SplitsRepeated

Logical matrix describing the bipartition splits
defined by a tree (see <a rd-options="" href="/link/Tree2Splits?package=TreeSearch&version=0.3.2" data-mini-rdoc="TreeSearch::Tree2Splits">Tree2Splits</a> for format). The first row
of <code>original</code> must be <code>FALSE</code> for all splits.

original, matches

Determines whether any of the splits described in <code>original</code> are present in
<code>matches</code>.

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

SplitsRepeated function

Logical matrix describing the bipartition splits
defined by a tree (see <a rd-options='' href='Tree2Splits'>Tree2Splits</a> for format). The first row
of <code>original</code> must be <code>FALSE</code> for all splits.

SplitsRepeated: Are Splits Repeated?

Description

Usage

Arguments

Value