the following optional values:
"col.edge" a vector of edge colors - this should be named with the right index of tree$edge;
"col.node" a vector of node colors.
Output
phylomorphospace() creates a phylomorphospace plot.
Citation
Function written by Liam J. Revell 2010 (updated 2011).
Based on: Sidlauskas, B. 2008. Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach. Evolution 12: 3135-3156.
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Last modified Mar. 8, 2011.