sls_main: Run the full sls routine

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

Description

Simulate an sls process and infer parameters maximizing the likelihood(s) for given function(s)

Usage

sls_main(sim_pars, cond = 1, l_2 = sim_get_standard_l_2(crown_age = 5,
  shift_time = 2), seed, start_pars = c(0.2, 0.1, 0.2, 0.1),
  optim_ids = rep(TRUE, length(start_pars)), models = get_logliks(),
  project_folder = NULL, verbose = FALSE)

Arguments

sim_pars	parameters of the simulation
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;
l_2	the matrix containing the information about how the subclades are nested into the main clade. See sls_sim.get_standard_l_2() for more info.
seed	the seed
start_pars	parameters to start from for the search of the likelihood maximum
optim_ids	ids of the parameters you want to optimize.
models	the models you want to use to define the likelihood
project_folder	the folder when you want to save data and results
verbose	set it to TRUE if you want to see the outputs on screen

Details

mle inference

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