ImposeConstraint

AddUnconstrained

Modify a tree such that it matches a specified constraint.
This is at present a somewhat crude implementation that attempts to retain
much of the structure of <code>tree</code> whilst guaranteeing compatibility with
each entry in <code>constraint</code>.

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

ImposeConstraint function

<dl><dt>tree</dt>
<dd>A tree of class <code>phylo</code>.</dd>
<dt>constraint</dt>
<dd>Either an object of class <code>phyDat</code>, in which case returned
trees will be perfectly compatible with each character in <code>constraint</code>;
or a tree of class <code>phylo</code>, in which each node in <code>constraint</code> will occur in
the returned tree.
See <a href="https://ms609.github.io/TreeSearch/articles/tree-search.html">vignette</a>
for further examples.</dd>
<dt>toAdd</dt>
<dd>Character vector specifying taxa to add to constraint.</dd>
<dt>asPhyDat</dt>
<dd>Logical: if <code>TRUE</code>, return a <code>phyDat</code> object; if <code>FALSE</code>,
return a matrix.</dd></dl>

Arguments

<ul>
<li><code>AddUnconstrained()</code>: Expand a constraint to include unconstrained
taxa.</li>
</ul>

Functions

<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

Force a tree to match a constraint — ImposeConstraint

<dl>

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


<dt>constraint</dt>
<dd>Either an object of class <code>phyDat</code>, in which case returned
trees will be perfectly compatible with each character in <code>constraint</code>;
or a tree of class <code>phylo</code>, in which each node in <code>constraint</code> will occur in
the returned tree.
See <a href='https://ms609.github.io/TreeSearch/articles/tree-search.html'>vignette</a>
for further examples.</dd>


<dt>toAdd</dt>
<dd>Character vector specifying taxa to add to constraint.</dd>


<dt>asPhyDat</dt>
<dd>Logical: if <code>TRUE</code>, return a <code>phyDat</code> object; if <code>FALSE</code>,
return 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>)

ImposeConstraint: Force a tree to match a constraint

Description

Usage

Value

Arguments

Functions

Author

See Also

Examples