diff_test.Rd

% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/diff_test.R
\name{diff_test}
\alias{diff_test}
\title{An exact test of population differentiation for genind objects}
\usage{
diff_test(x, sim = TRUE, nreps = 2000)
}
\arguments{
\item{x}{a genind object (from package adegenet)}

\item{sim}{boolean: if TRUE simulate p-value by using an MCMC sample of
those tables that have the same marginal totals as the observed data
(required for all but the smallest datasets)}

\item{nreps}{number of steps used to simulate p-value (default 2000)}
}
\value{
named vector of p-values testing the null hypothesis these samples
where drawn from a panmictic population.
}
\description{
This function uses Fisher's exact test to determine if alleles in
sub-populations are drawn randomly from a larger population (i.e. a
significance test for allelic differentiation among sub-populations).
}
\details{
Note, this test returns p-values for each locus in a dataset _not_
estimates of effect size. Since most populations have some degree of
population differentiation, very large samples are almost guaranteed to
return significant results. Refer to estimates of the various differentiation
statistics (D, G''ST and Phi'ST)to ascertain  how meaningful such results
might be.
}
\examples{
data(nancycats)
diff_test(seploc(nancycats)[[2]], nreps=100)
}
\seealso{
\code{\link{fisher.test}}, which this function wraps
}