sim.bd.age {TreeSim} | R Documentation |
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.
sim.bd.age(age, numbsim, lambda, mu, frac = 1, mrca = FALSE,
complete = TRUE, K = 0)
age |
Time since origin / most recent common ancestor. |
numbsim |
Number of trees to simulate. |
lambda |
Speciation rate. |
K |
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. |
mu |
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. |
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'. |
Tanja Stadler
T. Stadler. Simulating trees on a fixed number of extant species. Syst. Biol., 60: 676-684, 2011.
sim.bd.taxa, sim.rateshift.taxa, sim.gsa.taxa, birthdeath.tree, sim.age
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)