mantel_test: Compute Mantel test

In RPANDA: Phylogenetic ANalyses of DiversificAtion

Compute Mantel test

Description

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

Usage

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.

Details

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

Value

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).

Author(s)

Benoît Perez-Lamarque

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.

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)
      

RPANDA documentation built on Oct. 24, 2022, 5:06 p.m.