R/calc_rates.R

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

#' Calculate rates for island processes
#' @description Internal function that updates the all the rates at time t.
#'
#' @inheritParams default_params_doc
#'
#' @keywords internal
#' @return Named list with rates.
#' @author Joshua W. Lambert
calc_rates <- function(gam,
                       laa,
                       lac,
                       mu,
                       k,
                       num_spec,
                       num_immigrants,
                       mainland_n) {
  testit::assert(is.numeric(gam))
  testit::assert(is.numeric(laa))
  testit::assert(is.numeric(lac))
  testit::assert(is.numeric(mu))
  testit::assert(is.numeric(k))
  testit::assert(is.numeric(num_spec))
  testit::assert(is.numeric(num_immigrants))
  testit::assert(is.numeric(mainland_n))

  immig_rate <- max(0, mainland_n * gam * (1 - (num_spec / k)))
  ext_rate <- mu * num_spec
  ana_rate <- laa * num_immigrants
  clado_rate <- max(0, lac * num_spec * (1 - (num_spec / k)))

  testit::assert(immig_rate >= 0.0)
  testit::assert(ext_rate >= 0.0)
  testit::assert(ana_rate >= 0.0)
  testit::assert(clado_rate >= 0.0)

  return(list(
    immig_rate = immig_rate,
    ext_rate = ext_rate,
    ana_rate = ana_rate,
    clado_rate = clado_rate
  ))
}