## mantel.test.R (2006-07-28)
## Mantel Test for Similarity of Two Matrices
## Copyright 2002-2006 Ben Bolker and Julien Claude
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
perm.rowscols <- function(m1, n)
{
s <- sample(1:n)
m1[s, s]
}
### calculate the Mantel z-statistic for two square matrices m1 and m2
mant.zstat <- function(m1, m2) sum(lower.triang(m1 * m2))
lower.triang <- function(m)
{
d <- dim(m)
if (d[1] != d[2]) print("Warning: non-square matrix")
m[col(m) <= row(m)]
}
mantel.test <- function (m1, m2, nperm = 1000, graph = FALSE, ...)
{
n <- nrow(m1)
realz <- mant.zstat(m1, m2)
nullstats <- replicate(nperm, mant.zstat(m1, perm.rowscols(m2, n)))
pval <- sum(nullstats > realz)/nperm
if (graph) {
plot(density(nullstats), type = "l", ...)
abline(v = realz)
}
list(z.stat = realz, p = pval)
}
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