R/project_pop.R

In danStich/anadrofish: Anadromous Fish Population Responses to Habitat Changes

#' @title Project population
#'
#' @description Function used to project population forward 
#' one time step using vector multiplication.
#'
#' @param x A numeric vector containing age-specific 
#' abundance at end of year t.
#' 
#' @param age0 A numeric vector of length one containing number of new recruits 
#' at end of year t.
#' 
#' @param nM Numeric vector of instantaneous natural mortality.
#' 
#' @param fM Numeric vector of instantaneous fishing mortality.
#' 
#' @param max_age Numeric indicating maximum age of spawning fish.
#' 
#' @param species Species for which population dynamics will be simulated.
#' Choices include American shad (\code{"AMS"}), alewife (\code{"ALE"}), and
#' blueback herring (\code{"BBH"}).
#'
#' @return A numeric vector of age-structured abundance in time t + 1.
#'
#' @example inst/examples/projectpop_ex.R
#' 
#' @export
#'
project_pop <- function(x, age0, nM, fM, max_age, 
                        species = c("AMS", "ALE", "BBH")){
  
  # Error handling
  # Species error handling
  if(missing(species)){
    stop("
    
    Argument 'species' must be one of 'ALE', 'AMS', or 'BBH'.")   
  }
  
  if(!species %in% c('ALE', 'AMS', 'BBH')){
    stop("
         
    Argument 'species' must be one of 'ALE', 'AMS', or 'BBH'.") 
  }  
  
  # Calculate total mortality
  Z <- nM + fM

  # Survival rate
  if(species == "AMS"){
    s <- rep(1 - (1 - exp(-Z)), max_age)  
    s[1] <- (1 - (1 - exp(-nM))) ^ 3 

  }
  
  if(species %in% c("ALE", "BBH")){
    s <- 1 - (1 - exp(-Z))  
  }
      
  # Project population one time-step and drop
  # any fish > max_age
  tplus <- c(age0, x[1:(max_age-1)]) * s    
    
  # Return the result to R
  return(tplus[1:max_age])

}