likelihood_sgd: Likelihood of a phylogeny under the SGD model

Description Usage Arguments Value Author(s) References Examples

View source: R/likelihood_sgd.R

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

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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

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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 Nov. 8, 2018, 12:32 p.m.