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ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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OrdCode and ClaCode access #88

Closed amroco closed 8 years ago

amroco commented 8 years ago

Looking at whats available using the species function I can see GenCode, SpecCode and FamCode, but nothing for higher levels such as order and class.

Is there a way to access these? Thank you :)

cboettig commented 8 years ago

The species_list() function will allow you to search by Order etc by creating a list of species in the requested taxon level. The FishBase database doesn't define or use codes corresponding to Order or Class, but you should be able to make any query you need by just filtering on the corresponding species names as provided by species_list(). HTH,

amroco commented 8 years ago

Hi Carl, I no longer need this as I got a hold of the list, but in case anyone else would like to operate at higher level taxon, there are codes for higher levels used in fishbase and sealifebase, just thought I'd put it out there in case that's something other people may need sometime. Cheers

sckott commented 8 years ago

thanks @amroco - what are some examples of higher level codes?

amroco commented 8 years ago

Here is an example from SeaLifeBase:

Phylum: Arthropoda (0), Class: Maxillopoda (10046) Order: Harpacticoida (10046) Family: Novocriniidae (4540) Genus: Novocrinia (25029)

Cheers, A

sckott commented 8 years ago

thanks

amroco commented 8 years ago

Oop, the class and order codes are unique, I accidentally copied and pasted the same value there. Anyway, there are values for those : )