get_data: Get PBS data

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

Get PBS data

Description

Automates fisheries and research survey data extraction from DFO Pacific groundfish databases. The output datasets feed into other functions (tidy_, plot_, or fit_ functions) for data visualization, which can be used as products themselves or can be fed into automated DFO Pacific groundfish data synopsis report production.

Usage

get_survey_sets(
  species,
  ssid = c(1, 3, 4, 16, 2, 14, 22, 36, 39, 40),
  join_sample_ids = FALSE,
  verbose = FALSE,
  sleep = 0.05
)

get_ll_hook_data(species = NULL, ssid = NULL)

get_survey_samples(
  species,
  ssid = NULL,
  remove_bad_data = TRUE,
  unsorted_only = TRUE,
  usability = NULL,
  major = NULL
)

get_commercial_samples(
  species,
  unsorted_only = TRUE,
  return_all_lengths = FALSE,
  major = NULL,
  usability = NULL
)

get_catch(species, major = NULL)

get_cpue_historical(
  species = NULL,
  major = NULL,
  alt_year_start_date = "04-01",
  areas = c("3[CD]+", "5[AB]+", "5[CDE]+"),
  end_year = NULL
)

get_cpue_historical_hake(end_year = NULL)

get_cpue_historical_hl(
  species = NULL,
  major = NULL,
  alt_year_start_date = "04-01",
  areas = c("3[CD]+", "5[AB]+", "5[CDE]+"),
  end_year = NULL
)

get_cpue_spatial(species, major = NULL)

get_catch_spatial(species, major = NULL)

get_cpue_spatial_ll(species, major = NULL)

get_cpue_index(gear = "bottom trawl", min_cpue_year = 1996, major = NULL)

get_cpue_index_hl(min_cpue_year = 1980, major = NULL)

get_age_precision(species, major = NULL)

get_survey_index(species, ssid = NULL)

get_sable_landings(species, ssid = NULL)

get_survey_blocks(ssid = NULL)

get_eulachon_specimens()

get_gear_types()

get_management(
  species = NULL,
  species_group = NULL,
  fishery = NULL,
  area = NULL,
  start_year = NULL
)

cache_pbs_data(
  species,
  major = NULL,
  file_name = NULL,
  path = ".",
  compress = FALSE,
  unsorted_only = TRUE,
  historical_cpue = FALSE,
  survey_sets = FALSE,
  verbose = TRUE,
  return_all_lengths = FALSE
)

get_hake_survey_samples()

get_hake_catch(end_date = format(Sys.Date(), "%d/%m/%Y"))

get_sablefish_surveys()

Arguments

species	One or more species common names (e.g. "pacific ocean perch") or one or more species codes (e.g. 396). Species codes can be specified as numeric vectors ⁠c(396, 442⁠) or characters c("396", "442"). Numeric values shorter than 3 digits will be expanded to 3 digits and converted to character objects (1 turns into "001"). Species common names and species codes should not be mixed. If any element is missing a species code, then all elements will be assumed to be species common names.
ssid	A numeric vector of survey series IDs. Run get_ssids() for a look-up table of available survey series IDs with surveys series descriptions.
join_sample_ids	If TRUE then the sample IDs will be joined in. This may result in repeated rows of data if the same sample ID is part of different survey stratifications.
verbose	If TRUE then extra messages were reprinted during data extraction. Useful to monitor progress.
sleep	System sleep in seconds between each survey-year to be kind to the server.
remove_bad_data	Remove known bad data, such as unrealistic length or weight values.
unsorted_only	Remove sorted biological data ('keepers' and 'discards' and unknown). Default = TRUE.
usability	A vector of usability codes to include. Defaults to all. IPHC codes may be different to other surveys.
major	To select only the inside population (Strait of Georgia, area 4B only), set inside = 1. To select only the outside population, set inside = 0.
return_all_lengths	Include all length types, rather than just with most common measurement. Default = FALSE.
alt_year_start_date	Alternative year starting date specified as a month-day combination. E.g. "03-01" for March 1st. Can be used to create 'fishing years'.
areas	Area groupings as a vector of regular expressions. See base::regex().
end_year	Specify the last calendar year to be extracted.
gear	The gear type(s) to include for CPUE. Will be converted to uppercase. Run get_comm_gear_types() for a look-up table of available gear types to select from.
min_cpue_year	Minimum year for the CPUE data.
species_group	Species group code(s) to include (see lookup table get_species_groups()). Defaults to all.
fishery	The fishery_id code(s) (see lookup table get_fishery_ids()) for fisheries to include in data extraction. Defaults to all.
area	The fishery area(s) (see lookup table get_management_areas()) to include in data extraction (eg. '5A'; c('3C', '3D', '5A', '5B')).
start_year	The minimum year to include management actions. Defaults to all.
file_name	Optional filename(s) for the cached file. Defaults to the same as the species argument.
path	The folder where the cached data will be saved.
compress	Compress the .rds file? Defaults to FALSE for faster reading and writing at the expense of disk space.
historical_cpue	Logical for whether historical CPUE should be included.
survey_sets	Logical for whether the survey set data should be extracted. You might set this to FALSE if you don't need these data and you want to substantially speed up data extraction.
end_date	A string representing the date. Must be of the format dd/mm/yyyy

