quartetTallyCpp

This is a C++ function, called from quartetTable, to fill in the quartet counts.
From a list of topological distance matrices (1 for each gene tree) it determines all
gene quartets. It is not intended to be used as a stand-alone function, and hence not fully
documented. The faster looping in C++ over R gives substantial time improvements

Methods for analyzing and using quartets displayed on a collection
of gene trees, primarily to make inferences about the species tree or network
under the multi-species coalescent model. These include quartet hypothesis tests
for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>,
simplex plots of quartet concordance factors as presented by Allman et al. (2020)
<doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet
distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and
Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, the NANUQ algorithm for inference
of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>,
the TINNIK algorithm for inference of the tree of blobs of an arbitrary
network of Allman et al.(2022) <doi:10.1007/s00285-022-01838-9>, and
NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in
Allman et al.(2024) (forthcoming).
Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.

John Rhodes

MSCquartets

Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Elizabeth Allman

Hector Banos

Jonathan Mitchell

Kristina Wicke

quartetTallyCpp function

<dl><dt>dList</dt>
<dd>a list of distance matrices</dd>
<dt>M</dt>
<dd>number of sets of 4 taxa</dd>
<dt>nt</dt>
<dd>number of gene trees/distance matrices</dd>
<dt>Q</dt>
<dd>matrix to fill out as table of quartet counts</dd>
<dt>random</dt>
<dd>if 0 compute for all sets of 4 taxa, otherwise for M random ones</dd>
<dt>progressbar</dt>
<dd>if TRUE, display progress bar</dd></dl>

Arguments

Build quartet table from distances — quartetTallyCpp

<dl>

<dt>dList</dt>
<dd>a list of distance matrices</dd>


<dt>M</dt>
<dd>number of sets of 4 taxa</dd>


<dt>nt</dt>
<dd>number of gene trees/distance matrices</dd>


<dt>Q</dt>
<dd>matrix to fill out as table of quartet counts</dd>


<dt>random</dt>
<dd>if 0 compute for all sets of 4 taxa, otherwise for M random ones</dd>


<dt>progressbar</dt>
<dd>if TRUE, display progress bar</dd>

</dl>

quartetTallyCpp: Build quartet table from distances

Description

Usage

Arguments

See Also