.MASTSizeEdges

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

.MASTSizeEdges function

<dl><dt>edge1</dt>
<dd>Edge matrix of tree 1. Must be in postorder!</dd>
<dt>edge2</dt>
<dd>Edge matrix of tree 2.</dd>
<dt>nTip</dt>
<dd>Integer specifying the number of leaves in each split.</dd></dl>

Arguments

Calculate MAST size from edge matrices. — .MASTSizeEdges

<dl>

<dt>edge1</dt>
<dd>Edge matrix of tree 1. Must be in postorder!</dd>


<dt>edge2</dt>
<dd>Edge matrix of tree 2.</dd>


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

</dl>

Calculate MAST size from edge matrices.

.MASTSizeEdges: Calculate MAST size from edge matrices.

Description

Usage

Arguments