ncf (version 1.1-1)

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)

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.

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