pvalHist

Graphical exploration of extreme p-values from quartet hypothesis tests, to aid in choosing critical values
for hypothesis tests. Log base 10 of p-values exceeding some minimum are plotted, to explore gaps in
the tail of the distribution.

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

pvalHist function

<dl><dt>pTable</dt>
<dd>a quartet table with p-values, such as from <code>NANUQ</code>, <code>quartetTreeTestInd</code>,
or <code>quartetStarTestInd</code></dd>
<dt>model</dt>
<dd>one of <code>"T1"</code>, <code>"T3"</code>, or <code>"star"</code>, where <code>pTable</code>
contains a column <code>p_model</code> of p-values</dd>
<dt>pmin</dt>
<dd>include only p-values above <code>pmin</code> in the histogram</dd></dl>

Arguments

Plot histogram of log p-values in table — pvalHist

<dl>

<dt>pTable</dt>
<dd>a quartet table with p-values, such as from <code>NANUQ</code>, <code>quartetTreeTestInd</code>,
or <code>quartetStarTestInd</code></dd>


<dt>model</dt>
<dd>one of <code>"T1"</code>, <code>"T3"</code>, or <code>"star"</code>, where <code>pTable</code>
contains a column <code>p_model</code> of p-values</dd>


<dt>pmin</dt>
<dd>include only p-values above <code>pmin</code> in the histogram</dd>

</dl>

pvalHist: Plot histogram of log p-values in table

Description

Usage

Arguments

Details

See Also

Examples