likelihood_coal_var function

Likelihood of a birth-death model using a coalescent approch

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

likelihood_coal_var(Vtimes, ntips, lamb0, alpha, mu0, beta, N0, pos = TRUE)

Arguments

• Vtimes: a vector of branching times (sorted from present to past)
• ntips: number of species in the phylogeny
• lamb0: the speciation rate at present
• alpha: the parameter controlling the exponential variation in speciation rate.
• mu0: the extinction rate at present
• beta: the parameter controlling the exponential variation in extinction rate.
• N0: the number of extanct species
• pos: logical: should be set to FALSE only to not enforce positive speciation and extinction ratess

Returns

a list containing the following components: - res: the loglikelihood value of the phylogeny, given the parameters

• 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 alpha (for example) means that the speciation 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

Author(s)

H Morlon

Examples

data(Cetacea)
Vtimes <- sort(branching.times(Cetacea))
lamb0 <- 0.1
alpha <- 0.001
mu0<-0
beta<-0
ntips <- Ntip(Cetacea)
N0 <- 89
likelihood <- likelihood_coal_var(Vtimes, ntips, lamb0, alpha, mu0, beta, N0)