MatrixToPhyDat

PhyDatToMatrix

matrix of tokens, probably created with <code><a rd-options="=ReadCharacters" href="/link/ReadCharacters()?package=TreeTools&version=1.4.1&to=%3DReadCharacters" data-mini-rdoc="=ReadCharacters::ReadCharacters()">ReadCharacters()</a></code>
or <code><a rd-options="=ReadTntCharacters" href="/link/ReadTntCharacters()?package=TreeTools&version=1.4.1&to=%3DReadTntCharacters" data-mini-rdoc="=ReadTntCharacters::ReadTntCharacters()">ReadTntCharacters()</a></code>. Row names should correspond to tip
labels; column names may optionally correspond to
character labels.

tokens

A dataset of class <code>phyDat</code>.

dataset

<code>MatrixToPhyDat()</code> converts a matrix of tokens to a <code>phyDat</code> object;
<code>PhyDatToMatrix()</code> converts a <code>phyDat</code> object to a matrix of tokens.

internal

Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of node support;
calculation of ancestor-descendant relationships;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.

Martin R. Smith

TreeTools

Create, Modify and Analyse Phylogenetic Trees

Emmanuel Paradis

MatrixToPhyDat function

matrix of tokens, probably created with <code><a rd-options='=ReadCharacters' href='ReadCharacters()'>ReadCharacters()</a></code>
or <code><a rd-options='=ReadTntCharacters' href='ReadTntCharacters()'>ReadTntCharacters()</a></code>. Row names should correspond to tip
labels; column names may optionally correspond to
character labels.

MatrixToPhyDat: Convert between matrices and `phyDat` objects

Description

Usage

Arguments

Value

See Also