ReduceTrees

<code>ReduceTrees()</code> reduces trees according to the tree reduction rules of
Allen2001;textualTreeDist:<ul>
<li>Collapse identical pendant subtrees;</li>
<li>Compress equivalent internal chains.</li>
</ul>

Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median of sets of trees,
and for computing the information content of trees and splits.

Martin R. Smith

TreeDist

Calculate and Map Distances Between Phylogenetic Trees

Roy Jonker

Yong Yang

Yi Cao

ReduceTrees function

<dl><dt>tree1, tree2</dt>
<dd>Single trees of class <code>phylo</code> to undergo comparison.</dd>
<dt>check</dt>
<dd>Logical specifying whether to validate input. Specify
<code>FALSE</code> and you will encounter undefined behaviour if trees are not
binary <code>phylo</code> objects with identical leaf labels, rooted on leaf 1.</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=TreeDist&version=2.9.2" data-mini-rdoc="TreeDist::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Collapse areas of agreement between two trees — ReduceTrees

<dl>

<dt>tree1, tree2</dt>
<dd>Single trees of class <code>phylo</code> to undergo comparison.</dd>


<dt>check</dt>
<dd>Logical specifying whether to validate input. Specify
<code>FALSE</code> and you will encounter undefined behaviour if trees are not
binary <code>phylo</code> objects with identical leaf labels, rooted on leaf 1.</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>)

ReduceTrees: Collapse areas of agreement between two trees

Description

Usage

Value

Arguments

Author

Examples