KeptPaths

KeptPaths.data.frame

KeptPaths.matrix

Lists which paths present in a master tree are present when leaves are
dropped.

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

KeptPaths function

<dl><dt>paths</dt>
<dd><code>data.frame</code> of paths in master tree, perhaps generated using
<code>PathLengths()</code>.</dd>
<dt>keptVerts</dt>
<dd>Logical specifying whether each entry is retained in the
reduced tree, perhaps generated using <code>KeptVerts()</code>.</dd>
<dt>all</dt>
<dd>Logical: if <code>TRUE</code>, return all paths that occur in the reduced
tree; if <code>FALSE</code>, return only those paths that correspond to a single edge.
that correspond to edges in the reduced tree.
Ignored if <code>paths</code> is a matrix.</dd></dl>

Arguments

<a href="https://orcid.org/0000-0001-5660-1727">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeTools&version=1.12.0" data-mini-rdoc="TreeTools::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Paths present in reduced tree — KeptPaths

<dl>

<dt>paths</dt>
<dd><code>data.frame</code> of paths in master tree, perhaps generated using
<code>PathLengths()</code>.</dd>


<dt>keptVerts</dt>
<dd>Logical specifying whether each entry is retained in the
reduced tree, perhaps generated using <code>KeptVerts()</code>.</dd>


<dt>all</dt>
<dd>Logical: if <code>TRUE</code>, return all paths that occur in the reduced
tree; if <code>FALSE</code>, return only those paths that correspond to a single edge.
that correspond to edges in the reduced tree.
Ignored if <code>paths</code> is a matrix.</dd>

</dl>

<a href='https://orcid.org/0000-0001-5660-1727'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

KeptPaths: Paths present in reduced tree

Description

Usage

Value

Arguments

Author

See Also

Examples