tomatching: Convert representation of a phylogenetic tree as a moment...
In symmoments: Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution

Description Usage Arguments Details Value Author(s) References See Also Examples

Function converts a tree in moment format to matching format.

The input can be an L-matrix object, a square L matrix, or an L matrix in reduced upper-triangular (vector) form.

The toMatching function sets its list output to class L-matching, which has 5 components, including the tree in matching format.

1	toMatching(L, type = NULL, tip.label = NULL)

`L`	An `L-matrix` object, a square L matrix, or an L matrix in reduced upper-triangular (vector) form.
`type`	If object is not of class "L-matrix" and is a square L matrix, then type should be "square'. If it is an L matrix in upper triangular form, type should be "ut".
`tip.label`	Character vector containing labels for tips. If null, labels default to "a"-"z" it at most 26; otherwise, 3-letter labels of the form "aaa", "aab",...

An L-matrix object is a list with 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.

a matching representation of the phylogenetic tree corresponding to the input

Kem Phillips <kemphillips@comcast.net

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

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

functions toMoment and toNewick

# create a Newick object
exam.Newick      <- "(((a,b),c),d);"
# convert to a moment L-matrix
exam.moment <- toMoment(exam.Newick)
# convert to matching format
exam.matching <- toMatching(exam.moment)