sls_main_dummy: Run the full sls routine with dummy shift

In Giappo/sls: 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) with dummy shift

Usage

sls_main_dummy(
  sim_pars,
  cond = 3,
  l_2 = sim_get_standard_l_2(crown_age = 5, shift_time = 2),
  seed,
  start_pars = c(0.2, 0.1),
  optim_ids = rep(TRUE, length(start_pars)),
  loglik_functions = sls_logliks_dummy(),
  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 conditions on the survival of subclade and on the other crown descendents in the main clade; cond = 3 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 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.
loglik_functions	the loglik_functions you want to use
project_folder	the folder where you want to save data and results
verbose	set it to TRUE if you want to see the outputs on screen

Details

mle inference with dummy shift

Giappo/sls documentation built on Feb. 1, 2021, 9:55 a.m.