sim.bd.age: sim.bd.age: Simulating birth-death trees of a fixed age.

Description

sim.bd.age simulates trees conditioned on (i) the time since origin or (ii) the time since the most recent common ancestor of the extant tips. The method allows for incomplete sampling: only a fixed fraction of all tips is included in the sampled tree. The method assumes constant birth and death rates, or allows for a density-dependent birth rate. If you want to have species-age dependent rates, use sim.age in R package TreeSimGM.

Usage

sim.bd.age(age, numbsim, lambda, mu, frac = 1, mrca = FALSE,
 complete = TRUE, K = 0)

Arguments

age

Time since origin / most recent common ancestor.

numbsim

Number of trees to simulate.

lambda

Speciation rate.

If K=0, then lambda is constant. If K>0, density-dependent speciation is assumed, with speciation rate = lambda(1-m/K) when there are m extant species.

Extinction rate.

frac

Sampling fraction: The actual number of tips is n/frac, but only n tips are included (incomplete sampling).

mrca

If mrca=FALSE: age is the time since origin. If mrca=TRUE: age is the time since most recent common ancestor of the extant tips.

complete

If complete = TRUE, the tree with the extinct and non-sampled lineages is returned. If complete = FALSE, the extinct and non-sampled lineages are suppressed.

Value

treearray

Array of 'numbsim' trees with the time since origin / most recent common ancestor being 'age'. If tree goes extinct or no tips are sampled (only possible when mrca = FALSE), return value is '0'. If only one extant and no extinct tips are sampled, return value is '1'.

References

T. Stadler. Simulating trees on a fixed number of extant species. Syst. Biol., 60: 676-684, 2011.

Examples

Run this code

# NOT RUN {
age<-2
lambda <- 2.0
mu <- 0.5
frac <-0.6
numbsim<-3

##
# Simulating trees with time age since the origin:

sim.bd.age(age,numbsim,lambda,mu,mrca=FALSE,complete=TRUE)
# }
# NOT RUN {
<!-- % sim.bd.age(age,numbsim,lambda,mu,frac,mrca=FALSE,complete=FALSE) -->
# }
# NOT RUN {
# }
# NOT RUN {
<!-- % # Simulating trees with time age since the time of the most recent common  -->
# }
# NOT RUN {
<!-- % # ancestor of the extant and sampled species: -->
# }
# NOT RUN {
# }
# NOT RUN {
<!-- % sim.bd.age(age,numbsim,lambda,mu,mrca=TRUE,complete=TRUE) -->
# }
# NOT RUN {
<!-- % sim.bd.age(age,numbsim,lambda,mu,frac,mrca=TRUE,complete=FALSE) -->
# }