combineCycleResolutions

Given a list of resolutions of different multifurcations on a tree of blobs
(each as produced by <code>resolveCycle</code>), combine these with the tree
of blobs to form a network.

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

combineCycleResolutions function

<dl><dt>ToB</dt>
<dd>an unrooted tree of blobs for the network, with multifurcating nodes
labelled by <code>labelIntNodes</code></dd>
<dt>resolutions</dt>
<dd>a list of resolutions (each of which may be a list)
for different nodes with elements in format described in output of <code>resolveCycle</code></dd>
<dt>plot</dt>
<dd>if FALSE (0), no plots; if TRUE (&gt;0) plot networks</dd>
<dt>titletext</dt>
<dd>a string of text for plot</dd></dl>

Arguments

Combine several cycle resolutions on a tree of blobs to create a network — combineCycleResolutions

<dl>

<dt>ToB</dt>
<dd>an unrooted tree of blobs for the network, with multifurcating nodes
labelled by <code>labelIntNodes</code></dd>


<dt>resolutions</dt>
<dd>a list of resolutions (each of which may be a list)
for different nodes with elements in format described in output of <code>resolveCycle</code></dd>


<dt>plot</dt>
<dd>if FALSE (0), no plots; if TRUE (&gt;0) plot networks</dd>


<dt>titletext</dt>
<dd>a string of text for plot</dd>

</dl>

combineCycleResolutions: Combine several cycle resolutions on a tree of blobs to create a network

Description

Usage

Value

Arguments

Details

See Also

Examples