R/ocean_entry_success.R

In CVPIA-OSC/lateFallRunDSM: Structured Decision Fall Run Model for CVPIA

#' @title Ocean Entry Success
#' @description Calculates the number of juveniles that survive entering the ocean
#' @details See \code{\link{params}} for details on parameter sources
#' @param migrants Variable representing the number of juveniles at golden gate bridge
#' @param month Variable representing the current simulation month
#' @param avg_ocean_transition_month Variable representing the average month juveniles transition to the ocean
#' @param .ocean_entry_success_length Size related intercept representing the fork lengths for each size classes
#' @param ..ocean_entry_success_int Intercept
#' @param .ocean_entry_success_months Coefficient for \code{month} variable
#' @param stochastic \code{TRUE} \code{FALSE} value indicating if model is being run stochastically
#' @source IP-117068
#' @export
ocean_entry_success <- function(migrants, month, avg_ocean_transition_month,
                                .ocean_entry_success_length = lateFallRunDSM::params$.ocean_entry_success_length,
                                ..ocean_entry_success_int = lateFallRunDSM::params$..ocean_entry_success_int,
                                .ocean_entry_success_months = lateFallRunDSM::params$.ocean_entry_success_months,
                                stochastic){
  
  month_since <- ifelse(month <= avg_ocean_transition_month, 0, max(1, month - avg_ocean_transition_month))
  
  survival_probs <- NULL
  for(i in 1:dim(migrants)[1]) {
    survival_probs <- rbind(survival_probs,
                            boot::inv.logit(..ocean_entry_success_int[[i]] +
                                              .ocean_entry_success_months * month_since +
                                              .ocean_entry_success_length))
  }
  
  if (stochastic) {
    survived <- t(sapply(1:31, function(watershed) {
      rbinom(4, size = migrants[watershed, ], prob = survival_probs[watershed, ])
    }))
  } else {
    survived <- round(survival_probs * migrants)
  }
  
  if (month_since == 0) rep(0, 31) else rowSums(survived)
  
}