cpp_mutual_clustering_all_pairs

Internal function. Computes all pairwise MCI scores for a set of trees,
using OpenMP threads when available (falling back to single-threaded
execution otherwise). No interrupt checking is performed inside the
parallel region; the outer R call remains interruptible between batches.

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

Neil Kaye

cpp_mutual_clustering_all_pairs function

<dl><dt>splits_list</dt>
<dd>A list of split matrices (class <code>Splits</code> or <code>RawMatrix</code>),
one per tree, all covering the same tip set. Typically the object
returned by <code>as.Splits(trees, tipLabels = labs, asSplits = FALSE)</code>.</dd>
<dt>n_tip</dt>
<dd>Integer; number of tips shared by all trees.</dd></dl>

Arguments

Pairwise mutual clustering information — batch computation — cpp_mutual_clustering_all_pairs

<dl>

<dt>splits_list</dt>
<dd>A list of split matrices (class <code>Splits</code> or <code>RawMatrix</code>),
one per tree, all covering the same tip set. Typically the object
returned by <code>as.Splits(trees, tipLabels = labs, asSplits = FALSE)</code>.</dd>


<dt>n_tip</dt>
<dd>Integer; number of tips shared by all trees.</dd>

</dl>

cpp_mutual_clustering_all_pairs: Pairwise mutual clustering information — batch computation

Description

Usage

Value

Arguments