Clustering associated to a shift allocation, assuming no homoplasy.

Source: R/parsimonyNumber.R

clusters_from_shifts take a vector of shifts edges, and gives the clustering of the tips induced by them, in a "no homoplasy" model (i.e. no convergence is allowed).

clusters_from_shifts(tree, edges, part.list = enumerate_tips_under_edges(tree))

Arguments

tree

phylogenetic tree

edges

a vector of edges of the tree, where the shifts are

part.list

a list giving the descendant tips of each edge

Value

list of size n+m-1, entry i is the vector of tips bellow edge i.

Details

By default, this function uses enumerate_tips_under_edges to compute the list of tips under each edge.