sls_main: Run the full sls routine

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)

Usage

sls_main(
  sim_pars,
  cond = 3,
  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)),
  loglik_functions = sls::sls_logliks_div(),
  project_folder = NULL,
  verbose = FALSE,
  max_iterations = 10000
)

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;
crown_age	the age of the phylogeny
shift_time	the time of the shift
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
max_iterations	maximum number of iterations for the optimizer

Details

mle inference

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