GeneralizedRF

An internal function to calculate Generalized Robinson–Foulds
distances from splits.

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>;
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

GeneralizedRF function

<dl><dt>splits1, splits2</dt>
<dd>Logical matrices where each row corresponds to a leaf,
either listed in the same order or bearing identical names (in any sequence),
and each column corresponds to a split, such that each leaf is identified as
a member of the ingroup (<code>TRUE</code>) or outgroup (<code>FALSE</code>) of the respective
split.</dd>
<dt>nTip</dt>
<dd>Integer specifying the number of leaves in each split.</dd>
<dt>PairScorer</dt>
<dd>function taking four arguments, <code>splits1</code>, <code>splits2</code>,
<code>nSplits1</code>, <code>nSplits2</code>, which should return the score of each pair of splits
in a two-dimensional matrix. Additional parameters may be specified via
....</dd>
<dt>reportMatching</dt>
<dd>Logical specifying whether to return the clade
matchings as an attribute of the score.</dd>
<dt>...</dt>
<dd>Additional parameters to <code>PairScorer</code></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

Generalized Robinson–Foulds distance — GeneralizedRF

<dl>

<dt>splits1, splits2</dt>
<dd>Logical matrices where each row corresponds to a leaf,
either listed in the same order or bearing identical names (in any sequence),
and each column corresponds to a split, such that each leaf is identified as
a member of the ingroup (<code>TRUE</code>) or outgroup (<code>FALSE</code>) of the respective
split.</dd>


<dt>nTip</dt>
<dd>Integer specifying the number of leaves in each split.</dd>


<dt>PairScorer</dt>
<dd>function taking four arguments, <code>splits1</code>, <code>splits2</code>,
<code>nSplits1</code>, <code>nSplits2</code>, which should return the score of each pair of splits
in a two-dimensional matrix. Additional parameters may be specified via
....</dd>


<dt>reportMatching</dt>
<dd>Logical specifying whether to return the clade
matchings as an attribute of the score.</dd>


<dt>...</dt>
<dd>Additional parameters to <code>PairScorer</code></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>)

GeneralizedRF: Generalized Robinson–Foulds distance

Description

Usage

Value

Arguments

Author

Details