ExtractTaxa

NexusTokens

Extract leaf labels and character states from a Nexus-formatted matrix.

internal

Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://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

Robert Noble

ExtractTaxa function

<dl><dt>matrixLines</dt>
<dd>Character vector containing lines of a file that include
a phylogenetic matrix. See <code>ReadCharacters()</code> for expected format.</dd>
<dt>character_num</dt>
<dd>Index of character(s) to return.
<code>NULL</code>, the default, returns all characters.</dd>
<dt>continuous</dt>
<dd>Logical specifying whether characters are continuous.
Treated as discrete if <code>FALSE</code>.</dd>
<dt>tokens</dt>
<dd>Vector of character strings corresponding to phylogenetic
tokens.</dd></dl>

Arguments

Extract taxa from a matrix block — ExtractTaxa

<dl>

<dt>matrixLines</dt>
<dd>Character vector containing lines of a file that include
a phylogenetic matrix. See <code>ReadCharacters()</code> for expected format.</dd>


<dt>character_num</dt>
<dd>Index of character(s) to return.
<code>NULL</code>, the default, returns all characters.</dd>


<dt>continuous</dt>
<dd>Logical specifying whether characters are continuous.
Treated as discrete if <code>FALSE</code>.</dd>


<dt>tokens</dt>
<dd>Vector of character strings corresponding to phylogenetic
tokens.</dd>

</dl>

ExtractTaxa: Extract taxa from a matrix block

Description

Usage

Value

Arguments

Examples