Details

• get_survey_sets() extracts survey catch data and spatial data for plotting survey catchs on a map of British Columbia

• get_survey_samples() extracts all biological sample specimen records from research surveys for given species and survey series IDs from GFBio

• get_hake_survey_samples() extracts all biological sample specimen records from hake joint acoustic surveys from GFBio

• get_commercial_samples() extracts all biological sample specimen records from commercial data for given species from GFBio

• get_catch() extracts all landing and discard records for a given species from GFFOS.GF_MERGED_CATCH

• get_hake_catch() extracts all landing and discard records for Pacific Hake with some extra data used in the Hake assessment

• get_cpue_spatial() extracts catch, effort and spatial data from GFFOS.GF_D_OFFICIAL_CATCH for the groundfish trawl fishery

• get_cpue_spatial_ll() extracts catch, effort and spatial data from GFFOS.GF_D_OFFICIAL_CATCH for the longline fishery

• get_cpue_index() extracts catch and effort data from GFFOS.GF_MERGED_CATCH for the groundfish trawl fishery since 1996

• get_cpue_historical() extracts historical catch and effort data back into the 1950s. It's help file is on a separate page; see the link

• get_age_precision() extracts age readings from biological samples for a given species where there is a second ('precision') age reading

• get_sara_dat() scrubs Species At Risk website for up-to-date species status and listings

• get_survey_index() extracts survey catch data for given species and survey series IDs

• get_management() extracts management actions

• cache_pbs_data() runs all 'get' functions in the gfdata package

  (except those specific to IPHC data) and caches extracted data to a given folder

This cache_pbs_data() function caches data from

• get_survey_samples()

• get_commercial_samples()

• get_catch()

• get_cpue_spatial()

• get_cpue_spatial_ll()

• get_catch_spatial()

• get_survey_index()

• get_age_precision()

• and optionally from get_survey_sets() and get_cpue_historical()

Value

The ⁠get_*⁠ functions return a data frame. The cache_pbs_data() function writes an .rds file to path for each specified species. A data object for a single species is a named list object with each element containing a data frame from a ⁠get_*⁠ function. The element name of the list reflects the function name with the get_ part removed. For example, the output from get_survey_samples() is in a list element named survey_samples().

Authentication

⁠get_*⁠ functions only extract data when performed on a computer connected to the Pacific Biological Station DFO network. By default, the functions assume that you are on an authorized DFO Windows computer where authentication with the databases happens automatically. If instead, you wish to connect by username and password, see the details section in run_sql().

Examples

## Not run: 
## Import survey catch density and location data by tow or set for plotting
## Specify single or multiple species by common name or species code and
## single or multiple survey series id(s).
get_survey_sets(species = "lingcod", ssid = 1)

## Import survey or commercial biological data for various plots
## (e.g. length frequency, growth, age frequency, maturity, etc.)
get_survey_samples(species = 442, ssid = c(1, 3, 4, 16))

get_commercial_samples(c(442, 397))

## Import catch data by species for barcharts of landings by fishing area,
## geartype, and year.
get_catch("lingcod")

## Import spatial commercial catch per unit effort data for trawl or longline
## data by species for plotting along BC coast.
get_cpue_spatial("lingcod")
get_cpue_spatial_ll("yelloweye rockfish")

## Import catch and effort data by gear type for modelling commercial trawl
## cpue index.
get_cpue_index(gear = "bottom trawl", min_cpue_year = 2012)

## Import survey bootstrapped biomass estimates for plotting relative biomass
## indices by specified survey series.
get_survey_index("pacific cod", ssid = c(1, 3, 4, 16))

## End(Not run)

pbs-assess/gfdata documentation built on Feb. 16, 2025, 7:47 a.m.