RPANDA (version 1.2)

likelihood_coal_cst: Likelihood of a phylogeny under the equilibrium diversity model

Description

Computes the likelihood of a phylogeny under the equilibrium diversity model with potentially time-varying rates and potentially missing extant species. Notations follow Morlon et al. PloSB 2010.

Usage

likelihood_coal_cst(Vtimes, ntips, tau0, gamma, N0)

Arguments

Vtimes

a vector of branching times (sorted from present to past)

ntips

the number of tips in the phylogeny

tau0

the turnover rate at present

gamma

the parameter controlling the exponential variation in turnover rate. With gamma=0, the turnover rate is constant over time.

N0

the number of extant species

Value

a list containing the following components:

res

the loglikelihood value of the phylogeny, given tau0 and gamma

all

vector of all the individual loglikelihood values corresponding to each branching event

Details

Time runs from the present to the past. Hence, a positive gamma (for example) means that the turnover rate declines from past to present.

References

Morlon, H., Potts, M.D., Plotkin, J.B. (2010) Inferring the dynamics of diversification: a coalescent approach, PLoS B 8(9): e1000493

Examples

data(Cetacea)
Vtimes <- sort(branching.times(Cetacea))
tau0 <- 0.1
gamma <- 0.001
ntips <- Ntip(Cetacea)
N0 <- 89
likelihood <- likelihood_coal_cst(Vtimes,ntips,tau0,gamma,N0)