Revision e57f926191f2e69cb915090695d0d354c0639bc2 authored by Emmanuel Paradis on 04 February 2004, 00:00:00 UTC, committed by Gabor Csardi on 04 February 2004, 00:00:00 UTC
1 parent 2055920
mantel.test.Rd
\name{mantel.test}
\alias{mantel.test}
\title{Mantel Test for Similarity of Two Matrices}
\usage{
mantel.test(m1, m2, nperm = 1000, graph = FALSE, ...)
}
\arguments{
\item{m1}{a numeric matrix giving a measure of pairwise distances,
correlations, or similarities among observations.}
\item{m2}{a second numeric matrix giving another measure of pairwise
distances, correlations, or similarities among observations.}
\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{...}{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.
}
\details{
The function calculates a 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.
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 \code{...} 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).}
}
\references{
Mantel, N. (1967) The detection of disease clustering and a
generalized regression approach. \emph{Cancer Research}, \bold{27},
209--220.
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
to R by Julien Claude \email{claude@isem.univ-montp2.fr}}
\examples{
q1 <- matrix(runif(36), nrow = 6)
q2 <- matrix(runif(36), nrow = 6)
mantel.test(q1, q2, graph = TRUE,
main = "Mantel test: a random example with 6 X 6 matrices",
xlab = "z-statistic", ylab = "Density",
sub = "The vertical line shows the observed z-statistic")
}
\keyword{multivariate}
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