R: Number of Cherries and Null Models of Trees

cherry {ape} | R Documentation

## 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.

### See Also

`gammaStat`

[Package ape version 5.6-2 Index]