| likelihood_coal_cst {RPANDA} | R Documentation |
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 |
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.
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 |
Author(s)
H Morlon
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)