SplitsCompatible

Determine whether splits are compatible (concave); i.e. they can both occur
on a single tree.

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 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

SplitsCompatible function

<dl><dt>split1, split2</dt>
<dd>Logical vectors listing leaves in a consistent order,
identifying each leaf as a member of the ingroup (<code>TRUE</code>) or outgroup
(<code>FALSE</code>) of the split in question.</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=2.7.0" data-mini-rdoc="TreeDist::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Are splits compatible? — SplitsCompatible

<dl>

<dt>split1, split2</dt>
<dd>Logical vectors listing leaves in a consistent order,
identifying each leaf as a member of the ingroup (<code>TRUE</code>) or outgroup
(<code>FALSE</code>) of the split in question.</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>)

SplitsCompatible: Are splits compatible?

Description

Usage

Value

Arguments

Author

Examples