Fits the SGD model with exponential growth of the metacommunity, by maximum likelihood. Notations follow Manceau et al. (2015)
1 |
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. |
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) |
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.
M Manceau
Manceau, M., Lambert, A., Morlon, H. (2015) Phylogenies support out-of-equilibrium models of biodiversity Ecology Letters 18: 347-356
likelihood_sgd
1 2 3 4 5 |
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
All documentation is copyright its authors; we didn't write any of that.