MSCsimtester (version 1.0.0)

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. Background is given by Allman, Banos, and Rhodes (2019) .

Copy Link

Version

Install

install.packages('MSCsimtester')

Monthly Downloads

182

Version

1.0.0

License

MIT + file LICENSE

Maintainer

Elizabeth Allman

Last Published

December 15th, 2021

Functions in MSCsimtester (1.0.0)

plotPops

Plot species tree, with population sizes on edges.

print.rootedTripleOutput

Print function for objects of class rootedTripleOutput.

plotEdgeOrder

Plot species tree, with edge numbers on edges.

MSCsimtester

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

print.ADtestOutput

Print function for objects of class ADtestOutput.

pairwiseDist

Compute and plot sample and theoretical pairwise distance densities.

genetreeSample

Simulated gene tree dataset.

ADtest

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

rootedTriple

Compare expected and sample frequencies of topological rooted triples.