mbd_calc_max_lik: Do an MBD maximum likelihood estimate.

In richelbilderbeek/becosys: Unified Interface To Phylogenetics Models Of Speciation

Description

Do an MBD maximum likelihood estimate.

Usage

mbd_calc_max_lik(
  branching_times,
  init_param_values,
  fixed_params,
  opt_params,
  init_n_species = 2,
  conditioned_on = "nothing"
)

Arguments

branching_times	the branching times of the phylogeny
init_param_values	initial parameter values, as created with create_mbd_params
fixed_params	the parameters that are fixed. This is a list of the four parameter names, and a boolean to indicate if it is fixed yes/no. Use create_mbd_params_selector to create such a list
opt_params	the parameters that are optimized. This is a list of the four parameter names, and a boolean to indicate if it is optimized yes/no. Use create_mbd_params_selector to create such a list
init_n_species	the number of species at the moment of the first branching time. Can be either one or two: 1: stem 2: crown
conditioned_on	on what must be the likelihood estimation be conditioned: "nothing": the branch lengths were obtained from a random phylogeny that could also have gone extinct "non_extinction": the branch lengths were obtained from a phylogeny conditioned on non-extinction

Author(s)

Richel J.C. Bilderbeek

richelbilderbeek/becosys documentation built on Oct. 19, 2020, 9:20 a.m.