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Extract SPECIES information from CFDBS

Source: R/get_species.R
get_species.Rd

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

Usage

get_species(channel, species = "all")

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)

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:

data

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 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_areas(), get_gears(), get_locations(), get_ports(), get_species_itis(), get_vessels()

Examples

if (FALSE) { # \dontrun{
# 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)
get_species(channel,species=81)

# extracts info for cod ("COD")
get_species(channel,"cod")
get_species(channel,"co")
get_species(channel,"COD")


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