R/16-postSpawnMortality.R

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

#' @title Define in-river population matrices
#'
#' @description Internal function used to apply
#' post-spawning mortality to male and female
#' spawners, and juvenile mortality rates for
#' new recruits
#'
#' Not intended to be called directly, but visible
#' for the sake of model transparency.
#'
#' @return A list of lists, each holding the numbers of
#' males, females, or eggs in each age class in each
#' production unit of each of four migration routes
#' following the application of post spawning mortality.
#'
#' @export
#'
postSpawnMortality <- function() {
  if (river == "penobscot") {
    # Males
    males[[1]] <- Map("*", males[[1]], post_spawn_survival_males)
    males[[2]] <- Map("*", males[[2]], post_spawn_survival_males)
    males[[3]] <- Map("*", males[[3]], post_spawn_survival_males)
    males[[4]] <- Map("*", males[[4]], post_spawn_survival_males)

    # Females
    females[[1]] <- Map("*", females[[1]], post_spawn_survival_females)
    females[[2]] <- Map("*", females[[2]], post_spawn_survival_females)
    females[[3]] <- Map("*", females[[3]], post_spawn_survival_females)
    females[[4]] <- Map("*", females[[4]], post_spawn_survival_females)

    # Apply juvenile mortality up to outmigration. This will be a list object with
    # Piscataquis recruits in the first element and Mainstem recruits in second.
    recruits <- vector(mode = "list", length = length(fec_Max))
    recruits[[1]] <- Map("*", fec_Max[[1]], juvenile_survival)
    recruits[[2]] <- Map("*", fec_Max[[2]], juvenile_survival)
    recruits[[3]] <- Map("*", fec_Max[[3]], juvenile_survival)
    recruits[[4]] <- Map("*", fec_Max[[4]], juvenile_survival)

    return(list(
      males = males,
      females = females,
      recruits = recruits
    ))
  }

  if (river == "merrimack") {
    # Males
    males[[1]] <- Map("*", males[[1]], post_spawn_survival_males)
    males[[2]] <- Map("*", males[[2]], post_spawn_survival_males)

    # Females
    females[[1]] <- Map("*", females[[1]], post_spawn_survival_females)
    females[[2]] <- Map("*", females[[2]], post_spawn_survival_females)

    # Apply juvenile mortality up to outmigration. This will be a list object with
    # Piscataquis recruits in the first element and Mainstem recruits in second.
    recruits <- vector(mode = "list", length = length(fec_Max))
    recruits[[1]] <- Map("*", fec_Max[[1]], juvenile_survival)
    recruits[[2]] <- Map("*", fec_Max[[2]], juvenile_survival)

    return(list(
      males = males,
      females = females,
      recruits = recruits
    ))
  }

  if (river == "connecticut") {
    # Males
    males[[1]] <- Map("*", males[[1]], post_spawn_survival_males)
    males[[2]] <- Map("*", males[[2]], post_spawn_survival_males)

    # Females
    females[[1]] <- Map("*", females[[1]], post_spawn_survival_females)
    females[[2]] <- Map("*", females[[2]], post_spawn_survival_females)

    # Apply juvenile mortality up to outmigration. This will be a list object with
    # Piscataquis recruits in the first element and Mainstem recruits in second.
    recruits <- vector(mode = "list", length = length(fec_Max))
    recruits[[1]] <- Map("*", fec_Max[[1]], juvenile_survival)
    recruits[[2]] <- Map("*", fec_Max[[2]], juvenile_survival)

    return(list(
      males = males,
      females = females,
      recruits = recruits
    ))
  }

  if (river == "susquehanna") {
    # Males
    males[[1]] <- Map("*", males[[1]], post_spawn_survival_males)
    males[[2]] <- Map("*", males[[2]], post_spawn_survival_males)
    males[[3]] <- Map("*", males[[3]], post_spawn_survival_males)
    males[[4]] <- Map("*", males[[4]], post_spawn_survival_males)

