R/correct-ssids.R

In pbs-assess/gfdata: Data Extraction for DFO PBS Groundfish Stocks

# Custom fixes for problem surveys with shared trip ids resulting in assignment to wrong ssid
#
# @param dat df containing these columns: fishing_event_ids, survey_series_id, survey_id,
#  major_stat_area_code, minor_stat_area_code
# @param specimens Defaults to FALSE where checks for duplication of fishing_event_ids
#
correct_ssids <- function(dat, specimens = FALSE) {
  try(dat[dat$survey_series_id %in% c(6, 7), ]$survey_id <- NA, silent = TRUE)
  try(dat[((dat$survey_series_id %in% 6 & dat$major_stat_area_code %in% c("03", "04"))), ]$survey_series_id <- 7, silent = TRUE)
  try(dat[((dat$survey_series_id %in% 7 & dat$major_stat_area_code %in% c("05", "06"))), ]$survey_series_id <- 6, silent = TRUE)
  try(dat[((dat$survey_series_og %in% 6 & dat$major_stat_area_code %in% c("03", "04"))), ]$survey_series_og <- 7, silent = TRUE)
  try(dat[((dat$survey_series_og %in% 7 & dat$major_stat_area_code %in% c("05", "06"))), ]$survey_series_og <- 6, silent = TRUE)

  # SABLE doesn't work with SSIDs, use reason_desc and or grouping codes instead?
  try(dat[dat$survey_series_id %in% c(35, 41, 42, 43), ]$survey_id <- NA, silent = TRUE) # this throws a warning when others don't
  try(dat[dat$survey_series_id %in% c(35, 41, 42, 43), ]$survey_series_id <- 35, silent = TRUE)
  try(dat[dat$survey_series_og %in% c(35, 41, 42, 43), ]$survey_series_og <- 35, silent = TRUE)
  # try(dat[ ((dat$survey_series_id %in% c(35, 41, 42, 43) & dat$reason_desc %in% "EXPLORATORY")), ]$survey_series_id <- 35, silent = TRUE)
  # try(dat[ ((dat$survey_series_id %in% c(35, 41, 42, 43) & dat$reason_desc %in% "SABLEFISH STANDARDIZED OFFSHORE SURVEY")), ]$survey_series_id <- 42, silent = TRUE)

  # Jig surveys are split into too many separate survey series, so we'll assume all were assigned correctly and drop everything that doesn't match
  dat <- dat[(!(dat$survey_series_id %in% 82 & !(dat$minor_stat_area_code %in% c("12")))), ]
  dat <- dat[(!(dat$survey_series_id %in% 83 & !(dat$minor_stat_area_code %in% c("13")))), ]
  dat <- dat[(!(dat$survey_series_id %in% 84 & !(dat$minor_stat_area_code %in% c("15")))), ]
  dat <- dat[(!(dat$survey_series_id %in% 85 & !(dat$minor_stat_area_code %in% c("16")))), ]
  dat <- dat[(!(dat$survey_series_id %in% 86 & !(dat$minor_stat_area_code %in% c("18")))), ]
  dat <- dat[(!(dat$survey_series_id %in% 87 & !(dat$minor_stat_area_code %in% c("19")))), ]

  # for IPHC station specific ssids, drop everything that doesn't match
  dat <- dat[(!(dat$survey_series_id %in% 17 & !(dat$minor_stat_area_code %in% c("3")))), ] # 3CD
  dat <- dat[(!(dat$survey_series_id %in% 18 & !(dat$minor_stat_area_code %in% c("6")))), ] # 5AB
  dat <- dat[(!(dat$survey_series_id %in% 19 & !(dat$minor_stat_area_code %in% c("7")))), ] # 5CD

  dat |> dplyr::distinct()
}