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PhylogeneticEM (version 1.8.0)

sample_shifts_edges: Sample shifts edges in a parsimonious way.

Description

sample_shifts_edges attempts to find K shifts in the tree which allocations are parsimonious. The actual generation of edges is done by function sample_edges_intervals.

Usage

sample_shifts_edges(tree, K, part.list = enumerate_tips_under_edges(tree))

Value

vector of edges

Arguments

tree

: input tree

K

: number of edges to be sampled.

Details

This function uses function enumerate_tips_under_edges to generate a list of tips under each edge, and function check_parsimony to check for parsimony of a given solution, under the assumption of an "infinite site model".