    # Females
    females[[1]] <- Map("*", females[[1]], post_spawn_survival_females)
    females[[2]] <- Map("*", females[[2]], post_spawn_survival_females)
    females[[3]] <- Map("*", females[[3]], post_spawn_survival_females)
    females[[4]] <- Map("*", females[[4]], post_spawn_survival_females)

    # Apply juvenile mortality up to outmigration. This will be a list object with
    # Piscataquis recruits in the first element and Mainstem recruits in second.
    recruits <- vector(mode = "list", length = length(fec_Max))
    recruits[[1]] <- Map("*", fec_Max[[1]], juvenile_survival)
    recruits[[2]] <- Map("*", fec_Max[[2]], juvenile_survival)
    recruits[[3]] <- Map("*", fec_Max[[3]], juvenile_survival)
    recruits[[4]] <- Map("*", fec_Max[[4]], juvenile_survival)

    return(list(
      males = males,
      females = females,
      recruits = recruits
    ))
  }

  if (river == "saco") {
    # Males
    males[[1]] <- Map("*", males[[1]], post_spawn_survival_males)

    # Females
    females[[1]] <- Map("*", females[[1]], post_spawn_survival_females)

    # Apply juvenile mortality up to outmigration.
    recruits <- vector(mode = "list", length = length(fec_Max))
    recruits[[1]] <- Map("*", fec_Max[[1]], juvenile_survival)

    return(list(
      males = males,
      females = females,
      recruits = recruits
    ))
  }

  if (river == "kennebec") {
    # Males
    males[[1]] <- Map("*", males[[1]], post_spawn_survival_males)
    males[[2]] <- Map("*", males[[2]], post_spawn_survival_males)

    # Females
    females[[1]] <- Map("*", females[[1]], post_spawn_survival_females)
    females[[2]] <- Map("*", females[[2]], post_spawn_survival_females)

    # Apply juvenile mortality up to outmigration. This will be a list object with
    # Piscataquis recruits in the first element and Mainstem recruits in second.
    recruits <- vector(mode = "list", length = length(fec_Max))
    recruits[[1]] <- Map("*", fec_Max[[1]], juvenile_survival)
    recruits[[2]] <- Map("*", fec_Max[[2]], juvenile_survival)

    return(list(
      males = males,
      females = females,
      recruits = recruits
    ))
  }

  if (river == "hudson") {
    # Males
    males[[1]] <- Map("*", males[[1]], post_spawn_survival_males)
    males[[2]] <- Map("*", males[[2]], post_spawn_survival_males)

    # Females
    females[[1]] <- Map("*", females[[1]], post_spawn_survival_females)
    females[[2]] <- Map("*", females[[2]], post_spawn_survival_females)

    # Apply juvenile mortality up to outmigration. This will be a list object with
    # Piscataquis recruits in the first element and Mainstem recruits in second.
    recruits <- vector(mode = "list", length = length(fec_Max))
    recruits[[1]] <- Map("*", fec_Max[[1]], juvenile_survival)
    recruits[[2]] <- Map("*", fec_Max[[2]], juvenile_survival)

    return(list(
      males = males,
      females = females,
      recruits = recruits
    ))
  }
  
  if (river == "androscoggin") {
    # Males
    males[[1]] <- Map("*", males[[1]], post_spawn_survival_males)
    males[[2]] <- Map("*", males[[2]], post_spawn_survival_males)

    # Females
    females[[1]] <- Map("*", females[[1]], post_spawn_survival_females)
    females[[2]] <- Map("*", females[[2]], post_spawn_survival_females)

    # Apply juvenile mortality up to outmigration. This will be a list object with
    # Piscataquis recruits in the first element and Mainstem recruits in second.
    recruits <- vector(mode = "list", length = length(fec_Max))
    recruits[[1]] <- Map("*", fec_Max[[1]], juvenile_survival)
    recruits[[2]] <- Map("*", fec_Max[[2]], juvenile_survival)

    return(list(
      males = males,
      females = females,
      recruits = recruits
    ))
  }  
  
}