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phangorn

distanceHadamard

Distance Hadamard

Description

Distance Hadamard produces spectra of splits from a distance matrix.

Usage

distanceHadamard(dm, eps = 0.001)

Arguments

dm

A distance matrix.
eps

Threshold value for splits.

Value

distanceHadamard returns a matrix. The first column contains the distance spectra, the second one the edge-spectra. If eps is positive an object of with all splits greater eps is returned.

Author(s)

Klaus Schliep klaus.schliep@gmail.com, Tim White

References

Hendy, M. D. and Penny, D. (1993). Spectral Analysis of Phylogenetic Data. Journal of Classification, 10, 5-24.

See Also

Examples

data(yeast)
dm <- dist.hamming(yeast)
dm <- as.matrix(dm)
fit <- distanceHadamard(dm)
lento(fit)
plot(as.networx(fit), "2D")
phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0
GPL (>= 2)
Authors
Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]
Initial release

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