RPANDA (version 1.2)

fit_sgd: Maximum likelihood fit of the SGD model

Description

Fits the SGD model with exponential growth of the metacommunity, by maximum likelihood. Notations follow Manceau et al. (2015)

Usage

fit_sgd(phylo, tot_time, par, f=1, meth = "Nelder-Mead")

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)

par

a numeric vector of initial values for the parameters (b,d,nu) to be estimated (these values are used by the optimization algorithm)

f

the fraction of extant species included in the phylogeny

meth

optimization to use to maximize the likelihood function, see optim for more details.

Value

a list with the following components

model

the name of the fitted model

LH

the maximum log-likelihood value

aicc

the second order Akaike's Information Criterion

par

a numeric vector of estimated values of b (birth), b-d (growth) and nu (mutation)

References

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

See Also

likelihood_sgd

Examples

# Some examples may take a little bit of time. Be patient!
data(Calomys)
tot_time <- max(node.age(Calomys)$ages)
par_init <- c(1e7, 1e7-0.5, 1)
#fit_sgd(Calomys, tot_time, par_init, f=11/13)