likelihood_sgd function

Likelihood of a phylogeny under the SGD model

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).

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

Returns

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

Author(s)

M Manceau

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)