Extract SPECIES information from CFDBS (SPECIES_ITIS_NE, table)

Source: R/get_species_itis.R

Extract a list of species names, code, market category, etc from the NEFSC SPECIES_ITIS_NE table

get_species_itis(channel, species = "all", nameType = "common_name")

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. Defaults to "all" species. Numeric codes (SPECIES_ITIS) are converted to VARCHAR2(33) when creating the sql statement. Character codes are short character strings.
nameType

Character string. Upper or lower case. Either "common_name" (default), "scientific_name" or "nespp4". Determines which type of name to search under.

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.SPECIES_ITIS_NE" is used

Reference

Use the data dictionary for field name explanations.

See also

connect_to_database

Other get functions: get_areas(), get_gears(), get_locations(), get_ports(), get_species(), get_vessels()

Examples

if (FALSE) {
# extracts complete species table based on custom sql statement
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
get_species_itis(channel)

# extracts info for cod (164712)
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
get_species_itis(channel,species=164712)

# extracts info for cod ("COD")
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
get_species_itis(channel,"cod") #o r
get_species_itis(channel,"co") # or (note also return cockles, calico scallop etc.)
get_species_itis(channel,"COD")

# extracts info for cod ("gadus")
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
get_species_itis(channel,"gadus",nameType="scientific_name") #o r
get_species_itis(channel,"morh",nameType="scientific_name") #o r
get_species_itis(channel,"GADUS",nameType="scientific_name") #o r

#' # extracts info for cod ("0814") market category 4
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
get_species_itis(channel,"0814",nameType="NESPP4") #o r
get_species_itis(channel,814,nameType="NESPP4")


# extracts info for cod (164712)  and bluefish (168559)
channel <- connect_to_database(server="name_of_server",uid="individuals_username")
sqlStatement <- "select * from cfdbs.species_itis_ne"
get_species_itis(channel,species= c("164712","168559"))
}