Extracts Massachusetts inshore bottom trawl survey data

Pulls survey data

Usage

get_mass_inshore_survey_data(channel, filterByYear = NA)

Arguments

channel: an Object inherited from DBIConnection-class. This object is used to communicate with the database engine. (see connect_to_database)
filterByYear: Numeric vector. Subset of years from which to pull data. If not specified then all years are pulled. (Default = NA)

Value

A list containing a Data frame (data.table) (n x 19), a list of SQL queries used to pull the data, the date of the pull, and the call expression. Each row of the data.table represents the catch of a species on a specific tow along with physical attributes of the tow.

The data frame (Descriptions taken from NEFSC Data dictionary)

CRUISE6: Code uniquely identifying cruise. The first four digits indicate the year and the last two digit uniquely identify the cruise within the year. The 5th byte signifies cruises other than groundfish: Shrimp survey = 7 (i.e. 201470), State of Massachusetts survey = 9 (i.e. 201491), Food habits = 5 (i.e.199554)
STATION: Unique sequential order in which stations have been completed. Hangups and short tows each receive a non-repeated consecutive number.
STRATUM: A predefined area where a net dredge, or other piece of gear was deployed. Code consists of 2 parts: Stratum group code number (2 bytes) and stratum number (3 bytes). Stratum group refers to if area fished is inshore or offshore North or South of Cape Hatteras or the type of cruise (shellfish, State of MA, offshore deepwater). The stratum number (third and fourth digits of code) refers to area defined by depth zone. See SVDBS.SVMSTRATA. The fifth digit of the code increases the length of the stratum number for revised strata after the Hague Line was established. Stratum group code: 01 = Trawl, offshore north of Hatteras; 02 = BIOM; 03 = Trawl, inshore north of Hatteras; 04 = Shrimp; 05 = Scotian shelf; 06 = Shellfish; 07 = Trawl, inshore south of Hatteras; 08 = Trawl, Offshore south of Hatteras; 09 = MA DMF; 99 = Offshore deepwater (outside the stratified area). A change in Bottom Trawl Stratum for the Gulf of Maine-Bay of Fundy has been in effect since Spring 1987, and may be summarized as follows: Previous strata: 01350; Present strata: 01351, 01352.
TOW: Sequential number representing order in which station was selected within a stratum.
SVVESSEL: Standard two character code for a survey vessel. Refer to SVDBS.SV_VESSEL
YEAR: Year in which cruise was conducted.
SEASON: Season of the year in which cruise was conducted.
LAT: Beginning latitude of tow in decimal degrees.(DECDEG_BEGLAT)
LON: Beginning longitude of tow in decimal degrees.(DECDEG_BEGLON)
EST_TOWDATE: Date and time represented by Eastern Standard Time (EST) for the start of a tow or deployment.(BEGIN_EST_TOWDATE)
DEPTH: A four digit number recording the average depth, to the nearest meter, during a survey gear deployment.(AVGDEPTH)
SURFTEMP: Surface temperature of water (degrees Celcius).
BOTTEMP: Bottom temperature (degrees Celsius).
SURFSALINITY: Salinity at water surface in practical salinity units (PSU).
BOTSALINITY: Bottom salinity in Practical Salinity Units (PSU).
SVSPP: A standard code which represents a species caught in a trawl or dredge. Refer to the SVDBS.SVSPECIES_LIST
CATCHSEX: Code used to identify species that are sexed at the catch level. See SVDBS.SEX_CODES
ABUNDANCE: Expanded number of individuals of a species caught at a given station.(EXPCATCHNUM)
BIOMASS: Expanded catch weight of a species caught at a given station. (EXPCATCHWT)

The date:

pullDate: The date the data was pulled from the database

The expression:

functionCall: The call used to create the data pull

The version:

version: The version of survdat used to pull the data

Examples

if (FALSE) { # \dontrun{
channel <- dbutils::connect_to_database("serverName","userName")
get_mass_inshore_survey_data(channel)
} # }

Usage

Arguments

Value

See also

Examples