RPANDA (version 1.2)

likelihood_sgd: Likelihood of a phylogeny under the SGD model

Description

Computes the likelihood of a phylogeny under the SGD model with exponential increasing of the metacommunity, and potentially missing extant species. Notations follow Manceau et al. (2015).

Usage

likelihood_sgd(phylo, tot_time, b, d, nu, f)

Arguments

phylo

an object of type 'phylo' (see ape documentation)

tot_time

the age of the phylogeny (crown age, or stem age if known). If working with crown ages, tot_time is given by max(node.age(phylo)$ages).

b

the (constant) birth rate of individuals in the model.

d

the (constant) death rate of individuals in the model.

nu

the (constant) mutation rate of individuals in the model.

f

the fraction of extant species included in the phylogeny

Value

the likelihood value of the phylogeny, given the model and the parameter values b, d, nu.

References

Manceau M., Lambert A., Morlon H. (2015) Phylogenies support out-of-equilibrium models of biodiversity Ecology Letters 18: 347-356

Examples

data(Cetacea)
tot_time <- max(node.age(Cetacea)$ages)
b <- 1e6
d <- 1e6-0.5
nu <- 0.6
f <- 87/89
#lh <- likelihood_sgd(Cetacea, tot_time, b, d, nu, f)