Converts a tree from Newick or matching to moment format

Share:

Description

Converts a tree from Newick or matching to moment format

Usage

1
toMoment(inputobject, tip.label = NULL)

Arguments

inputobject

a tree in Newick format or a matching object defined in the ape package

tip.label

rearranged labels for tips; these must be the original labels

Details

The L-matrix class consists of $5$ components: "L" is the L-matrix in square form. "L.ut" is the L-matrix in upper-triangular form. "Newick" is the Newick representation of the tree. "tip.label" is the character vector of tip labels. "tip.label.n" is the number of tips.

Value

a moment L-matrix corresponding to the input phylogentic tree object

Author(s)

Kem Phillips <kemphillips@comcast.net>

References

K Phillips, Symbolic Computation of the Central Moments of the Multivariate Normal Distribution, Journal of Statistical Software, 2010.

J. Felsenstein, The Newick tree format, 1990, http://evolution.genetics.washington.edu/phylip/newicktree.html

P.W. Diaconis and S. Holmes, Matchings and Phylogenetic Trees, Proc. Natl. Acad. Sci., 1998, 95(25), 14600-14602

See Also

functions toNewick and toMatching

Examples

1
2
3
4
5
6
7
8
# create a Newick object
exam.Newick      <- "(((a,b),c),d);"
# convert to a moment L-matrix
exam.moment <- toMoment(exam.Newick)
# convert to matching object
exam.matching <- toMatching(exam.moment)
# convert back to moment object
backto.moment <- toMoment(exam.matching)