R/1-orfhistory.R

In elisekeppel/gfhistorical: What the Package Does (One Line, Title Case)

# This is to get the historical rockfish catch data (Cdn, US & foreign)
# Author: Elise Keppel
# Last edited: November 2019

get_orf_history <- function(foreign = FALSE){
# Import raw catch data from Catch-Historical.xls spreadsheet from Rowan Haigh
#   containing orf/pop landings from various sources. Convert all landings
#   to kg and arrange in similar format.
# Note that the number of Yamanaka and Obradovich records differ from Rowan Haigh's orfhistory due to his
# multiple lines for catch in a given major area divided up by regions D1-3. The catches
# sum to the same values.
  ketchen76 <- read_xls("inst/extdata/Catch-Historical.xls", sheet = "Ketchen76", range = "A4:G614")

  stewart <- suppressMessages(read_xls("inst/extdata/Catch-Historical.xls",
    sheet = "Stewart",
    range = "I4:O36"))

  yamanaka <- read_xls("inst/extdata/Catch-Historical.xls",
    sheet = "Yamanaka",
    range = "AZ5:BH38")

  obradovich <- read_xls("inst/extdata/Catch-Historical.xls",
    sheet = "Obradovich",
    range = "A5:K81")

  ketchen80 <- read_xls("inst/extdata/Catch-Historical.xls",
    sheet = "Ketchen80",
    range = "A3:G113")

  leaman80 <- read_xls("inst/extdata/Catch-Historical.xls",
    sheet = "Leaman80",
    range = "A3:G67")
  #-----------------------------------------------------------------------------------

  names(yamanaka) <- c('year', 1, 3, 4, 5, 6, 7, 8, 9)
  orf_yamanaka <- yamanaka %>%
    gather('1', '3', '4', '5', '6', '7', '8', '9', key = major, value = catch) %>%
    mutate(
      year = year,
      spp = '391',
      major = as.numeric(major),
      region = case_when(
        major == 1 ~ '4B',
        major == 2 ~ '4A',
        major == 3 ~ '3C',
        major == 4 ~ '3D',
        major == 5 ~ '5A',
        major == 6 ~ '5B',
        major == 7 ~ '5C',
        major == 8 ~ '5D',
        major == 9 ~ '5E'),
      nation = 'CA',
      catch = as.numeric(catch)*1000, # convert tons to kg
      units = "kg",
      source = "yamanaka",
      action = "add",
      fishery = "combined"
    )

  orf_ketchen76 <- ketchen76 %>%
    mutate(catch = catch/2.20459, # convert lbs to kg (off by a little from Rowan's)
      units = "kg",
      source = "ketchen76",
      fishery = "trawl",
      action = "max") %>%
    select(year:nation, catch, units, source, action, fishery)

  orf_obradovich <- obradovich %>%
    gather('1', '2', '3', '4', '5', '6', '7', '8', '9', key = major, value = catch) %>%
    mutate(
      year = year,
      spp = '391',
      major = as.numeric(major),
      region = case_when(
        major == 1 ~ '4B',
        major == 2 ~ '4A',
        major == 3 ~ '3C',
        major == 4 ~ '3D',
        major == 5 ~ '5A',
        major == 6 ~ '5B',
        major == 7 ~ '5C',
        major == 8 ~ '5D',
        major == 9 ~ '5E'),
      nation = 'CA',
      catch = as.numeric(catch)*1000, # convert tons to kg
      units = "kg",
      source = "obradovich",
      action = "max",
      fishery = gear
    ) %>%
    filter(!is.na(catch)) %>%
    select(-gear)

  orf_ketchen80 <- ketchen80 %>%
    mutate(catch = catch*1000, # convert tons to kg
      units = "kg",
      source = "ketchen80",
      fishery = "trawl",
      action = "add") %>%
    select(year:nation, catch, units, source, action, fishery)

  orf_leaman80 <- leaman80 %>%
    mutate(catch = catch*1000, # convert tons to kg
      units = "kg",
      source = "leaman80",
      fishery = "trawl",
      action = "add") %>%
    select(year:nation, catch, units, source, action, fishery)

  #----------------------------------------------------------------------------------
  # estimate US ORF landings by major areas 3CD5ABCD for 1930-1964 using ratios calculated from ketchen76 1950-1953 area landings data and US total landings data

