partial.mantel.test {ncf}R Documentation

Partial Mantel test

Description

A simple function to calculate permutation-based partial mantel tests for three matrices, the partial mantel test is calculated to test for relationships between M1 and M2 (M3) cotrolling for M3 (M2). syntax and logic follows Legendre and Legendre (1998) pp 557-558

Usage

partial.mantel.test(M1, M2, M3, resamp = 1000, method = "pearson", quiet = FALSE)

Arguments

M1, M2, M3 similarity/distance matrices 1, 2 and 3.
resamp the number of resamples for the null distribution.
method The method to be used for calculating the correlations.
quiet if TRUE the counter is supressed during execution.

Details

Missing values are are treated through pairwise deletion. The method must be one of pearson (default), spearman or kendall

Value

An object of class "partial.Mantel" is returned, consisting of a list with two components:

MantelR the vector of observed Mantel and partial Mantel correlations.
p is the vector of two-sided p-value under randomization (of M1).

Author(s)

Ottar N. Bjornstad onb1@psu.edu

References

Legendre, P., and L. Legendre. 1998. Numerical Ecology, 2nd edition. Elsevier, Amsterdam

See Also

mantel.test

Examples

#first generate some sample data and dissimilarity matrices
    x <- rnorm(10)
    y <- rnorm(10)
    z <- rnorm(10)
    M1 <- sqrt(outer(x, x, "-")^2)
    M2 <- sqrt(outer(y, y, "-")^2)
    M3 <- sqrt(outer(z, z, "-")^2)

    partial.mantel.test(M1=M1, M2=M2, M3=M3, resamp=10)

[Package ncf version 1.1-3 Index]