infExpoTree: Likelihood calculation without density dependence.
In expoTree: Calculate density dependent likelihood of a phylogenetic tree

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/infExpoTree.R

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.

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

`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.

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.

Likelihood

Gabriel E Leventhal

Tanja Stadler, Journal of Theoretical Biology, 2010

expoTree

  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)