ncf (version 1.1-2)

partial.mantel.test: 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.

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).

Details

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

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)