NonDuplicateRoot

the first column of the edge matrix of 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>, i.e. tree$edge[, 1]

parent

the second column of the edge matrix of 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>, i.e. tree$edge[, 2]

child

(optional) integer specifying the number of edges of 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>, i.e. <code>dim(tree$edge)[1]</code>

nEdge

Identify, for each edge, whether it is not a duplicate of the root edge

internal

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

NonDuplicateRoot function

the first column of the edge matrix of a tree of class <code><a rd-options='' href='phylo'>phylo</a></code>, i.e. tree$edge[, 1]

the second column of the edge matrix of a tree of class <code><a rd-options='' href='phylo'>phylo</a></code>, i.e. tree$edge[, 2]

(optional) integer specifying the number of edges of a tree of
class <code><a rd-options='' href='phylo'>phylo</a></code>, i.e. <code>dim(tree$edge)[1]</code>

NonDuplicateRoot: Non-duplicate root

Description

Usage

Arguments