R/update_island_endemics.R

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

#' Checks and updates if any changes on the mainland change the state of the
#' island species.
#'
#' @inheritParams default_params_doc
#'
#' @return Data frame of island species
#' @author Joshua W. Lambert
update_island_endemics <- function(timeval,
                                   total_time,
                                   island_tbl,
                                   mainland_clade) {
  testit::assert(is.numeric(timeval))
  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)

  if (any(island_tbl[, "spec_type"] == "I")) {
    immig_spec <-
      island_tbl[which(island_tbl[, "spec_type"] == "I"), "spec_id"]
    mainland_ex_time <-
      mainland_clade[
        which(mainland_clade[, "spec_id"] %in% immig_spec),
        "spec_ex_t"
      ]
    mainland_spec_type <-
      mainland_clade[
        which(mainland_clade[, "spec_id"] %in% immig_spec),
        "spec_type"
      ]
    for (i in seq_along(mainland_ex_time)) {
      if (timeval > mainland_ex_time[i] && total_time > mainland_ex_time[i]) {
        if (mainland_spec_type[i] != "US") {
          island_tbl[island_tbl[, "spec_id"] == immig_spec[i], "spec_type"] <-
            "A"
          island_tbl[island_tbl[, "spec_id"] == immig_spec[i], "ana_origin"] <-
            "mainland_extinction"
        }
      }
    }
  }
  return(island_tbl)
}