fit_sgd: Maximum likelihood fit of the SGD model

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

View source: R/fit_sgd.R

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)

RPANDA documentation built on May 29, 2017, 3:34 p.m.

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