fit_sgd: Maximum likelihood fit of the SGD model

Description Usage Arguments Value Note Author(s) References See Also Examples

Description

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

Usage

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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)

Note

While b-d and nu can in general be well estimated, the likelihood surface is quite flat whith respect to b, such that the estimated b can vary a lot depending on the choice of the initial parameter values. Estimates of b should not be trusted.

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

See Also

likelihood_sgd

Examples

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# 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)


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