ml: sls Maximum Likelihood

In richelbilderbeek/splendid: Likelihood model for diversification processes with single lineage rate shifts

Description

Calculates maximum likelihood

Usage

ml(loglik_function = get_logliks(), brts, start_pars = c(0.5, 0.3, 0.5,
  0.3), n_0 = 2, cond = 1, verbose = TRUE, optim_ids = rep(TRUE,
  length(start_pars)), true_pars = start_pars)

Arguments

loglik_function	the loglik function you want to use
brts	branchin times
start_pars	parameters to start from for the search of the likelihood maximum
n_0	starting number of lineages
cond	type of conditioning: cond = 0 no conditiong; cond = 1 conditions on the survival of crown descendents; cond = 2 not available; cond = 3 conditions on the survival of subclade and on the other crown descendents in the main clade; cond = 4 conditions on the survival of the subclade and both crown descendents in the main clade;
verbose	set it to TRUE if you want to see the outputs on screen
optim_ids	ids of the parameters you want to optimize.
true_pars	true parameter values when running the ml process.

Value

best parameters

richelbilderbeek/splendid documentation built on May 20, 2019, 9:42 a.m.