evolqg: PhyloMantel – R documentation

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PhyloMantel

Mantel test with phylogenetic permutations

Description

Performs a matrix correlation with significance given by a phylogenetic Mantel Test. Pairs of rowns 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
)

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
`...`	aditional 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.

Value

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

Note

This method should only be used when there is no option other than representing data as pair-wise. It suffers from low power, and alternatives should be used when available.

Author(s)

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:
## Not run: 
PhyloMantel(dentus.tree, comparisons, mh.dist, k = 10000)
MantelCor(comparisons, mh.dist)

## End(Not run)

evolqg

Tools for Evolutionary Quantitative Genetics

v0.2-8

MIT + file LICENSE

Authors

Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Andrade Machado, Guilherme Garcia

Initial release

2020-11-14