R/run_oceanic_sim.R

In Neves-P/DAISIErobustness: Test the Robustness of DAISIE to Geodynamics and Traits

#' Runs original clade-specific oceanic DAISIE simulation
#'
#' @inheritParams default_params_doc
#' @author Joshua W. Lambert, Pedro Santos Neves, Shu Xie
#' @return Output from \code{\link[DAISIE]{DAISIE_sim_cr}()}
run_oceanic_sim <- function(ml,
                            sim_pars) {
  if ("trait_pars" %in% names(sim_pars)) {
    mainland_species <- sim_pars$M + sim_pars$trait_pars$M2 # nolint
  } else {
    mainland_species <- sim_pars$M
  }
  oceanic_sim <- DAISIE::DAISIE_sim_cr(
    time = sim_pars$time,
    M = mainland_species,
    pars = as.numeric(ml[1:5]),
    hyper_pars = DAISIE::create_hyper_pars(d = 0, x = 0),
    replicates = 1,
    divdepmodel = "CS",
    plot_sims = FALSE,
    cond = 5,
    verbose = FALSE,
    sample_freq = Inf
  )
  return(oceanic_sim)
}