get_comland_data: Extracts and processes commercial data from Database

In NOAA-EDAB/comlandr: Pulls and processes commercial fishing data from the Northeast US

Extracts and processes commercial data from Database

Description

Connects to Population dynamics Database STOCKEFF to pull US landings data. Data is also pulled from NAFO (foreign landings) and the State of Maine (Herring). These sources of data are then aggregated, species value is adjusted to a user defined reference year, skate and hake landings (often reported as an unclassified category) are split based on bottom trawl survey, and missing values are imputed. For more information regarding these methods see vignette("Overview")

Usage

get_comland_data(
  channel,
  filterByYear = NA,
  filterByArea = NA,
  useLanded = T,
  removeParts = T,
  useHerringMaine = T,
  useForeign = T,
  refYear = NA,
  refMonth = NA,
  disagSkatesHakes = T,
  aggArea = F,
  userAreas = comlandr::mskeyAreas,
  areaDescription = "EPU",
  propDescription = "MeanProp",
  applyProp = F,
  aggGear = F,
  userGears = comlandr::mskeyGears,
  fleetDescription = "Fleet",
  unkVar = c("MONTH", "NEGEAR", "AREA"),
  knStrata = c("HY", "QY", "MONTH", "NEGEAR", "TONCL2", "AREA")
)

Arguments

channel	an Object inherited from ROracle::Oracle. This object is used to connect to communicate with the database engine. (see dbutils::connect_to_database)
filterByYear	numeric vector. Years to be retrieved (Default = NA, pull all years)
filterByArea	numeric vector. Statistical Areas to be retrieved (Default = NA, pull all areas)
useLanded	boolean. Use landed or live weight for shellfish (Default = T, landed)
removeParts	boolean. Remove species parts (Heads, wings, etc), Default = T
useHerringMaine	boolean. Pull data from Maine Herring database or use herring data in commercial landings database (Default = T)
useForeign	boolean. Pull foreign data from NAFO. (Default = T)
refYear	numeric. Reference year to use when adjusting species value
refMonth	numeric. Reference month to use when adjusting species value
disagSkatesHakes	boolean. Partition skates and hake unclassified landings into species (Default = T)
aggArea	boolean. Aggregate Statistical Areas into larger spatial units (Default = F)
userAreas	data frame. Spatial units in which Statistical areas should be aggregated (eg. mskeyAreas)
areaDescription	character string. Field name in userAreas denoting spatial unit. (Default = "EPU")
propDescription	character string. Field name in userAreas denoting the scaling factor. (Default = "MeanProp")
applyProp	boolean. Apply the proportions in userAreas to the landings and value (Default = T)
aggGear	boolean. Aggregate NEGEAR codes to larger "fleets" (Default = F)
userGears	data frame. Fleet designations in which NEGEAR codes should be grouped (eg. mskeyGears)
fleetDescription	character string. Field name in userGears denoting Fleet. (Default = "Fleet")
unkVar	character vector. Variables in the data, with have missing values, that you wish to assign a value to. (unkVar = NULL skips assigning unknowns)
knStrata	character vector. Variables in the data that you wish to use to use to assign values to unkVar

Value

A list of 3 objects

• Data frame (data.table) (n x 12)

comland	Each row of the data.table defines a group of trips fishing in the same YEAR, MONTH, AREA using the same NEGEAR and MESH, on the same sized vessel, TONCL2, catching species (NESPP3) with MARKET_CODE for the same purpose (UTILCD). The sum of the landings and value are returned for each 'group'
YEAR	Year of trips
MONTH	Month of trips
NEGEAR/Fleet	Fishing gear used on trips or aggregated to Fleet
TONCL2	Tonnage class of the fishing vessel (2 digit value)
NESPP3	Species code (3 characters)
MARKET_CODE	Market code or species caught (2 characters)
MESHCAT	Code to describe the mesh size for a trawl vessel
AREA/EPU	Statistical area/ Ecological Production Unit in which species was reportly caught
UTILCD	Utilization code. Eg. The utilization code: 0=food fish or unknown; 2=aquaculture; 3=canned pet food (1984+); 4=Biomedical (2002+); 5=animal food (1984+); 7=bait; 8=industrial, other (2002+); 9=industrial, reduction.
US	Landing from the USA vessels or foreign vessels
SPPLIVMT	Weight in metric tons.
SPPVALUE	The value of landed catch to the nearest dollar (U.S.), paid to fisherman by dealer, for a given species.

• Character string

sql	Defines the SQL query used to pull the data

• Function call

call	The function call used to create the data

Argument choices

Some of the arguments rely on the choice of others.

If aggArea = T then the user must also supply a userAreas data frame and a areaDescription string to denote the field in userArea which maps the statistical area to the larger spatial unit.

If aggGear = T then the user must also supply a userGears data frame and a fleetDescription string to denote the field in userGears which maps the NEGEAR codes to the fleet designation.

NOAA-EDAB/comlandr documentation built on March 1, 2025, 8 p.m.