TreeSim (version 2.4)

sim.bd.taxa.age: sim.bd.taxa.age: Simulating birth-death trees with a given age on a fixed number of extant taxa.

Description

sim.bd.taxa.age simulates trees on n species with a (i) fixed time since origin or (ii) fixed time since the most recent common ancestor of the sampled species under the constant rate birth-death process. The method allows for incomplete sampling, i.e. each extant tip from a complete tree is included with a fixed probability. The tree is conditioned to have n tips after sampling and a fixed time since origin or since the most recent common ancestor of the sampled species.

Usage

sim.bd.taxa.age(n, numbsim, lambda, mu, frac = 1, age, mrca = FALSE)

Arguments

n

Number of extant sampled tips.

numbsim

Number of trees to simulate.

lambda

Speciation rate.

mu

Extinction rate.

frac

Each tip is included into the final tree with probability frac.

age

The time since origin / most recent common ancestor.

mrca

If mrca = FALSE: The time since the origin of the process. If mrca = TRUE: The time since the most recent common ancestor of the sampled species.

Value

treearray

Array of numbsim trees with n>1 tips with a given age. The extinct lineages are not included.

References

T. Stadler: On incomplete sampling under birth-death models and connections to the sampling-based coalescent. J. Theo. Biol. (2009) 261: 58-66.

See Also

sim.bd.age, sim.rateshift.taxa, sim.gsa.taxa, birthdeath.tree

Examples

# NOT RUN {
n<-10
lambda <- 2.0
mu <- 0.5
frac <-0.6
numbsim<-2
age<-2

##
# Simulating numbsim reconstructed trees with n sampled species under a
# birth-death process with speciation rate lambda, extinction rate mu,
# sampling probability frac, and time age since origin:

sim.bd.taxa.age(n, numbsim, lambda, mu, frac, age, mrca = FALSE)

# Simulating numbsim reconstructed trees with n sampled species under a
# birth-death process with speciation rate lambda, extinction rate mu,
# sampling probability frac, and time age since the most recent 
# common ancestor of the extant sampled species:

sim.bd.taxa.age(n, numbsim, lambda, mu, frac, age, mrca = TRUE)

# }