CladeSizes

<code>CladeSizes()</code> reports the number of nodes in each clade in a tree.

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

CladeSizes function

<dl><dt>tree</dt>
<dd>A tree of class <code>phylo</code>.</dd>
<dt>internal</dt>
<dd>Logical specifying whether internal nodes should be counted
towards the size of each clade.</dd>
<dt>nodes</dt>
<dd>Integer specifying indices of nodes at the base of clades
whose sizes should be returned.
If unspecified, counts will be provided for all nodes (including leaves).</dd></dl>

Arguments

Clade sizes — CladeSizes

<dl>

<dt>tree</dt>
<dd>A tree of class <code>phylo</code>.</dd>


<dt>internal</dt>
<dd>Logical specifying whether internal nodes should be counted
towards the size of each clade.</dd>


<dt>nodes</dt>
<dd>Integer specifying indices of nodes at the base of clades
whose sizes should be returned.
If unspecified, counts will be provided for all nodes (including leaves).</dd>

</dl>

CladeSizes: Clade sizes

Description

Usage

Value

Arguments

See Also

Examples