R/clean_catch.r

In ben-williams/scallopr: ADF&G scallop survey assessment

# 3 scal.catch (need tows first)
clean_catch <- function(catch_data, tows, YEAR){

  if(YEAR < 2019){
    catch_data %>%
      dplyr::filter(YEAR == YEAR,
             RACE_CODE == 74120,
             CONDITION_CODE_RII %in% c("01", "1", "52"),
             EVENT_ID %in% tows$tow_id) %>%  # filter out uneccessary data
      dplyr::transmute(tow_id = EVENT_ID,
                size = dplyr::case_when(SCAL_SIZE_CLASS==2 ~ "small",
                                 SCAL_SIZE_CLASS==1 ~ "large",
                                 SCAL_SIZE_CLASS==3 ~ "clapper"),
                count = COUNT,
                wt_lb = SAMPLE_WT_KG * 2.20462) %>%
      dplyr::group_by(tow_id, size) %>%
      dplyr::summarize(count = sum(count), wt_lb = sum(wt_lb)) %>%
      dplyr::right_join(expand.grid(size = c("clapper", "small", "large", "all"),
                             tow_id = tows$tow_id)) %>%
      dplyr::mutate_if(is.numeric, funs(replace(., is.na(.), 0))) %>%
      within(count[size == "all"] <- count[size == "small"] +
               count[size == "large"]) %>% # add "all" to counts
      within(wt_lb[size == "all"] <- wt_lb[size == "small"] +
               wt_lb[size == "large"]) %>% # add "all" to wts
      dplyr::mutate(Size = factor(size, levels = Size_levels)) %>%
      dplyr::select(-size) %>%
      dplyr::left_join(tows, by = "tow_id") %>%
      dplyr::ungroup() -> x

  } else {
    catch_data %>%
      dplyr::filter(rcode == 74120,
             samp_grp %in% c(1, 2),
             tow %in% tows$tow_id) %>%  # filter out uneccessary data
      dplyr::transmute(tow_id = tow,
                size = dplyr::case_when(samp_grp == 1 ~ "large",
                                 samp_grp == 2 ~ "small"),
                count = samp_cnt,
                wt_lb = samp_wt * 2.20462) %>%
      dplyr::group_by(tow_id, size) %>%
      dplyr::summarize(count = sum(count), wt_lb = sum(wt_lb)) %>%
      dplyr::right_join(expand.grid(size = c("small", "large"),
                             tow_id = tows$tow_id)) %>%
      dplyr::mutate_if(is.numeric, funs(replace(., is.na(.), 0))) %>%
      # within(count[size == "all"] <- count[size == "small"] + count[size == "large"]) %>% # add "all" to counts
      # within(wt_lb[size == "all"] <- wt_lb[size == "small"] + wt_lb[size == "large"]) %>% # add "all" to wts
      dplyr::mutate(Size = factor(size, levels = Size_levels)) %>%
      dplyr::select(-size) %>%
      dplyr::left_join(tows, by = "tow_id") %>%
      dplyr::ungroup() -> x

  }

  write_csv(x, here::here(paste0("output/",YEAR,"/scal_catch.csv")))
  x

}