CollessLike-package: Distribution and Percentile of Sackin, Cophenetic and...

In CollessLike: Distribution and Percentile of Sackin, Cophenetic and Colless-Like Balance Indices of Phylogenetic Trees

Description

Computation of Colless-Like, Sackin and cophenetic balance indices of a phylogenetic tree and study of the distribution of these balance indices under the alpha-gamma model. For more details see A. Mir, F. Rossello, L. Rotger (2013) <doi:10.1016/j.mbs.2012.10.005> and (2018) <doi:10.1371/journal.pone.0203401>, M. J. Sackin (1972) <doi:10.1093/sysbio/21.2.225>, D. H. Colless (1982) <doi:10.2307/2413420>.

Details

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Author(s)

Arnau Mir, Francesc Rossello, Lucia Rotger

Maintainer: Lucia Rotger <[e-mail]>

References

B. Chen, D. Ford, M. Winkel, A new family of Markov branching trees: the alpha-gamma model. Electr. J. Probab. 14 (2009), 400-430.

A. Mir, F. Rossello, L. Rotger, A Colless-like balance index for multifurcating phylogenetic trees.

A. Mir, F. Rossello, L. Rotger, A new balance index for phylogenetic trees. Mathematical Biosciences 241 (2013), 125-136.

M. J. Sackin, "Good" and "bad" phenograms. Sys. Zool, 21 (1972), 225-226.

Examples

# A random phylogenetic tree of 5 leaves between all trees with 5 leaves 
# following the alpha-gamma model with alpha=0.5 and gamma=0.3
a.g.tree = a.g.model(5,0.5,0.3)
# To compute the percentile of that tree of the Colless-Like,
# Sackin and cophenetic normalized balance indices under the alpha-gamma
# model with alpha=0.5 and gamma=0.3, and a distribution plot.
#distribution(a.g.tree,0.5,0.3,db.path=getwd())
# For a percentile plot set the parameter percentile.plot as TRUE
#distribution(a.g.tree,0.5,0.3,db.path=getwd(),percentile.plot=TRUE)
 
# Computation of the Colless-Like, Sackin and cophenetic balance indices
# of a sample of 50 trees that follow the alpha-gamma distribution
# with alpha=0.5 and gamma=0.3 with 5 leaves.
  indices.data = indices.simulation(5,0.5,0.3,50)
# Computation of the percentile of the random tree using the previous 
# generated sample  
  distribution(a.g.tree,0.5,0.3,set.indices=indices.data)

CollessLike documentation built on Oct. 30, 2019, 12:05 p.m.