Evaluate

A tree of class <code><a rd-options="" href="/link/phylo?package=TreeSearch&version=0.2.2" data-mini-rdoc="TreeSearch::phylo">phylo</a></code>.

tree

A phylogenetic data matrix of class <code><a rd-options="phangorn" href="/link/phyDat?package=TreeSearch&version=0.2.2&to=phangorn" data-mini-rdoc="phangorn::phyDat">phyDat</a></code>, whose names 
correspond to the labels of any accompanying tree.

dataset

Boolean (<code>TRUE</code>/<code>FALSE</code>): display warnings when concavity 
functions are generated by approximation.

warn

Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith
(2019) <doi:10.1093/sysbio/syy083>.

Martin R. Smith

TreeSearch

Phylogenetic Tree Search Using Custom Optimality Criteria

Emmanuel Paradis

Klaus Schliep

Martin Brazeau

Evaluate function

A tree of class <code><a rd-options='' href='phylo'>phylo</a></code>.

A phylogenetic data matrix of class <code><a rd-options='phangorn' href='phyDat'>phyDat</a></code>, whose names 
correspond to the labels of any accompanying tree.

Evaluate: Evaluate tree

Description

Usage

Arguments