tmPDA function

Generation of rooted binary trees under the PDA model

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.

genPDATree(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

genPDATree A single tree of class phylo is returned.

Examples

genPDATree(n = 5)

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.