mantel.test: Mantel Test for Similarity of Two Matrices
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Author(s) References Examples

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.

1	mantel.test(m1, m2, nperm = 1000, graph = FALSE, ...)

`m1`	a numeric matrix giving a measure of pairwise distances, correlations, or similarities among observations.
`m2`	a second numeric matrix giving another measure of pairwise distances, correlations, or similarities among observations.
`nperm`	the number of times to permute the data.
`graph`	a logical indicating whether to produce a summary graph (by default the graph is not plotted).
`...`	further arguments to be passed to `plot()` (to add a title, change the axis labels, and so on).

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 graph = TRUE, the functions plots the density estimate of the permutation distribution along with the observed Z-statistic as a vertical line.

The ... argument allows the user to give further options to the plot function: the title main be changed with main=, the axis labels with xlab =, and ylab =, and so on.

`z.stat`	the Z-statistic (sum of rows*columns of lower triangle) of the data matrices.
`p`	P-value (quantile of the observed Z-statistic in the permutation distribution).

Original code in S by Ben Bolker bolker@zoo.ufl.edu, ported to R by Julien Claude claude@isem.univ-montp2.fr

Mantel, N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209–220.

Manly, B. F. J. (1986) Multivariate statistical methods: a primer. London: Chapman & Hall.

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")