initBquartets

This is a C++ function, called from <code>TINNIKdist</code>, to initialize for
inference of B and T quartets.

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

initBquartets function

<dl><dt>pTable</dt>
<dd>a quartet table with p-values</dd>
<dt>m</dt>
<dd>number of rows in pTable</dd>
<dt>alpha</dt>
<dd>critical value for tree test</dd>
<dt>beta</dt>
<dd>critical value for star tree test</dd>
<dt>colptest</dt>
<dd>column with p value for tree test</dd>
<dt>colpstar</dt>
<dd>column with p value for star tree test</dd>
<dt>Bquartets</dt>
<dd>0/1 vector encoding initial B quartets</dd></dl>

Arguments

Initialize vector of B quartets — initBquartets

<dl>

<dt>pTable</dt>
<dd>a quartet table with p-values</dd>


<dt>m</dt>
<dd>number of rows in pTable</dd>


<dt>alpha</dt>
<dd>critical value for tree test</dd>


<dt>beta</dt>
<dd>critical value for star tree test</dd>


<dt>colptest</dt>
<dd>column with p value for tree test</dd>


<dt>colpstar</dt>
<dd>column with p value for star tree test</dd>


<dt>Bquartets</dt>
<dd>0/1 vector encoding initial B quartets</dd>

</dl>

initBquartets: Initialize vector of B quartets

Description

Usage

Arguments

See Also