R/create_daisie_data.R

In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

#' Converts simulation output into island output
#'
#' @inheritParams default_params_doc
#'
#' @return List with the island information, composed of
#' branching times of extant species, status of species on
#' the island and number of missing species.
#' @keywords internal
#' @author Joshua W. Lambert
create_daisie_data <- function(total_time,
                               island_tbl,
                               mainland_clade,
                               mainland_sample_prob,
                               mainland_sample_type) {
  testit::assert(is.numeric(total_time))
  testit::assert(is.data.frame(island_tbl))
  testit::assert(ncol(island_tbl) == 7)
  testit::assert(is.data.frame(mainland_clade))
  testit::assert(ncol(mainland_clade) == 7)
  testit::assert(is.numeric(mainland_sample_prob))
  testit::assert(is.character(mainland_sample_type))

  if (nrow(island_tbl) == 0) {
    ideal_island <- empirical_island <-
      list(list(
        branching_times = total_time,
        stac = 0,
        missing_species = 0
      ))
  } else {
    islands <- create_non_empty_island(
      total_time = total_time,
      island_tbl = island_tbl,
      mainland_clade = mainland_clade,
      mainland_sample_prob = mainland_sample_prob,
      mainland_sample_type = mainland_sample_type
    )
    ideal_island <- islands$ideal_island
    empirical_island <- islands$empirical_island
  }
  return(list(
    ideal_island = ideal_island,
    empirical_island = empirical_island
  ))
}