% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/MSCsimtester.R
\docType{package}
\name{MSCsimtester-package}
\alias{MSCsimtester}
\alias{MSCsimtester-package}
\title{Validity tests of simulators of the multspecies coalescent model in phylogenomics.}
\description{
The package performs comparisons of certain summary statistics for simulated gene tree samples to
theoretical predictions under the multispecies coalescent model.
The primary functions are \code{rootedTriple} for comparison of frequencies of topological rooted triples
on gene trees, and \code{pairwiseDist} and \code{ADtest} for comparison of the distributions of pairwise
distances between taxa on gene trees.
}
\details{
Required input is a collection of gene trees, stored as a \code{multiPhylo} object by the \code{ape} package,
and a rooted species tree, as a \code{Phylo} object,
with edge lengths in generations, together with constant population sizes for each edge.

\code{MSCsimtester} builds on the packages \code{ape} and \code{kSamples}.

For further examples of use and citation purposes, see \insertRef{2022allman-MSCsimtester}{MSCsimtester}.
}
\references{
\insertRef{2022allman-MSCsimtester}{MSCsimtester}
}
\author{
\strong{Maintainer}: Elizabeth Allman \email{e.allman@alaska.edu} [copyright holder]

Authors:
\itemize{
  \item Elizabeth Allman \email{e.allman@alaska.edu} [copyright holder]
  \item Hector Banos \email{hbassnos@gmail.com} [copyright holder]
  \item John Rhodes \email{j.rhodes@alaska.edu} [copyright holder]
}

}
