R/bact_shell_harvest.R

In donco/odeqassessment:

#' Bacteria Shell Harvest Analysis
#'
#' Assesses Ecoli data against the standard
#' @param df dataframe with Ecoli data
#' @param criteria POSIXCT column name containing criteria values
#' @return a dataframe with relevant Ecoli criteria and excursion variables added
#' @export
#' @examples function(df = your_ecoli_data, criteria = "bact-shell-crit")

Shell_Harvest <- function(df, per_criteria = "bact_crit_percent", ss_criteria = "bact_crit_ss") {

  print("Begin shellfish harvesting analysis")

  Perc_Crit <- as.symbol(per_criteria)
  SS_Crit <- as.symbol(ss_criteria)

  shell_harvest <- df %>%
    dplyr::filter(BacteriaCode == 3,
                  Char_Name == "Fecal Coliform") %>%
    dplyr::mutate(perc_exceed = ifelse(Result_cen > !!Perc_Crit, 1, 0),
                  ss_excursion = ifelse(Result_cen > !!SS_Crit, 1, 0))

  # if(nrow(shell_harvest) == 0) {
  #   stop("No available data")
  # }

  return(shell_harvest)

  # shell_harvest_analysis <- shell_harvest %>%
  #   group_by(MLocID, OWRD_Basin) %>%
  #   summarise(num_samples = n(),
  #             median = ifelse(num_samples >= 5, median(Result_cen), NA ),
  #             num_exceed = sum(perc_exceed),
  #             Perc_Crit = first(!!Perc_Crit),
  #             SS_Crit = first(SS_Crit)
  #   )
  #
  # return(shell_harvest_analysis)

}