PhyloMantel: Mantel test with phylogenetic permutations In evolqg: Tools for Evolutionary Quantitative Genetics

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

 ```1 2 3``` ```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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16``` ```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) ```

Example output

```Loading required package: plyr
Rsquared Probability
0.4891338   0.0690000
Rsquared Probability
0.4891338   0.0680000
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Rsquared Probability
0.4891338   0.0750000
Warning message:
In MantelCor.default(comparisons, mh.dist) :
Matrices do not appear to be correlation matrices. Use with caution.
```

evolqg documentation built on May 30, 2017, 1:52 a.m.