R: getx: Calculating the vector of speciation / transmission...
getx
R Documentation
getx: Calculating the vector of speciation / transmission times and sampling times for a phylogenetic tree.
Description
getx calculates the vector of branching (speciation / transmission) times and sampling times for a phylogenetic tree (which may have polytomies). This vector is the input for the TreePar methods.
Usage
getx(datatree,sersampling)
Arguments
datatree
Phylogenetic tree.
sersampling
Set sersampling = 0 if all tips are from one timepoint; 1 otherwise.
Value
x
Vector of branching times where 0 is the present and time increasing into the past; If sersampling = 1: Vector of branching and tip sampling times. Second column indicates for each time if branching event (1) or tip (0).
Author(s)
Tanja Stadler
Examples
### tree with tips sampled at one timepoint
n<-10
lambda <- 2.0
mu <- 0.5
frac <-0.6
numbsim<-1
trees<-sim.bd.taxa(n, numbsim, lambda, mu, frac,complete=FALSE,stochsampling=TRUE)
branching<-getx(trees[[1]])
### tree with tips sampled sequentially through time
set.seed(1)
n<-10
lambda <- c(2,1,2)
mu <- c(1,0.5,1.5)
sampprob <-c(0.5,0.5,0.5)
times<-c(0,1,2)
numbsim<-2
trees<-lapply(rep(n,numbsim),sim.bdsky.stt,lambdasky=lambda,deathsky=mu,
timesky=times,sampprobsky=sampprob,rho=0,timestop=0)
branchingserial<-getx(trees[[1]][[1]],sersampling=1)
providing 
.