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MSCsimtester (version 1.1)

Tests of Multispecies Coalescent Gene Tree Simulator Output

Description

Statistical tests for validating multispecies coalescent gene tree simulators, using pairwise distances and rooted triple counts. See Allman ES, Baños HD, Rhodes JA 2023. Testing multispecies coalescent simulators using summary statistics, IEEE/ACM Trans Comput Biol Bioinformat, 20(2):1613–1618. .

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Version

Install

install.packages('MSCsimtester')

Monthly Downloads

181

Version

1.1

License

MIT + file LICENSE

Maintainer

Elizabeth Allman

Last Published

June 2nd, 2025

Functions in MSCsimtester (1.1)

ADtest

Anderson-Darling test comparing sample and theoretical pairwise distance distributions.
genetreeSample

Simulated gene tree dataset.
print.ADtestOutput

Print function for objects of class ADtestOutput.
print.rootedTripleOutput

Print function for objects of class rootedTripleOutput.
rootedTriple

Compare expected and sample frequencies of topological rooted triples.
pairwiseDist

Compute and plot sample and theoretical pairwise distance densities.
plotEdgeOrder

Plot species tree, with edge numbers on edges.
plotPops

Plot species tree, with population sizes on edges.
MSCsimtester

Validity tests of simulators of the multspecies coalescent model in phylogenomics.