sim.genespeciestree {TreeSim} | R Documentation |
sim.genespeciestree: Simulating birth-death species trees with nested coalescent gene trees.
Description
sim.genespeciestree simulates birth-death species trees (using sim.bd.taxa or sim.bd.taxa.age). Within each species tree, a gene tree is simulated, assuming a coalescent with coalescent rate being 1. The method returns summary statistics for the gene tree.
Usage
sim.genespeciestree(n, numbsim, lambda, mu, frac = 1, age=0)
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 species tree with probability frac. |
age |
The time since origin / most recent common ancestor. If age = 0 (default) a uniform prior for the time since origin is assumed. |
Value
statistics |
For each simulated gene tree the following statistics are returned (with "gammaspecies" being the gamma statistic for the corresponding species tree): "Colless","s","Sackin","cherries","matching of species tree and gene tree","gammaspecies","gamma". |
Author(s)
Tanja Stadler
References
T. Stadler, J. Degnan, N. Rosenberg. Manuscript.
Examples
#Simulate two gene trees within two species trees:
n<-10
lambda <- 2.0
mu <- 0.5
frac <-0.6
numbsim<-2
age<-2
# Simulation is conditioned on 10 final tips
sim.genespeciestree(n, numbsim, lambda, mu, frac, 0)
# Simulation is conditioned on 10 final tips and tree age 2
sim.genespeciestree(n, numbsim, lambda, mu, frac, age)