R/lesa.flokkar.R

In einarhjorleifsson/fjolst2:

#' Read from the table faeda.f_flokkar or the dataframe fflokkar.
#'
#' @param ranfiskur xxx
#' @param lenfl xxx
#' @param synis.id xxx
#' @param fjoldi xxx
#' @param total xxx
#' @param flokk.id xxx
#' @param oracle xxx
#' @param old.stomach.breaks xxx
#'
#' @export

lesa.flokkar <- function (ranfiskur,
                          lenfl = NULL,
                          synis.id = NULL,
                          fjoldi = T,
                          total = T,
                          flokk.id = NULL,
                          oracle = fjolstOracle,
                          old.stomach.breaks=old.stomach.breaks)
{
  if (!oracle) {
    result <- fflokkar[, c("synis.id", "flokk.id", "ranfiskur",
                           "lenfl", "fj.fmaga", "fj.omelt", "fj.tomra", "fj.aelt",
                           "faerslunumer")]
    result <- result[result$ranfiskur == ranfiskur, ]
    if (!is.null(synis.id))
      result <- result[!is.na(match(result$synis.id, synis.id)),
                       ]
    if (!is.null(lenfl))
      result <- result[!is.na(match(result$lenfl, lenfl)),
                       ]
    i <- is.na(result$fj.aelt)
    if (any(i))
      result$fj.aelt[i] <- 0
    i <- is.na(result$fj.omelt)
    if (any(i))
      result$fj.omelt[i] <- 0
    print(nrow(result))
    cat("start total")
    if (total) {
      if (!is.null(synis.id))
        tmp <- fhopar[!is.na(match(fhopar$flokk.id, result$flokk.id)),
                      ]
      else tmp <- fhopar
      x <- apply.shrink(tmp$thyngd, tmp$flokk.id, sum,
                        names = c("flokk.id", "total"))
      result <- join(result, x, "flokk.id", set = 0)
    }
    cat("start fjoldi")
    if (fjoldi) {
      s.id = unique(result$synis.id)
      tmp <- lesa.lengdir(s.id, ranfiskur)
      tmp1 <- lesa.numer(s.id, ranfiskur)
      tmp <- Skala.med.toldum(tmp, tmp1)
      tmp <- tmp[, c("synis.id", "lengd", "fj.alls")]
      tmp$lenfl <- as.numeric(cut(tmp$lengd, old.stomach.breaks$breaks))
      tmp <- apply.shrink(tmp$fj.alls, list(tmp$synis.id,
                                            tmp$lenfl), sum, names = c("synis.id", "lenfl",
                                                                       "fjoldi"))
      tmp$index <- paste(tmp$synis.id, tmp$lenfl)
      result$index <- paste(result$synis.id, result$lenfl)
      tmp <- tmp[!is.na(match(tmp$index, result$index)),
                 ]
      result <- join(result, tmp[, c("index", "fjoldi")],
                              "index", set = 0)
      j <- match("index", names(result))
      result <- result[, -j]
      result$fjoldi[is.na(result$fjoldi)] <- 0
    }
    i <- is.na(result$fj.aelt)
    if (any(i))
      result$fj.aelt[i] <- 0
    return(result)
  }
  ranf <- paste(ranfiskur, collapse = ",")
  lfl <- c(5, 8, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90,
           100, 120, 200)
  x <- 0
  nafn <- c("synis.id", "flokk.id", "ranfiskur", "lenfl", "fj.fmaga",
            "fj.omelt", "fj.tomra", "fj.aelt", "faerslunumer")
  nafn1 <- c("synis_id", "flokk_id", "ranfiskur", "len_fl",
             "fj_fmaga", "fj_omelt", "fj_tomra", "fj_aelt", "faerslunumer")
  dn <- nafn1
  dn2 <- nafn
  dn1 <- paste(dn, collapse = ",")
  skipun <- paste("select", dn1, "from faeda.f_flokkar where ranfiskur in (",
                  ranf, ")")
  if (!is.null(synis.id))
    skipun <- paste(skipun, "and synis_id in (", paste(synis.id,
                                                       collapse = ","), ")")
  if (!is.null(flokk.id))
    skipun <- paste(skipun, "and flokk_id > ", flokk.id)
  if (!is.null(lenfl))
    skipun <- paste(skipun, "and lenfl in (", paste(lenfl,
                                                    collapse = ","), ")")
  x <- run.sqlskipun(skipun, synis.id, "synis_id")
  ind <- match(dn, nafn1)
  nafn <- nafn[ind]
  if (total) {
    print("total")
    table <- "faeda.f_hopar"
    skipun <- paste("select sum(NVL(thyngd,0)) total,flokk_id from",
                    table)
    y <- run.sqlskipun(skipun, x$flokk.id, "flokk_id", "where", "group by flokk_id")
    x <- join(x, y, "flokk.id", set = 0)
  }
  row.names(x) <- x$flokk.id
  print("fjoldi")
  if (fjoldi)
    x <- fjoldi.i.flokkum(x, ranfiskur,oracle=oracle)
  i <- is.na(x$fj.aelt)
  if (any(i))
    x$fj.aelt[i] <- 0
  i <- is.na(x$fj.omelt)
  if (any(i))
    x$fj.omelt[i] <- 0
  return(x)
}