expoTree (version 1.0.1)

infExpoTree: Likelihood calculation without density dependence.

Description

Calculates the likelihood of a phylogenetic tree without density dependence. It takes branching and sampling times as an argument and integrates the likelihoood function over the whole tree.

Usage

infExpoTree(pars,times,ttypes,survival=TRUE,vflag=0,root.lineages=0)

Arguments

pars

Vector of parameters. pars = (beta,mu,psi,rho). See 'Details'.

times

Vector of event times.

ttypes

Vector of event types.

survival

Condition on survival of the tree.

vflag

Set verbosity level.

root.lineages

Number of lineages that are extant at the 'root' of the tree.

Value

Likelihood

Details

The parameters are: - beta : Branching rate. For epidemic trees, this is the infection rate. For species trees, this is the speciation rate. - mu : Extinction rate. For epidemic trees, this is the death/recovery rate. For species trees, this is the extinction rate. - psi : Sampling rate. - rho : Initial sampling rate.

References

Tanja Stadler, Journal of Theoretical Biology, 2010

See Also

expoTree

Examples

  times <- cumsum(runif(10))
  ttypes <- rep(1,10)

  N <- 15
  beta <- 1
  mu <- 0.1
  psi <- 0
  rho <- 1

  lik <- infExpoTree(beta,mu,psi,rho,times,ttypes)