genPDATree {poweRbal}

Generation of rooted binary trees under the PDA model

Description

genPDATree - Generates a rooted binary tree in phylo format with the given number of n leaves under the proportional-to-distinguishable-arrangements model. Given n, all phylogenies (trees with labeled leaves) with n leaves are equiprobable under the PDA.
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.

Usage

genPDATree(n)

Arguments

n

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

Value

genPDATree A single tree of class phylo is returned.

Author(s)

Sophie Kersting

References

• This function uses the rtopology(..., rooted = T) 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).
  

• D. E. Rosen. Vicariant patterns and historical explanation in biogeography. Systematic Zoology, 27(2):159, 1978.

Examples

genPDATree(n = 5)