R/ts_biomass.R

In BenWilliams-NOAA/groundfishr: What the Package Does (One Line, Title Case)

#' survey biomass
#'
#' @param year of interest
#' @param area e.g., "goa"
#' @param file if not using the design-based abundance, the file name must be stated (e.g. "GAP_VAST.csv")
#' @param rmv_yrs any survey years to exclude
#' @param save
#'
#' @return
#' @export ts_biomass
#'
#' @examples
#'
ts_biomass <- function(year, area = "goa", file = NULL, rmv_yrs = NULL, id = NULL, save = TRUE){

  if(is.null(file)){

    read.csv(here::here(year, "data", "raw", "goa_ts_biomass_data.csv")) %>%
      dplyr::rename_all(tolower)  -> df

    # sablefish are different...
    if("summary_depth" %in% names(df)){
      df %>%
      dplyr::filter(summary_depth < 995, year != 2001) %>%
        dplyr::group_by(year) %>%
        dplyr::summarise(biom = sum(area_biomass) / 1000,
                         se = sqrt(sum(biomass_var)) / 1000) %>%
        dplyr::mutate(lci = biom - 1.96 * se,
                      uci = biom + 1.96 * se) -> sb
  } else {
      df %>%
        dplyr::group_by(year) %>%
        dplyr::summarise(biomass = sum(total_biomass),
                       se = sqrt(sum(biomass_var)),
                       lci = biomass - 1.96 * se,
                       uci = biomass + 1.96 * se) %>%
        dplyr::mutate(lci = ifelse(lci < 0, 0, lci)) %>%
        dplyr::mutate_if(is.double, round) %>%
        dplyr::filter(biomass > 0) -> sb
    }
  } else {
    read.csv(here::here(year, "data", "user_input", file)) -> sb
  }

  if(!is.null(rmv_yrs)){
    sb |>
      dplyr::filter(!(year %in% rmv_yrs)) -> sb
  }

  if(isTRUE(save)){
    if(!is.null(id)){
        write.csv(sb, here::here(year, "data", "output", paste0(area, "_ts_biomass_", id, ".csv")), row.names = FALSE)
      } else {
        write.csv(sb, here::here(year, "data", "output", paste0(area, "_ts_biomass.csv")), row.names = FALSE)
      }
      sb
  } else {
    sb
  }
}