get_default_initpars: Get default initial parameter values for run_optim...

In TheoPannetier/DDvTDtools: Compare diversity-dependent (DD) and time-dependent (TD) diversification models

Description

Returns default initial parameter values used to fit optim models to phylogenies with run_optim. Called by run_optim().

Usage

get_default_initpars(true_pars, optim, brts)

Arguments

true_pars	numeric vector. The true parameter values used to simulate the trees.
optim	character, name of the optimisation model, either "DD" or "TD".
brts	numeric vector, a set of branching times as given by ape::branching_times().

Details

For the DD and TD models, initial parameter values are by default set to the true values used to simulate the trees. For thr CR model, la0 is set to the expected speciation rate, knowing the age, number of tips and the extinction rate for the tree. This is computed using equation (15) from Kendall (1948) for the expected number of particles over time in a constant-rate birth-death process.

Author(s)

Théo Pannetier

References

Kendall, David G. On the Generalized "Birth-and-Death" Process. Ann. Math. Statist. 19 (1948), no. 1, 1–15. doi:10.1214/aoms/1177730285

TheoPannetier/DDvTDtools documentation built on Oct. 22, 2020, 2:31 p.m.