| likelihood_sgd {RPANDA} | R Documentation |
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)