mantel_test function

Compute Mantel test

Compute Mantel test

This function computes a Mantel test between two dissimilarity matrices. The available correlations are Pearson, Spearman, and Kendall.

mantel_test(formula = formula(data), data = sys.parent(),
correlation = "Pearson", nperm = 1000)

Arguments

  • formula: formula y ~ x describing the test to be conducted where y and x are distance matrices (as "dist" objects).
  • data: an optional data frame containing the variables in the model as columns of dissimilarities. By default, the variables are taken from the current environment.
  • correlation: indicates which correlation (R) must be used among Pearson (default), Spearman, and Kendall correlations.
  • nperm: a number of permutations to evaluate the significance of the correlation. By default, it equals 1000, but this can be very long for the Kendall correlation.

Returns

  • mantelr: Mantel correlation (R).

  • pval1: one-tailed p-value (null hypothesis: R <= 0).

  • pval2: one-tailed p-value (null hypothesis: R >= 0).

  • pval3: two-tailed p-value (null hypothesis: R = 0).

Details

This function is adapted from the function mantel in the R-package ecodist (Goslee & Urban, 2007).

References

Perez-Lamarque B, Maliet O, Pichon B, Selosse M-A, Martos F, Morlon H. 2022. Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks. bioRxiv, 2021.08.30.458192, ver. 6 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.08.30.458192

Goslee, S.C. & Urban, D.L. (2007). The ecodist package for dissimilarity-based analysis of ecological data. J. Stat. Softw., 22, 1–19.

Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27:209-220.

Author(s)

Benoît Perez-Lamarque

See Also

phylosignal_network

phylosignal_sub_network

Examples

# Measuring phylogenetic signal in species interactions using a Mantel test 
# (do closely related species interact with similar partners?)

library(RPANDA)

# Load the data
data(mycorrhizal_network)

network <- mycorrhizal_network[[1]] # bipartite interaction matrix 
tree_orchids <- mycorrhizal_network[[2]] # phylogenetic tree (phylo object)

network <- network[,tree_orchids$tip.label]

ecological_distances <- as.matrix(vegan::vegdist(t(network), "jaccard", binary=FALSE))
    
phylogenetic_distances <- cophenetic.phylo(tree_orchids)

mantel_test(as.dist(ecological_distances) ~ as.dist(phylogenetic_distances), 
correlation="Pearson",  nperm = 10000)
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