R/DAISIE_sim_trait_dep_cpp.R

In thijsjanzen/TRAISIERCPP: Test RCPP Version TRAISIE

#' @title Simulate islands with given parameters.
#' @description This function simulates islands with given cladogenesis,
#' extinction, Kprime, immigration and anagenesis parameters. If a single
#' parameter set is provided (5 parameters) it simulates islands where all
#' species have the same macro-evolutionary process. If two paramater sets
#' (10 parameters) are provided, it simulates islands where two different
#' macro-evolutionary processes operate, one applying to type 1 species and
#' other to type 2 species. If two parameter sets and a time shift (11
#' parameters) are provided, it simulates islands where at the given time
#' a shift between the parameter sets will occur.
#'
#' Returns R list object that contains the simulated islands
#'
#' @inheritParams default_params_doc
#' @param max_n maximum number of species
#'
#' @return Each simulated dataset is an element of the list, which can be
#' called using [[x]]. For example if the object is called island_replicates,
#' the last replicates is a list in itself. The first (e.g.
#' \code{island_replicates[[x]][[1]]}) element of that list has the following
#' components: \cr \code{$island_age} - the island age \cr Then, depending on
#' whether a distinction between types is made, we have:\cr \code{$not_present}
#' - the number of mainland lineages that are not present on the island \cr
#' or:\cr \code{$not_present_type1} - the number of mainland lineages of type 1
#' that are not present on the island \cr \code{$not_present_type2} - the
#' number of mainland lineages of type 2 that are not present on the island \cr
#' \code{$stt_all} - STT table for all species on the island (nI - number of
#' non-endemic species; nA - number of anagenetic species, nC - number of
#' cladogenetic species, present - number of independent colonisations present
#' )\cr \code{$stt_stt_type1} - STT table for type 1 species on the island -
#' only if 2 types of species were simulated (nI - number of non-endemic
#' species; nA - number of anagenetic species, nC - number of cladogenetic
#' species, present - number of independent colonisations present )\cr
#' \code{$stt_stt_type2} - STT table for type 2 species on the island - only if
#' 2 types of species were simulated (nI - number of non-endemic species; nA -
#' number of anagenetic species, nC - number of cladogenetic species, present -
#' number of independent colonisations present )\cr \code{$brts_table} - Only
#' for simulations under 'IW'. Table containing information on order of events
#' in the data, for use in maximum likelihood optimization.)\cr
#'
#' The subsequent elements of the list each contain information on a single
#' colonist lineage on the island and has 4 components:\cr
#' \code{$branching_times} - island age and stem age of the population/species
#' in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic
#' species. For cladogenetic species these should be island age and branching
#' times of the radiation including the stem age of the radiation.\cr
#' \code{$stac} - the status of the colonist \cr * Non_endemic_MaxAge: 1 \cr *
#' ndemic: 2 \cr * Endemic&Non_Endemic: 3 \cr * Non_endemic: 4 \cr
#' \code{$missing_species} - number of island species that were not sampled for
#' particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
#' - whether the colonist belongs to type 1 or type 2 \cr
#' @author Luis Valente and Albert Phillimore
#' @seealso \code{\link{DAISIE_format_CS}} \code{\link{DAISIE_plot_sims}}
#' @references Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
#' Equilibrium and non-equilibrium dynamics simultaneously operate in the
#' Galapagos islands. Ecology Letters 18: 844-852.
#' Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (submitted).
#' Lake expansion increases equilibrium diversity via the target effect of
#' island biogeography.
#' @keywords models
#' @export
DAISIE_sim_trait_dep_cpp <- function(
    time,
    M,
    pars,
    replicates,
    divdepmodel = "CS",
    sample_freq = 25,
    plot_sims = TRUE,
    island_ontogeny = "const",
    sea_level = "const",
    hyper_pars = TRAISIERCPP::create_hyper_pars(d = 0, x = 0),
    area_pars = TRAISIERCPP::create_area_pars(
      max_area = 1,
      current_area = 1,
      proportional_peak_t = 0,
      total_island_age = 0,
      sea_level_amplitude = 0,
      sea_level_frequency = 0,
      island_gradient_angle = 0),
    extcutoff = 1000,
    cond = 0,
    verbose = TRUE,
    trait_pars = NULL,
    max_n = 1e4,
    ...
) {
  total_time <- time
  island_replicates <- list()
  island_ontogeny <- translate_island_ontogeny(island_ontogeny)
  sea_level <- translate_sea_level(sea_level)


  #### CS ####
  if (divdepmodel == "CS") {
    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) {
        if (M == 0 || is.null(trait_pars)) {
          stop("One state exist on mainland, should use constant rate DAISIE.")
        }else{
          for (m_spec in 1:M) {
           # cat(m_spec, "\n")
            ### M1 = 1, M2 = 0
            trait_pars_onecolonize <- create_trait_pars(
              trans_rate = trait_pars$trans_rate,
              immig_rate2 = trait_pars$immig_rate2,
              ext_rate2 = trait_pars$ext_rate2,
              ana_rate2 = trait_pars$ana_rate2,
              clado_rate2 = trait_pars$clado_rate2,
              trans_rate2 = trait_pars$trans_rate2,
              M2 = 0)

            full_list[[m_spec]] <- DAISIE_sim_core_trait_dep_cpp(
              time = total_time,
              mainland_n = 1,
              pars = pars,
              island_ontogeny = island_ontogeny,
              sea_level = sea_level,
              hyper_pars = hyper_pars,
              area_pars = area_pars,
              extcutoff = extcutoff,
              trait_pars = trait_pars_onecolonize,
              max_n = max_n
            )
          }

          for (m_spec in (M + 1):(M + trait_pars$M2)) {
          #  cat(m_spec, "\n")
            ### M1 = 0, M2 = 1
            trait_pars_onecolonize <- create_trait_pars(
              trans_rate = trait_pars$trans_rate,
              immig_rate2 = trait_pars$immig_rate2,
              ext_rate2 = trait_pars$ext_rate2,
              ana_rate2 = trait_pars$ana_rate2,
              clado_rate2 = trait_pars$clado_rate2,
              trans_rate2 = trait_pars$trans_rate2,
              M2 = 1)
            full_list[[m_spec]] <- DAISIE_sim_core_trait_dep_cpp(
              time = total_time,
              mainland_n = 0,
              pars = pars,
              island_ontogeny = island_ontogeny,
              sea_level = sea_level,
              hyper_pars = hyper_pars,
              area_pars = area_pars,
              extcutoff = extcutoff,
              trait_pars = trait_pars_onecolonize,
              max_n = max_n
            )
          }
        }
        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) {
        print(paste("Island replicate ", rep, sep = ""))
      }
    }
    island_replicates <- DAISIE_format_CS(
      island_replicates = island_replicates,
      time = total_time,
      M = M,
      sample_freq = sample_freq,
      verbose = verbose,
      trait_pars = trait_pars
    )
  }

  if (plot_sims == TRUE) {
    DAISIE_plot_sims(
      island_replicates = island_replicates,
      sample_freq = sample_freq,
      trait_pars = trait_pars
    )
  }
  return(island_replicates)
}