R/DAISIE_sim_time_dep_cs.R

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

#' Simulates island replicates with an clade-specific (CS) diversity-dependent
#' time-dependent process
#'
#' @inheritParams default_params_doc
#'
#' @return A list. The highest level of the least corresponds to each individual
#' replicate. See return for `DAISIE_sim_time_dep()` for details.
DAISIE_sim_time_dep_cs <- function(total_time,
                                   M,
                                   pars,
                                   replicates,
                                   area_pars,
                                   hyper_pars,
                                   nonoceanic_pars,
                                   sample_freq,
                                   island_ontogeny,
                                   sea_level,
                                   peak,
                                   Amax,
                                   Amin,
                                   extcutoff,
                                   cond,
                                   verbose) {
  island_replicates <- list()
  for (rep in 1:replicates) {
    island_replicates[[rep]] <- list()
    full_list <- list()
    if (cond == 0) {
      number_present <- -1
    } else {
      number_present <- 0
    }
    while (number_present < cond) {
      for (m_spec in 1:M) {
        full_list[[m_spec]] <- DAISIE_sim_core_time_dep(
          time = total_time,
          mainland_n = 1,
          pars = pars,
          nonoceanic_pars = nonoceanic_pars,
          island_ontogeny = island_ontogeny,
          sea_level = sea_level,
          hyper_pars = hyper_pars,
          area_pars = area_pars,
          peak = peak,
          Amax = Amax,
          Amin = Amin,
          extcutoff = extcutoff
        )
      }
      stac_vec <- unlist(full_list)[which(names(unlist(full_list)) == "stac")]
      present <- which(stac_vec != 0)
      number_present <- length(present)
    }
    island_replicates[[rep]] <- full_list
    if (verbose == TRUE) {
      message("Island replicate ", rep)
    }
  }
  island_replicates <- DAISIE_format_CS(
    island_replicates = island_replicates,
    time = total_time,
    M = M,
    sample_freq = sample_freq,
    verbose = verbose
  )

  return(island_replicates)
}