Algorithm for simulating a phylogenetic tree under the SGD model

Share:

Description

Simulates a phylogeny arising from the SGD model with exponentially increasing metapopulation size. Notations follow Manceau et al. (2015).

Usage

1
sim_sgd(tau, b, d, nu)

Arguments

tau

the simulation time, which corresponds to the length of the phylogeny

b

the (constant) per-individual birth rate

d

the (constant) per-individual death rate

nu

the (constant) per-individual mutation rate

Value

a phylogenetic tree of class "phylo" (see ape documentation)

Author(s)

M Manceau

References

Manceau M., Lambert A., Morlon H. (2015) Phylogenies support out-of-equilibrium models of biodiversity Ecology Letters 18: 347-356

Examples

1
2
3
4
5
6
tau <- 10
b <- 1e6
d <- b-0.5
nu <- 0.6
tree <- sim_sgd(tau,b,d,nu)
plot(tree)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.