quartetCutTestInd

Perform a hypothesis test for all quartet counts in an input table, as if the counts for different choices of 4 taxa
are independent.

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

quartetCutTestInd function

<dl><dt>rqt</dt>
<dd>table of resolved quartet counts, as produced by <code>quartetTableResolved</code>, or <code>quartetStarTestInd</code></dd>
<dt>lambda</dt>
<dd>power divergence statistic parameter (e.g., 0 for likelihood ratio statistic, 1 for Chi-squared statistic)</dd>
<dt>method</dt>
<dd><code>"MLest"</code>, <code>"conservative"</code>, or <code>"bootstrap"</code>; see <code>quartetCutTest</code> for explanation</dd>
<dt>smallcounts</dt>
<dd><code>"bootstrap"</code> or <code>"approximate"</code>, method of obtaining p-value when some counts are small, so
the chosen <code>method</code> is inappropriate</dd>
<dt>bootstraps</dt>
<dd>number of samples for bootstrapping</dd></dl>

Arguments

Multiple independent hypothesis tests for quartet counts fitting the Cut model under the NMSC — quartetCutTestInd

<dl>

<dt>rqt</dt>
<dd>table of resolved quartet counts, as produced by <code>quartetTableResolved</code>, or <code>quartetStarTestInd</code></dd>


<dt>lambda</dt>
<dd>power divergence statistic parameter (e.g., 0 for likelihood ratio statistic, 1 for Chi-squared statistic)</dd>


<dt>method</dt>
<dd><code>"MLest"</code>, <code>"conservative"</code>, or <code>"bootstrap"</code>; see <code>quartetCutTest</code> for explanation</dd>


<dt>smallcounts</dt>
<dd><code>"bootstrap"</code> or <code>"approximate"</code>, method of obtaining p-value when some counts are small, so
the chosen <code>method</code> is inappropriate</dd>


<dt>bootstraps</dt>
<dd>number of samples for bootstrapping</dd>

</dl>

quartetCutTestInd: Multiple independent hypothesis tests for quartet counts fitting the Cut model under the NMSC

Description

Usage

Value

Arguments

Details

References

See Also

Examples