R/23_prob_rebuilt_goal.R

In ktmurray1219/mmrefpoints: Project Marine Mammal Populations and Calculate Reference Points

#' Calculate the probability of reaching a rebuilding goal
#'
#' @description function that calculates the probability of recovery (in terms of 1+ numbers) to MNPL (or other population size) at \code{rebuilt.yr} years
#'
#' @param traj a matrix of trajectories, with rows=nsims and cols=nyears
#' @param goal  rebuilding goal as an absolute number of animals
#' @param rebuild.yr the year by which you want pop to be recovered (calculate probability that pop will recover to MNPL by rebuild.yr)
#'
#' @return - the probability that the stock will be rebuilt to the goal population size by year \code{rebuilt.yr}
#'
#' @examples
#' lh.params <- list(
#'   S0 = 0.944, S1plus = 0.99, 
#'   AgeMat = 17,
#'   nages = 19, z = 2.39, 
#'   lambdaMax = 1.04, K1plus = 9000
#' )
#' Projection <- projections(
#'   NOut = 100,
#'   ConstantBycatch = list(Catch = 40, CV = 01),
#'   InitDepl = 0.3,
#'   lh.params = lh.params,
#'   nyears = 40, obs_CV = 0.2
#' )
#' @export
prob_rebuilt_goal <- function(traj, goal = 2000, rebuild.yr = 100) {
  if (ncol(traj) < rebuild.yr) stop("Need more years of projection")
  nsims <- nrow(traj)
  prob <- length(which(traj[, rebuild.yr] > goal)) / nsims
  prob <- round(prob, digits = 2)
  return(prob)
}