Description Usage Arguments Details Value Author(s) References See Also Examples
Converts a tree from Newick or matching to moment format
1 |
inputobject |
a tree in Newick format or a |
tip.label |
rearranged labels for tips; these must be the original labels |
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.
a moment L-matrix corresponding to the input phylogentic tree object
Kem Phillips <kemphillips@comcast.net>
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
functions toNewick and toMatching
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)
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