clone

clone.HPart

Clone / duplicate an object
<code>clone()</code> physically duplicates objects

internal

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>;
the Hierarchical Mutual Information (Perotti et al. 2015)
<doi:10.1103/PhysRevE.92.062825>;
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

clone function

<dl><dt>x</dt>
<dd>the object to be cloned</dd>
<dt>...</dt>
<dd>additional parameters for methods</dd>
<dt>tipLabels</dt>
<dd>Character vector specifying sequence in which to order
tip labels.</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=2.11.1" data-mini-rdoc="TreeDist::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Clone / duplicate an object
clone() physically duplicates objects — clone

<dl>

<dt>x</dt>
<dd>the object to be cloned</dd>


<dt>...</dt>
<dd>additional parameters for methods</dd>


<dt>tipLabels</dt>
<dd>Character vector specifying sequence in which to order
tip labels.</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>)

clone: Clone / duplicate an object `clone()` physically duplicates objects

Description

Usage

Value

Arguments

Author