This function returns a matrix in which the first column contains all the internal nodes for tr1 and the second column contains the matching nodes from tr2, inasmuch as they can be identified. For method="descendants", pairs of matching nodes are defined by sharing all descendant leaves in common. for method="distances", nodes are considered to matched if the share the same set of distances (or proportional distances, for optional argument corr=TRUE) to all tips. matchLabels is functionally equivalent but matches node (tip) numbers based on the labels only.
matchNodes(tr1, tr2, method=c("descendants","distances"), ...)
matchLabels(tr1, tr2)first tree.
second tree.
method to use to match nodes between trees. "descendants" uses the tip species descended from each node; "distances" uses the distances from the nodes to the tips. Any umambiguous shortening of "descendants" or "distances" is allowed.
optional arguments which may or may not be used depending on method. tol is a tolerance value for the difference from exact matching that is allowed for method="distances". corr, which is FALSE by default, indicates whether to match nodes under method="distances" using the correlation (corr=TRUE) or the absolute similarity of distances.
A matrix in which the first column contains the nodes of tr1 with the second column containing matching nodes in tr2, with the criterion for matching defined by method.
Primarily designed to be used internally by fastAnc.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.