\alias{mantel.test}
\title{Mantel Test for Similarity of Two Matrices}
\usage{
-mantel.test(m1, m2, nperm = 1000, graph = FALSE, ...)
+mantel.test(m1, m2, nperm = 1000, graph = FALSE,
+ alternative = "two.sided", ...)
}
\arguments{
\item{m1}{a numeric matrix giving a measure of pairwise distances,
\item{nperm}{the number of times to permute the data.}
\item{graph}{a logical indicating whether to produce a summary graph
(by default the graph is not plotted).}
+ \item{alternative}{a character string defining the alternative
+ hypothesis: \code{"two.sided"} (default), \code{"less"},
+ \code{"greater"}, or any unambiguous abbreviation of these.}
\item{\dots}{further arguments to be passed to \code{plot()} (to add a
title, change the axis labels, and so on).}
}
\description{
This function computes Mantel's permutation test for similarity of two
matrices. It permutes the rows and columns of the two matrices
- randomly and calculates a Z-statistic.
+ randomly and calculates a \eqn{Z}-statistic.
}
\details{
- The function calculates a Z-statistic for the Mantel test, equal to
+ The function calculates a \eqn{Z}-statistic for the Mantel test, equal to
the sum of the pairwise product of the lower triangles of the
permuted matrices, for each permutation of rows and columns. It
- compares the permuted distribution with the Z-statistic observed for
- the actual data.
+ compares the permuted distribution with the \eqn{Z}-statistic observed
+ for the actual data.
If \code{graph = TRUE}, the functions plots the density estimate of
- the permutation distribution along with the observed Z-statistic as a
- vertical line.
+ the permutation distribution along with the observed \eqn{Z}-statistic
+ as a vertical line.
- The \code{...} argument allows the user to give further options to
+ The \code{\dots} argument allows the user to give further options to
the \code{plot} function: the title main be changed with \code{main=},
the axis labels with \code{xlab =}, and \code{ylab =}, and so on.
}
\value{
- \item{z.stat}{the Z-statistic (sum of rows*columns of lower triangle)
- of the data matrices.}
- \item{p}{P-value (quantile of the observed Z-statistic in the
- permutation distribution).}
+ \item{z.stat}{the \eqn{Z}-statistic (sum of rows*columns of lower
+ triangle) of the data matrices.}
+ \item{p}{\eqn{P}-value (quantile of the observed \eqn{Z}-statistic in
+ the permutation distribution).}
+ \item{alternative}{the alternative hypothesis.}
}
\references{
Mantel, N. (1967) The detection of disease clustering and a
Manly, B. F. J. (1986) \emph{Multivariate statistical methods: a primer.}
London: Chapman & Hall.
}
-\author{Original code in S by Ben Bolker \email{bolker@zoo.ufl.edu}, ported
+\author{
+ Original code in S by Ben Bolker \email{bolker@zoo.ufl.edu}, ported
to \R by Julien Claude \email{claude@isem.univ-montp2.fr}
}
\examples{