sim_sgd: Algorithm for simulating a phylogenetic tree under the SGD...

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Algorithm for simulating a phylogenetic tree under the SGD model

Description

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

Usage

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

tau <- 10
b <- 1e6
d <- b-0.5
nu <- 0.6
tree <- sim_sgd(tau,b,d,nu)
plot(tree)

hmorlon/PANDA documentation built on March 8, 2024, 8:36 p.m.