likelihood_sgd: Likelihood of a phylogeny under the SGD model

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

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.

Author(s)

M Manceau

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)

hmorlon/PANDA documentation built on Jan. 13, 2025, 5:35 a.m.