ncf (version 1.1-2)

mantel.test: Mantel Test

Description

A simple function to do a permutation-based Mantel test. The data can either be two distance/similarity matrices or (x, y, z) data.

Usage

mantel.test(M1 = NULL, M2 = NULL, x = NULL, y = NULL, z = NULL,
    resamp = 1000, latlon = FALSE, quiet = FALSE)

Arguments

M1, M2

similarity/distance matrix 1, and similarity/distance matrix 2

x

vector of length n representing the x coordinates (or longitude; see latlon).

y

vector of length n representing the y coordinates (or latitude).

z

matrix of dimension n x p representing p observation at each location.

resamp

the number of resamples for the null distribution.

latlon

if TRUE, coordinates are latitude and longitude.

quiet

if TRUE the counter is supressed during execution.

Value

• An object of class "Mantel" is returned, consisting of a list with two components:
• correlation
  is the value for the Mantel correlation.
• p
  the randomization-based two-sided p-value.

Details

Typical usages are mantel.test(M1, M2, x = NULL, y = NULL, z = NULL, resamp = 1000, latlon = FALSE, quiet = FALSE) mantel.test(x, y, z, M1=NULL, M2=NULL, resamp = 1000, latlon = FALSE, quiet = FALSE) Missing values are are treated through pairwise deletion.

Examples

#first generate some sample data
    x <- expand.grid(1:20, 1:5)[,1]
    y <- expand.grid(1:20, 1:5)[,2]
#z data from an exponential random field
    z <- cbind(
        rmvn.spa(x=x, y=y, p=2, method="exp"),
        rmvn.spa(x=x, y=y, p=2, method="exp")
        )

#the Mantel test
    mantel.test(x=x, y=y, z=z[,1], resamp=10)