| mantel_test {RPANDA} | R Documentation |
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
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)