| genAltBirthDeathTree {poweRbal} | R Documentation |
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.
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
genAltBirthDeathTree(n, BIRTHRATE = 1, DEATHRATE = 0, TRIES = 5)
Arguments
n |
Integer value that specifies the desired number of leaves, i.e., vertices with in-degree 1 and out-degree 0. |
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 |
Value
genAltBirthDeathTree A single tree of class phylo is
returned.
Author(s)
Sophie Kersting
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
genAltBirthDeathTree(n = 7, DEATHRATE = 1)