mantel: Mantel and Partial Mantel Tests for Dissimilarity Matrices

In vegan: Community Ecology Package

Description

Function mantel finds the Mantel statistic as a matrix correlation between two dissimilarity matrices, and function mantel.partial finds the partial Mantel statistic as the partial matrix correlation between three dissimilarity matrices. The significance of the statistic is evaluated by permuting rows and columns of the first dissimilarity matrix.

Usage

mantel(xdis, ydis, method="pearson", permutations=999, strata = NULL,
    na.rm = FALSE, parallel = getOption("mc.cores"))
mantel.partial(xdis, ydis, zdis, method = "pearson", permutations = 999, 
    strata = NULL, na.rm = FALSE, parallel = getOption("mc.cores"))

Arguments

xdis, ydis, zdis	Dissimilarity matrices or a dist objects.
method	Correlation method, as accepted by cor: "pearson", "spearman" or "kendall".
permutations	a list of control values for the permutations as returned by the function how, or the number of permutations required, or a permutation matrix where each row gives the permuted indices.
strata	An integer vector or factor specifying the strata for permutation. If supplied, observations are permuted only within the specified strata.
na.rm	Remove missing values in calculation of Mantel correlation. Use this option with care: Permutation tests can be biased, in particular if two matrices had missing values in matching positions.
parallel	Number of parallel processes or a predefined socket cluster. With parallel = 1 uses ordinary, non-parallel processing. The parallel processing is done with parallel package.

Details

Mantel statistic is simply a correlation between entries of two dissimilarity matrices (some use cross products, but these are linearly related). However, the significance cannot be directly assessed, because there are N(N-1)/2 entries for just N observations. Mantel developed asymptotic test, but here we use permutations of N rows and columns of dissimilarity matrix. See permutations for additional details on permutation tests in Vegan.

Partial Mantel statistic uses partial correlation conditioned on the third matrix. Only the first matrix is permuted so that the correlation structure between second and first matrices is kept constant. Although mantel.partial silently accepts other methods than "pearson", partial correlations will probably be wrong with other methods.

The function uses cor, which should accept alternatives pearson for product moment correlations and spearman or kendall for rank correlations.

Value

The function returns a list of class mantel with following components:

Call	Function call.
method	Correlation method used, as returned by cor.test.
statistic	The Mantel statistic.
signif	Empirical significance level from permutations.
perm	A vector of permuted values. The distribution of permuted values can be inspected with permustats function.
permutations	Number of permutations.
control	A list of control values for the permutations as returned by the function how.

Note

Legendre & Legendre (2012, Box 10.4) warn against using partial Mantel correlations.

Author(s)

Jari Oksanen

References

The test is due to Mantel, of course, but the current implementation is based on Legendre and Legendre.

Legendre, P. and Legendre, L. (2012) Numerical Ecology. 3rd English Edition. Elsevier.

See Also

cor for correlation coefficients, protest (“Procrustes test”) for an alternative with ordination diagrams, anosim and mrpp for comparing dissimilarities against classification. For dissimilarity matrices, see vegdist or dist. See bioenv for selecting environmental variables.

Examples

## Is vegetation related to environment?
data(varespec)
data(varechem)
veg.dist <- vegdist(varespec) # Bray-Curtis
env.dist <- vegdist(scale(varechem), "euclid")
mantel(veg.dist, env.dist)
mantel(veg.dist, env.dist, method="spear")

Example output

Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3

Mantel statistic based on Pearson's product-moment correlation 

Call:
mantel(xdis = veg.dist, ydis = env.dist) 

Mantel statistic r: 0.3047 
      Significance: 0.001 

Upper quantiles of permutations (null model):
  90%   95% 97.5%   99% 
0.112 0.144 0.176 0.206 
Permutation: free
Number of permutations: 999


Mantel statistic based on Spearman's rank correlation rho 

Call:
mantel(xdis = veg.dist, ydis = env.dist, method = "spear") 

Mantel statistic r: 0.2838 
      Significance: 0.001 

Upper quantiles of permutations (null model):
  90%   95% 97.5%   99% 
0.108 0.144 0.166 0.202 
Permutation: free
Number of permutations: 999

vegan documentation built on May 2, 2019, 5:51 p.m.