mantel_test_nbpartners: Compute Mantel test

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Compute Mantel test

Description

This function tests for phylogenetic signal in species interactions in guild A using a Mantel test that keep constant the number of partners per species.

Usage

mantel_test_nbpartners(network, tree_A, tree_B = NULL, method="Jaccard_binary",
nperm = 1000, correlation = "Pearson", verbose=TRUE)

Arguments

network	a matrix representing the bipartite interaction network with species from guild A in columns and species from guild B in rows. Row names (resp. columns names) must correspond to the tip labels of tree B (resp. tree A).
tree_A	a phylogenetic tree of guild A (the columns of the interaction network). It must be an object of class "phylo".
tree_B	(optional) a phylogenetic tree of guild B (the rows of the interaction network). It must be an object of class "phylo".
method	indicates which method is used to compute the phylogenetic signal in species interactions. If you want to perform a Mantel test between the phylogenetic distances and some ecological distances (do closely related species interact with similar partners?), you can choose "Jaccard_weighted" (default) for computing the ecological distances using Jaccard dissimilarities (or "Jaccard_binary" to not take into account the abundances of the interactions), "Bray-Curtis" for computing the Bray-Curtis dissimilarity, or "GUniFrac" for computing the weighted (or generalized) UniFrac distances ("UniFrac_unweighted" to not take into account the interaction abundances).
nperm	a number of permutations to evaluate the significance of the correlation. By default, it equals 1000.
correlation	indicates which correlation (R) must be used among Pearson (default) and Spearman correlations.
verbose	if TRUE, enables printing of messages.

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. Peer Community Journal, Volume 2, article no. e59. doi : 10.24072/pcjournal.179. https://peercommunityjournal.org/articles/10.24072/pcjournal.179/

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

mantel_test

Examples

# Measuring phylogenetic signal in species interactions using a Mantel test 
# with permutations keeping constant the number of partners per species

library(RPANDA)

# Load the data
data(mycorrhizal_network)

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


mantel_test_nbpartners(network, tree_orchids, method="Jaccard_weighted", 
correlation="Pearson",  nperm = 1000)
   

hmorlon/PANDA documentation built on Jan. 13, 2025, 5:35 a.m.