fitCycleOrders

Compute residual sum of squares (RSS) comparing empirical distance for a blob
to an expected one for a cycle with each given order/designated hybrid. This is used
in NANAUQ+ commands for resolving multifurcations in a tree of blobs to a cycle

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

fitCycleOrders function

<dl><dt>D</dt>
<dd>an empirical distance table</dd>
<dt>E</dt>
<dd>an expected distance table, to be reordered</dd>
<dt>orders</dt>
<dd>a vector indicating an order, or matrix whose rows give orders, to fit</dd></dl>

Arguments

Compute fit of circular orders to distance with least squares — fitCycleOrders

<dl>

<dt>D</dt>
<dd>an empirical distance table</dd>


<dt>E</dt>
<dd>an expected distance table, to be reordered</dd>


<dt>orders</dt>
<dd>a vector indicating an order, or matrix whose rows give orders, to fit</dd>

</dl>

fitCycleOrders: Compute fit of circular orders to distance with least squares

Description

Usage

Value

Arguments

See Also