3 \title{Mantel Test for Similarity of Two Matrices}
5 mantel.test(m1, m2, nperm = 1000, graph = FALSE, ...)
8 \item{m1}{a numeric matrix giving a measure of pairwise distances,
9 correlations, or similarities among observations.}
10 \item{m2}{a second numeric matrix giving another measure of pairwise
11 distances, correlations, or similarities among observations.}
12 \item{nperm}{the number of times to permute the data.}
13 \item{graph}{a logical indicating whether to produce a summary graph
14 (by default the graph is not plotted).}
15 \item{...}{further arguments to be passed to \code{plot()} (to add a
16 title, change the axis labels, and so on).}
19 This function computes Mantel's permutation test for similarity of two
20 matrices. It permutes the rows and columns of the two matrices
21 randomly and calculates a Z-statistic.
24 The function calculates a Z-statistic for the Mantel test, equal to
25 the sum of the pairwise product of the lower triangles of the
26 permuted matrices, for each permutation of rows and columns. It
27 compares the permuted distribution with the Z-statistic observed for
30 If \code{graph = TRUE}, the functions plots the density estimate of
31 the permutation distribution along with the observed Z-statistic as a
34 The \code{...} argument allows the user to give further options to
35 the \code{plot} function: the title main be changed with \code{main=},
36 the axis labels with \code{xlab =}, and \code{ylab =}, and so on.
39 \item{z.stat}{the Z-statistic (sum of rows*columns of lower triangle)
40 of the data matrices.}
41 \item{p}{P-value (quantile of the observed Z-statistic in the
42 permutation distribution).}
45 Mantel, N. (1967) The detection of disease clustering and a
46 generalized regression approach. \emph{Cancer Research}, \bold{27},
49 Manly, B. F. J. (1986) \emph{Multivariate statistical methods: a primer.}
50 London: Chapman & Hall.
52 \author{Original code in S by Ben Bolker \email{bolker@zoo.ufl.edu}, ported
53 to R by Julien Claude \email{claude@isem.univ-montp2.fr}
56 q1 <- matrix(runif(36), nrow = 6)
57 q2 <- matrix(runif(36), nrow = 6)
58 mantel.test(q1, q2, graph = TRUE,
59 main = "Mantel test: a random example with 6 X 6 matrices",
60 xlab = "z-statistic", ylab = "Density",
61 sub = "The vertical line shows the observed z-statistic")
63 \keyword{multivariate}