get_species: Extract SPECIES information from CFDBS

In andybeet/cfdbs: Pulls data from the NEFSC commercial database

Extract SPECIES information from CFDBS

Description

Extract a list of speices names, code, market category, etc from the NEFSC cfspp table

Usage

get_species(channel, species = "all")

Arguments

channel	DBI Object. Inherited from DBIConnection-class. This object is used to connect to communicate with the database engine. (see connect_to_database)
species	a specific species code or set of codes. Either numeric or character vector. (NESPP3 codes) Numeric codes are converted to VARCHAR2(3 BYTE) when creating the sql statement. A Species common name can also be supplied. The character string is used to pull from SPPNM field. Defaults to "all" species.

Value

A list is returned:

species	containing the result of the executed $sql statement
sql	containing the sql call
colNames	a vector of the table's column names

The default sql statement "select * from cfdbs.cfspp" is used

Reference

Use the data dictionary (http://nova.nefsc.noaa.gov/datadict/) for field name explanations. Note: species codes (nespp3) are stored in the database as VARCHAR2(3 BYTE)

See Also

connect_to_database

Other get functions: get_age_length(), get_anything_sql(), get_areas(), get_gears(), get_landings_length(), get_landings_palmer(), get_landings(), get_locations(), get_ports(), get_species_itis(), get_vessels()

Examples

## Not run: 
# extracts complete species table based on custom sql statement
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
get_species(channel)

# extracts info for cod (081) 
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
get_species(channel,species=81)

# extracts info for cod ("COD") 
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
get_species(channel,"cod") or
get_species(channel,"co") or
get_species(channel,"COD")


# extracts info for cod (081)  and bluefish (023)
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
sqlStatement <- "select * from cfdbs.cfspp"
get_species(channel,species= c("081","023"))

## End(Not run)

andybeet/cfdbs documentation built on Sept. 19, 2023, 9:34 p.m.