zero_constrained: Generates the "zero-constrained" tree described by Susko 2014...

In caseywdunn/hutan: A Collection of Tools for Phylogenetic Tree Manipulation

Description

Generates the "zero-constrained" tree described by Susko 2014 (http://dx.doi.org/10.1093/molbev/msu039)

Usage

zero_constrained(phy_resolved, phy_constraint, epsilon = 1e-06)

Arguments

phy_resolved	A fully resolved phylogeny stored as a phylo object, e.g. an ML tree.
phy_constraint	A partially resolved constraint tree.
epsilon	The value to replace the branch length with

Value

A phylo object containing a tree that is the same as phy_resolved, except that the length of edges that are incompatible with phy_constraint are replaced with epsilon.

Examples

data( siphonophore_ml )
data( siphonophore_constraint )
zc <- zero_constrained( siphonophore_ml, siphonophore_constraint )

caseywdunn/hutan documentation built on June 12, 2020, 3:12 a.m.