edge_to_splits

Wrapper for internal C++ function for maximum efficiency.
Improper input may crash R. Behaviour not guaranteed.
It is advisable to contact the package maintainers before
relying on this function.

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

edge_to_splits function

<dl><dt>edge</dt>
<dd>A matrix with two columns, with each row listing the parent and
child node of an edge in a phylogenetic tree. Property <code>edge</code> of objects
of class <code>phylo</code>.</dd>
<dt>edgeOrder</dt>
<dd>Integer vector such that <code>edge[edgeOrder, ]</code> returns a
postorder ordering of edges.</dd>
<dt>tipLabels</dt>
<dd>Character vector specifying sequence in which to order
tip labels. Label order must (currently) match to combine or compare separate
<code>Splits</code> objects.</dd>
<dt>asSplits</dt>
<dd>Logical specifying whether to return a <code>Splits</code> object,
or an unannotated two-dimensional array (useful where performance is
paramount).</dd>
<dt>nTip</dt>
<dd>Integer specifying number of leaves in tree.</dd>
<dt>...</dt>
<dd>Presently unused.</dd></dl>

Arguments

Efficiently convert edge matrix to splits — edge_to_splits

<dl>

<dt>edge</dt>
<dd>A matrix with two columns, with each row listing the parent and
child node of an edge in a phylogenetic tree. Property <code>edge</code> of objects
of class <code>phylo</code>.</dd>


<dt>edgeOrder</dt>
<dd>Integer vector such that <code>edge[edgeOrder, ]</code> returns a
postorder ordering of edges.</dd>


<dt>tipLabels</dt>
<dd>Character vector specifying sequence in which to order
tip labels. Label order must (currently) match to combine or compare separate
<code>Splits</code> objects.</dd>


<dt>asSplits</dt>
<dd>Logical specifying whether to return a <code>Splits</code> object,
or an unannotated two-dimensional array (useful where performance is
paramount).</dd>


<dt>nTip</dt>
<dd>Integer specifying number of leaves in tree.</dd>


<dt>...</dt>
<dd>Presently unused.</dd>

</dl>

edge_to_splits: Efficiently convert edge matrix to splits

Description

Usage

Value

Arguments

See Also