evolqg (version 0.3-4)

PhyloMantel: Mantel test with phylogenetic permutations

Description

Performs a matrix correlation with significance given by a phylogenetic Mantel Test. Pairs of rows and columns are permuted with probability proportional to their phylogenetic distance.

Usage

PhyloMantel(
  tree,
  matrix.1,
  matrix.2,
  ...,
  permutations = 1000,
  ComparisonFunc = function(x, y) cor(x[lower.tri(x)], y[lower.tri(y)]),
  k = 1
)

Value

returns a vector with the comparison value and the proportion of times the observed comparison is smaller than the correlations from the permutations.

Arguments

tree

phylogenetic tree. Tip labels must match names in input matrices

matrix.1

pair-wise comparison/distance matrix

matrix.2

pair-wise comparison/distance matrix

...

additional parameters, currently ignored

permutations

Number of permutations used in significance calculation

ComparisonFunc

comparison function, default is MatrixCor

k

determines the influence of the phylogeny. 1 is strong influence, and larger values converge to a traditional mantel test.

Author

Diogo Melo, adapted from Harmon & Glor 2010

References

Harmon, L. J., & Glor, R. E. (2010). Poor statistical performance of the Mantel test in phylogenetic comparative analyses. Evolution, 64(7), 2173-2178.

Lapointe, F. J., & Garland, Jr, T. (2001). A generalized permutation model for the analysis of cross-species data. Journal of Classification, 18(1), 109-127.

Examples

data(dentus)
data(dentus.tree)
tree = dentus.tree
cor.matrices = dlply(dentus, .(species), function(x) cor(x[-5]))
comparisons = MatrixCor(cor.matrices)

sp.means = dlply(dentus, .(species), function(x) colMeans(x[-5]))
mh.dist = MultiMahalanobis(means = sp.means, cov.matrix = PhyloW(dentus.tree, cor.matrices)$'6')
PhyloMantel(dentus.tree, comparisons, mh.dist, k = 10000)

#similar to MantelCor for large k:
if (FALSE) {
PhyloMantel(dentus.tree, comparisons, mh.dist, k = 10000)
MantelCor(comparisons, mh.dist)
}