check_parsimony: Check Parsimony, assuming no homoplasy

In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Check Parsimony, assuming no homoplasy

Description

check_parsimony take a vector of shifts edges, and check whether the number of groups of the tips induced by this allocation is exactly the number of shifts plus one. This is equivalent to parsimony when there is no homoplasy (i.e. no convergent regimes).

Usage

check_parsimony(tree, edges, ...)

Arguments

tree	phylogenetic tree
edges	a vector of edges of the tree, where the shifts are
...	possibly, a list giving the descendant tips of each edge

Details

This function computes explicitly the clustering of the tips, using function clusters_from_shifts. By default, this function uses enumerate_tips_under_edges to compute the list of tips under each edge, but a list can be provided (to avoid extra computation, if many tests on the same tree are done).

Value

boolean : TRUE if the allocation is parsimonious.

PhylogeneticEM documentation built on Aug. 31, 2022, 9:16 a.m.