tmYule function

Generation of rooted binary trees under the Yule model

genYuleTree - Generates a rooted binary tree in phylo

format with the given number of n leaves under the Yule model. The Yule process is a simple birth-process in which all species have the same speciation rate.

genYuleTree(n)

Arguments

• n: Integer value that specifies the desired number of leaves, i.e., vertices with in-degree 1 and out-degree 0.

  Due to the restrictions of the phylo or multiphylo format, the number of leaves must be at least 2 since there must be at least one edge.

Returns

genYuleTree A single tree of class phylo is returned.

Examples

genYuleTree(n = 5)

References

• This function uses the rtree function of the ape package (E. Paradis, K. Schliep. “ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.” Bioinformatics, 35, 526-528, 2019).
• G. U. Yule. A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S. Philosophical Transactions of the Royal Society of London. Series B, Containing Papers of a Biological Character, 213(402-410):21–87, 1925.
• E. F. Harding. The probabilities of rooted tree-shapes generated by random bifurcation. Advances in Applied Probability, 3(1):44–77, 1971.