R/15-01-00-processPopulation.R

In danStich/shadia: American shad dam passage performance standard model for R

#' @title Process population
#'
#' @description A function that uses \code{\link{createPUMatrix}},
#' \code{\link{assignFishToRoutes}}, and
#' \code{\link{additionalEggsProcessing}} to return the
#' number of fish in each cohort in each PU prior to
#' application of annual mortality rates and downstream
#' migration.  Called by \code{\link{processCohorts}}.
#' Not intended to be called directly. Visible for
#' model transparency.
#'
#' @export
#'
processPopulation <- function(isFemale, isEgg = FALSE) {
  environment(createPUMatrix) <- .shadia
  environment(assignFishToPU) <- .shadia
  environment(additionalEggsProcessing) <- .shadia

  # uses generalized function for creating PU matrix
  # of males, females, or eggs
  for (i in 1:nRoutes) {
    assign(paste0("PUS_", i), createPUMatrix(isFemale, i, isEgg), envir = .shadia)
  }

  # Collect age-structured male, female, or egg population
  # in each PU.
  population <- vector(mode = "list", length = nRoutes)

  for (i in 1:nRoutes) {
    population[[i]] <- vector(mode = "list", length = (nPU[[i]]))
    population[[i]] <- assignFishToPU(i, get(paste0("PUS_", i), envir = .shadia))
  }

  # Remove NA values and replace with zeroes because
  # that's what they are.
  population <- rapply(
    population,
    f = function(x) {
      ifelse(is.na(x), 0, x)
    },
    how = "replace"
  )
  if (!isEgg) {
    return(population)
  } else {
    fec_Max <- additionalEggsProcessing(population)
    return(fec_Max)
  }
}