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.
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.
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)