genAltBirthDeathTree: Generation of rooted binary trees under the alternative birth-death model

Description

genAltBirthDeathTree - Generates a rooted binary tree in phylo format with the given number of n leaves under the alternative birth-death model. In the alternative birth-death process all species have the same speciation BIRTHRATE and extinction rates DEATHRATE. Extinct species remain as fossils inside the tree with zero speciation and extinction rates.

Usage

genAltBirthDeathTree(n, BIRTHRATE = 1, DEATHRATE = 0, TRIES = 5)

Value

genAltBirthDeathTree A single tree of class phylo is returned.

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.
BIRTHRATE: Positive numeric value (default = 1) which specifies the rate at which the speciation events occur.
DEATHRATE: Positive numeric value (default = 0) which specifies the rate at which the extinction events occur.
TRIES: Integer value (default = 5) that specifies the number of attempts to generate a tree with n leaves.

References

S. J. Kersting, K. Wicke, and M. Fischer. Tree balance in phylogenetic models. arXiv:2406.05185, 2024.
S. J. Kersting, K. Wicke, and M. Fischer. Tree balance in phylogenetic models: Supplementary material. https://tinyurl.com/278cwdh8, 2024.

Examples

Run this code

genAltBirthDeathTree(n = 7, DEATHRATE = 1)

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