hadamard {phangorn}R Documentation

Hadamard Matrices and Fast Hadamard Multiplication

Description

A collection of functions to perform Hadamard conjugation.

Usage

hadamard(x)
fhm(v)
h2st(obj, levels=c("r","y"))
h4st(obj, levels = c("a","c","g","t"))
write.nexus.splits(obj, file="")

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.
file a file name.

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 K.P.Schliep@massey.ac.nz

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.

See Also

distanceHadamard

Examples

H = hadamard(3)
v = 1:8
H
fhm(v)
## Not run: 
data(Laurasiatherian)
dat = as.character(Laurasiatherian)[1:10,]
# RY-coding
dat[dat=="a"] = "r"
dat[dat=="g"] = "r"
dat[dat=="c"] = "y"
dat[dat=="t"] = "y"

fit = h2st(dat)
write.nexus.splits(fit[fit$edges>1e-4, ][-1,], file = "test.nxs")
# read this file into Spectronet or Splitstree to show the network
unlink("test.nxs") 
## End(Not run)


[Package phangorn version 0.0-5 Index]