toNewick: Convert a Phylogenetic Tree from a Moment L-Matrix to Newick...

In symmoments: Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution

Convert a Phylogenetic Tree from a Moment L-Matrix to Newick Form

Description

Converts a tree structure represented in a moment format back into a Newick format string.

Usage

toNewick(L, type = NULL, tip.label = NULL)

Arguments

L	The input tree structure. This can be an L-matrix object, a square L matrix, or an L matrix in reduced upper-triangular (vector) form.
type	A character string, either 'square' or 'ut'. This must be specified if L is a raw matrix or vector rather than a formal L-matrix object. Defaults to NULL.
tip.label	A character vector containing custom labels for the tips. If NULL (the default), labels fallback to "a" through "z" if there are at most 26 tips; otherwise, 3-letter combinations of the form "aaa", "aab", etc., are generated.

Details

An L-matrix object is a list containing the following 5 components:

• L: The L-matrix in full square form.

• L.ut: The L-matrix in reduced upper-triangular form.

• Newick: The Newick string representation of the tree structure.

• tip.label: A character vector of the tip labels.

• tip.label.n: An integer specifying the total number of tips.

Value

A character string representing the Newick format of the phylogenetic tree corresponding to the input. The output list is assigned the class 'L-Newick', which contains 5 components including the tree string.

Author(s)

Kem Phillips [e-mail]

References

\insertRef

Phillips2010symmoments

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

\insertRefDiaconis1998symmoments

See Also

toMoment, toMatching

Examples

# Create a Newick character string
exam.Newick <- "(((a,b),c),d);"

# Convert to a moment L-matrix
exam.moment <- toMoment(exam.Newick)

# Convert back to Newick format
backto.Newick <- toNewick(exam.moment)

symmoments documentation built on May 27, 2026, 9:06 a.m.