Main function to query the survey database

Main function to query the survey database

get_data(
  common = NULL,
  scientific = NULL,
  itis_id = NULL,
  regions = NULL,
  surveys = NULL,
  years = NULL
)

Arguments

common

A string, or vector of strings, of common names for species. This is NULL by default, so that all species are returned.

scientific

A string, or vector of strings, of scientific names for species. This is NULL by default, so that all species are returned.

itis_id

An integer, or vector of integers, corresponding to ITIS identifiers. This is NULL by default, so that all species are returned.

regions

A string, or vector of strings of common names for regions. May be one or more of "afsc", "nwfsc", "pbs". Surveys are nested within region, so returning data from a region may return more than one survey. This is NULL by default, so that all surveys are returned.

surveys

A string, or vector of strings of common names for surveys. May be one or more of "Aleutian Islands", "Bering Sea Slope", "eastern Bering Sea", "Gulf of Alaska", "northern Bering Sea", "NWFSC.Combo", "NWFSC.Shelf", "NWFSC.Slope", "NWFSC.Hypoxia", "Triennial", "SYN QCS", "SYN HS", "SYN WCVI", "SYN WCHG". If NULL, all are returned.

years

a vector of years, e.g. year = 2013:2018. If NULL, all are returned.

Value

a data frame of joined haul and catch data

  • event_id: Unique haul identifier.

  • itis: ITIS identifier for species.

  • catch_numbers: Numbers of fish for this haul - species.

  • catch_weight: Weight (kg) of fish for this haul - species.

  • region: Region this survey originated in ("pbs", "nwfsc", "afsc").

  • scientific_name: Scientific name for this species.

  • common_name: Common name for this species.

  • survey_name: Name of the survey this haul is part of.

  • date: String representation of the date, format YYYY-MM-DD.

  • pass: Optional pass identifier (1 or 2), only used for NWFSC surveys.

  • vessel: Optional unique vessel identifier, not included in all surveys.

  • lat_start: Starting latitude of haul, decimal degrees.

  • lon_start: Starting longitude of haul, decimal degrees.

  • lat_end: Ending latitude of haul, decimal degrees.

  • lon_end: Ending longitude of haul, decimal degrees.

  • depth_m: Haul bottom depth (meters).

  • effort: Amount of units corresponding to this haul.

  • effort_units: Units of effort.

  • performance: Optional performance indicator for each haul, not used for all surveys. If not indicated, assume performance is satisfactory

  • bottom_temp_c: Bottom temperature recorded at the gear, in degrees Celsius.

  • year: Calendar year corresponding to the haul.

Examples

if (FALSE) { # \dontrun{
d <- get_data()
} # }