phangorn: hadamard – R documentation

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hadamard

Hadamard Matrices and Fast Hadamard Multiplication

Description

A collection of functions to perform Hadamard conjugation. Hadamard matrix H with a vector v using fast Hadamard multiplication.

Usage

hadamard(x)

fhm(v)

h4st(obj, levels = c("a", "c", "g", "t"))

h2st(obj, eps = 0.001)

Arguments

`x`	a vector of length 2^n, where n is an integer.
`v`	a vector of length 2^n, where n is an integer.
`obj`	a data.frame or character matrix, typical a sequence alignment.
`levels`	levels of the sequences.
`eps`	Threshold value for splits.

Details

h2st and h4st perform Hadamard conjugation for 2-state (binary, RY-coded) or 4-state (DNA/RNA) data. write.nexus.splits writes splits returned from h2st or distanceHadamard to a nexus file, which can be processed by Spectronet or Splitstree.

Value

hadamard returns a Hadamard matrix. fhm returns the fast Hadamard multiplication.

Author(s)

Klaus Schliep klaus.schliep@gmail.com

References

Hendy, M.D. (1989). The relationship between simple evolutionary tree models and observable sequence data. Systematic Zoology, 38 310–321.

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

Hendy, M. D. (2005). Hadamard conjugation: an analytical tool for phylogenetics. In O. Gascuel, editor, Mathematics of evolution and phylogeny, Oxford University Press, Oxford

Waddell P. J. (1995). Statistical methods of phylogenetic analysis: Including hadamard conjugation, LogDet transforms, and maximum likelihood. PhD thesis.

Examples

H <- hadamard(3)
v <- 1:8
H %*% v
fhm(v)

data(yeast)

# RY-coding
dat_ry <- acgt2ry(yeast)
fit2 <- h2st(dat_ry)
lento(fit2)

# write.nexus.splits(fit2, file = "test.nxs")
# read this file into Spectronet or Splitstree to show the network
## Not run: 
dat <- as.character(yeast)
dat4 <- phyDat(dat, type="USER", levels=c("a","c", "g", "t"), ambiguity=NULL)
fit4 <- h4st(dat4)
old.par <- par(no.readonly = TRUE)
par(mfrow=c(3,1))
lento(fit4[[1]], main="Transversion")
lento(fit4[[2]], main="Transition 1")
lento(fit4[[3]], main="Transition 2")
par(old.par)

## End(Not run)

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