Get PBS data

Source: R/get-dat.R

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.

get_ssids()

get_major_areas()

get_management_areas()

get_fishery_ids()

get_species_groups()

get_gear_types()

get_age_methods()

get_species()

get_sensor_attributes()

get_other_surveys()

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

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

get_commercial_samples(species, unsorted_only = TRUE, usability = NULL)

get_catch(species)

get_hake_catch()

get_cpue_spatial(species)

get_cpue_spatial_ll(species)

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

get_age_precision(species, inside = NULL)

get_survey_index(species, ssid = NULL)

get_sensor_data_trawl(ssid = NULL, attribute = c("temperature",
  "depth", "dissolved oxygen", "salinity"), spread_attributes = FALSE)

get_sensor_data_fe_trawl(fishing_event_id = NULL,
  attribute = c("temperature", "depth", "dissolved oxygen", "salinity"),
  sensor_name = NULL)

get_sensor_data_ll_td(ssid = NULL, attribute = c("temperature",
  "depth"), sensor_min_max = FALSE)

get_sensor_data_ll_td(ssid = NULL, attribute = c("temperature",
  "depth"), sensor_min_max = FALSE)

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

get_sara_dat()

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

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.
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.
inside

To select only the inside population (Strait of Georgia, area 4B only), set inside = 1. To select only the outside population, set inside = 0.
gear

The gear type(s) to include for CPUE. Will be converted to uppercase. Run get_gear_types() for a look-up table of available gear types to select from.
min_cpue_year

Minimum year for the CPUE data.
attribute

A character vector of sensor attributes to filter for. Run get_sensor_attributes() for a look-up table of available attributes.
spread_attributes

Logical for whether the attributes should be returned in a wider format.
fishing_event_id

A vector of fishing events to filter for
sensor_name

A character vector of sensor names to filter for.
sensor_min_max

Allows for user to choose whether data are output in wide format (= TRUE) with min and max values for each attribute for each fishing event, or in long format (= FALSE) with only mean values for each attribute and fishing event.
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.

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().

Details

  • get_ssids() produces a lookup table for survey series IDs and descriptions

  • get_age_methods() produces a lookup table for ageing method codes and descriptions

  • get_sample_trips()produces a lookup table for sample ID and fishing event ID

  • get_strata_areas() produces a lookup table for surveyed area for each stratum within surveys

  • get_survey_ids() produces lookup table for survey IDs for a given survey series ID

  • 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_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

  • cache_pbs_data() runs all 'get' functions in the gfplot 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_survey_index()

  • get_age_precision()

  • and optionally from get_survey_sets() and get_cpue_historical()

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))
# }