equivCut: Drop duplicated matched nodes

In eliotmiller/shiftPlot: Phylogenetic shift plotting

Drop duplicated matched nodes

Description

Identify which of the duplicated nodes you want to retain.

Usage

equivCut(tree1, tree2, id.results, least.inclusive)

Arguments

tree1	The first tree.
tree2	The second tree.
id.results	Results from a run of the idMatches function.
least.inclusive	Do you want to keep the smallest or largest set of matched taxa. See details.

Details

The point of this function is to drop duplicated nodes that appear more than once in the results for tree 2. If there are multiple nodes in tree 2 which could potentially be mapped to a node in tree 1, do you want to keep the smallest or the largest one? for example: ((A,B),Z) vs (((A,B),Z),C), where C doesn't occur in tree 1. Do you want the matched node from tree 2 to be A,B,Z or A,B,Z,C.

Author(s)

Eliot Miller

eliotmiller/shiftPlot documentation built on March 30, 2023, 4:26 a.m.