sample_shifts_edges: Sample shifts edges in a parsimonious way.

In pbastide/PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

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))

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".

Value

vector of edges

pbastide/PhylogeneticEM documentation built on Feb. 12, 2024, 1:27 a.m.