cpp_transfer_consensus

Transfer consensus (C++ implementation)

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_transfer_consensus function

<dl><dt>splits_list</dt>
<dd>List of raw matrices (one per tree), each from as.Splits().</dd>
<dt>n_tip</dt>
<dd>Number of tips.</dd>
<dt>scale</dt>
<dd>Logical: use scaled transfer distance?</dd>
<dt>greedy_best_flag</dt>
<dd>Logical: TRUE for "best", FALSE for "first".</dd>
<dt>init_majority</dt>
<dd>Logical: TRUE to start from majority-rule splits.</dd></dl>

Arguments

Transfer consensus (C++ implementation) — cpp_transfer_consensus

<dl>

<dt>splits_list</dt>
<dd>List of raw matrices (one per tree), each from as.Splits().</dd>


<dt>n_tip</dt>
<dd>Number of tips.</dd>


<dt>scale</dt>
<dd>Logical: use scaled transfer distance?</dd>


<dt>greedy_best_flag</dt>
<dd>Logical: TRUE for "best", FALSE for "first".</dd>


<dt>init_majority</dt>
<dd>Logical: TRUE to start from majority-rule splits.</dd>

</dl>

cpp_transfer_consensus: Transfer consensus (C++ implementation)

Description

Usage

Value

Arguments