sim.bd.taxa.age: sim.bd.taxa.age: Simulating birth-death trees with a given...
In TreeSim: Simulating Phylogenetic Trees

Description Usage Arguments Value Note Author(s) References See Also Examples

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.

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

`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.

treearray

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

The algorithm is fast for the critical process, lambda=mu.

Tanja Stadler

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

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

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)