cherry | R Documentation |

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).

cherry(phy)

`phy` |
an object of class |

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.

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

Emmanuel Paradis

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

`gammaStat`

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