ape: cherry – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

cherry

Number of Cherries and Null Models of Trees

Description

This function calculates the number of cherries (see definition below) on a phylogenetic tree, and tests the null hypotheses whether this number agrees with those predicted from two null models of trees (the Yule model, and the uniform model).

Usage

cherry(phy)

Arguments

phy

an object of class "phylo".

Details

A cherry is a pair of adjacent tips on a tree. The tree can be either rooted or unrooted, but the present function considers only rooted trees. The probability distribution function of the number of cherries on a tree depends on the speciation/extinction model that generated the tree.

McKenzie and Steel (2000) derived the probability distribution function of the number of cherries for two models: the Yule model and the uniform model. Broadly, in the Yule model, each extant species is equally likely to split into two daughter-species; in the uniform model, a branch is added to tree on any of the already existing branches with a uniform probability.

The probabilities are computed using recursive formulae; however, for both models, the probability density function converges to a normal law with increasing number of tips in the tree. The function uses these normal approximations for a number of tips greater than or equal to 20.

Value

A NULL value is returned, the results are simply printed.

Author(s)

Emmanuel Paradis

References

McKenzie, A. and Steel, M. (2000) Distributions of cherries for two models of trees. Mathematical Biosciences, 164, 81–92.

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24