quartetTableResolved

Converts table of all quartet counts, including unresolved ones,
by either dropping unresolved ones, or distributing them uniformly
among the three resolved counts.

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

quartetTableResolved function

<dl><dt>qt</dt>
<dd>table, as produced by <code>quartetTable</code> for <code>n</code> taxa, with <code>n+4</code> columns</dd>
<dt>omit</dt>
<dd><code>TRUE</code> deletes unresolved quartets column;
<code>FALSE</code> deletes the column but redistributes unresolved counts as (1/3,1/3,1/3) to resolved counts</dd></dl>

Arguments

Modify quartet table to show only resolved quartets — quartetTableResolved

<dl>

<dt>qt</dt>
<dd>table, as produced by <code>quartetTable</code> for <code>n</code> taxa, with <code>n+4</code> columns</dd>


<dt>omit</dt>
<dd><code>TRUE</code> deletes unresolved quartets column;
<code>FALSE</code> deletes the column but redistributes unresolved counts as (1/3,1/3,1/3) to resolved counts</dd>

</dl>

quartetTableResolved: Modify quartet table to show only resolved quartets

Description

Usage

Value

Arguments

See Also

Examples