  # calculate total US ORF landings by areas 3CD5ABCD (5E not recorded) 1950-1953
  bc_us_landings <- ketchen76 %>% filter(nation == 'US', major %in% c(3,4,5,6,7,8,9)) %>%
    select(-nation, -region) %>%
    # filter for species 391 = ORF
    filter(year %in% c(1950:1953), spp %in% c(391)) %>%
    # convert from lbs to kg
    group_by(major) %>%
    summarise(catch = sum(catch)/2.2046) %>%
    mutate(units = "kg")
  sum_bc_us_landings <- as.numeric(bc_us_landings %>%
      summarise(catch = sum(catch)))

  # calculate total WA ORF landings from 1950-1953

  all_wa_landings <- stewart %>% select(1,6) %>%
    rename(year = "Year", wa_orf_lbs = "WA Rockfishes (lbs)") %>%
    mutate(wa_orf_kg = wa_orf_lbs/2.2046) # convert from lbs to kg
  sum_all_wa_landings <- all_wa_landings %>%
    filter(year %in% c(1950:1953)) %>%
    summarise(catch = sum(wa_orf_kg)) %>%
    as.numeric()

  # calculate ratio of US ORF catch that came from Canadian waters 1950-1953
  bc_us <- as.numeric(sum_bc_us_landings/sum_all_wa_landings) # 0.7148079

  # apply bc/wa ratio to annual total wa landings 1930-1964
  hist_bc_us_landings <- all_wa_landings %>%
    mutate(bc_wa_orf_kg = wa_orf_kg*bc_us)

  # calculate ratio of US ORF landings in each Canadian fishing area vs. total US catch in BC 1950-1953
  area_ratios <- bc_us_landings %>%
    mutate(bc_wa_area = catch/sum_bc_us_landings)

  # apply area ratios to total us catch in BC to obtain us catch by bc fishing area for 1930-1949

  bc_us_landings_by_area <- hist_bc_us_landings %>% select(-wa_orf_lbs, -wa_orf_kg) %>%
    mutate('3' = bc_wa_orf_kg*area_ratios$bc_wa_area[which(area_ratios$major == 3)]) %>%
    mutate('4' = bc_wa_orf_kg*area_ratios$bc_wa_area[which(area_ratios$major == 4)]) %>%
    mutate('5' = bc_wa_orf_kg*area_ratios$bc_wa_area[which(area_ratios$major == 5)]) %>%
    mutate('6' = bc_wa_orf_kg*area_ratios$bc_wa_area[which(area_ratios$major == 6)]) %>%
    mutate('7' = bc_wa_orf_kg*area_ratios$bc_wa_area[which(area_ratios$major == 7)]) %>%
    mutate('8' = bc_wa_orf_kg*area_ratios$bc_wa_area[which(area_ratios$major == 8)]) %>%
    select(-bc_wa_orf_kg) %>%
    gather('3', '4', '5', '6', '7', '8', key = major, value = catch) %>%
    mutate(spp = '391', nation = 'US', units = "kg", source = "stewart",
      fishery = "trawl", action = "max", major = as.numeric(major),
      region = case_when(
        major == 1 ~ '4B',
        major == 2 ~ '4A',
        major == 3 ~ '3C',
        major == 4 ~ '3D',
        major == 5 ~ '5A',
        major == 6 ~ '5B',
        major == 7 ~ '5C',
        major == 8 ~ '5D',
        major == 9 ~ '5E'))

  # As pre-1954 data are not included in GF_MERGED_CATCH table in GFFOS,
  #   for now will use pre-1954 data from Rowan's orfhistory
  #   TO DO: check for any updates to pre-1954 gfcatch data and create function
  #     to extract this.
  gfcatch53 <- orfhistory %>% filter(source == 'GFCatch', year <1954) %>%
    mutate(units = "kg")
  gfcatch54 <- orfhistory %>% filter(source == 'GFCatch', year >1953) %>% # TO DO: recreate gfcatch 1954+
    mutate(units = "kg")
  pacharv3 <- orfhistory %>% filter(source == 'PacHarv3') %>% # TO DO: recreate pacharv3
    mutate(units = "kg")
  orf <- rbind(orf_yamanaka, orf_ketchen76, orf_obradovich, orf_ketchen80,
    orf_leaman80, bc_us_landings_by_area, gfcatch53, gfcatch54, pacharv3)
  orf <- if(!foreign) {filter(orf, nation %in% c("CA", "US"))}
}