Chapter 20 NOAA/NMFS species codes

Table

LTabundR provides the standard table of NOAA/NMFS species codes as a built-in dataset:

This version of the species codes table was provided by Amanda Bradford (Pacific Islands Fisheries Science Center) in 2021.

For an easier way to find a species of interest, look into the species_translator() function on the Miscellaneous functions page.

species_translator()

To streamline the management of species codes, scientific names, common names, etc., in the functions throughout this package, we have developed a “translator” function that returns the various identifiers for a species according to a variety of search terms.

You can search by species code:

# source('R/species_translator.R`)
species_translator(id = '035') %>% t()
                35                                        
code            "035"                                     
short_name      "LONG_PILOT"                              
scientific_name "Globicephala melas"                      
common          "Long-finned pilot whale"                 
description     "Atlantic pilot whale; blackfish; pothead"

By the short code name:

species_translator(id = 'LONG_PILOT') %>% t()
                35                                        
code            "035"                                     
short_name      "LONG_PILOT"                              
scientific_name "Globicephala melas"                      
common          "Long-finned pilot whale"                 
description     "Atlantic pilot whale; blackfish; pothead"

By the scientific name:

species_translator(id = 'Globicephala melas') %>% t()
                35                                        
code            "035"                                     
short_name      "LONG_PILOT"                              
scientific_name "Globicephala melas"                      
common          "Long-finned pilot whale"                 
description     "Atlantic pilot whale; blackfish; pothead"

Or by one of the species’ common names:

species_translator(id = 'Long-finned pilot whale') %>% t()
                35                                        
code            "035"                                     
short_name      "LONG_PILOT"                              
scientific_name "Globicephala melas"                      
common          "Long-finned pilot whale"                 
description     "Atlantic pilot whale; blackfish; pothead"

The function will return any species for which there is a partial match:

species_translator(id = 'megap') %>% t()
                76                      
code            "076"                   
short_name      "HUMPBACK_W"            
scientific_name "Megaptera novaeangliae"
common          "Humpback whale"        
description     ""                      
                70                                              
code            "070"                                           
short_name      "UNID_RORQL"                                    
scientific_name "Balaenopterid sp"                              
common          "Unidentified rorqual (Balaenoptera; Megaptera)"
description     ""                                              

species_translator(id = 'killer')
    code short_name      scientific_name                        common
32   032 PYGMY_KLLR     Feresa attenuata            Pygmy killer whale
33   033 FALSE_KLLR Pseudorca crassidens            False killer whale
37   037 KILLER_WHA         Orcinus orca                  Killer whale
110  110                    Orcinus orca        Transient killer whale
111  111                    Orcinus orca         Resident killer whale
112  112                    Orcinus orca         Offshore killer whale
113  113                    Orcinus orca Type A Antarctic killer whale
114  114                    Orcinus orca Type B Antarctic killer whale
115  115                    Orcinus orca Type C Antarctic killer whale
          description
32  slender blackfish
33                   
37                   
110                  
111                  
112                  
113                  
114                  
115                  

Note that if species_codes is NULL, as in the examples above, the list of codes used in ABUND9 will be used as a default.