TreeSim (version 2.4)

corsim: corsim: Simulating the missing speciation events in an incomplete phylogenies.

Description

corsim simulates the missing speciation event in an incomplete phylogeny assuming a constant speciation and extinction rate. These rates can be estimated with the functions bd.shifts.optim (if random speciation events are missing) and bd.groups.optim (if only young speciation events are missing) provided in TreePar. corsim allows to specify an upper and lower bound for the times of the missing speciation events.

Usage

corsim(x,lambda,mu,missing,told=0,tyoung=0)

Arguments

x

Vector of the speciation times in the incomplete phylogeny (where time is measured such that 0 is the present and increasing going into the past).

lambda

Speciation rate.

mu

Extincion rate.

missing

Number of missing species (i.e. missing speciation events).

told

Upper bound for the time of missing speciation events. Default is 0 which means no upper bound.

tyoung

Lower bound for the time of missing speciation events. Default is 0 which means no lower bound. tyoung<told unless tyoung=told=0 is required.

Value

x

Vector of speciation times: input and simulated speciation times.

References

N. Cusimano, T. Stadler, S. Renner. A new method for handling missing species in diversification analysis applicable to randomly or non-randomly sampled phylogenies. Syst. Biol., 61(5): 785-792, 2012.

See Also

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

Examples

# NOT RUN {
# Speciation times of a tree with five species:
x<-c(1,1.5,3,5)
# We simulate using the following parameters:
lambda<-2
mu<-1
tyoung<-0.5
told<-4.5
# We simulate 5 additional speciation times (i.e. five additional species):
missing<-5

# xcompleted is x plus 5 additional speciation events between 0.5 and 4.5 timesteps 
# in the past. xcompleted corresponds to a 10-species tree:
xcompleted<-corsim(x,lambda,mu,missing,told,tyoung)
# }