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PhylogeneticEM (version 1.0.0)

clusters_from_shifts: Clustering associated to a shift allocation, assuming no homoplasy.

Description

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).

Usage

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.