Set up a connection to the Species+/CITES Checklist API

To set up a connection to the Species+/CITES Checklist API, an authentication token is required. Each user should obtain his or her own personal token to run the code below (see https://api.speciesplus.net/documentation for more details). To obtain a token, sign up on the Species+ API website.

Set the token

Now, we assume that you already have a token. For illustrative purposes, we will use the generic token value 8QW6Qgh57sBG2k0gtt from the API documentation.

A token is mandatory and needs to be passed to the header of all URL requests. They are three different ways to set the token in rcites:

1. set an environment variable SPECIESPLUS_TOKEN in your .Renviron file (preferred for frequent users);

2. use set_token() to set up the token as a character string (with quotes). If not entered in the function, the token can be passed without quotes (not as a character string) after the prompt. This way, the token SPECIESPLUS_TOKEN is interactively set up only for the current R session, meaning a login will be required for the future R sessions (preferred);

library(rcites)
set_token("8QW6Qgh57sBG2k0gtt")
1. use the token argument inside the functions, i.e. the token is passed manually to each function call.

Note that if you set a wrong token and you wish to set it again interactively, you must first forget the previous token with forget_token().

Use of key features

Retrieve a taxon identifiers with spp_taxonconcept()

Basic calls to spp_taxonconcept()

In order to efficiently query information from the CITES database, you first need to retrieve the unique taxon identifier taxon_id from the Species+ taxon concept. To do so, you should first call spp_taxonconcept() and provide the scientific name of the taxon you are looking for. Let us start by requesting the identifier of the African bush elephant, i.e. Loxodonta africana.

res1 <- spp_taxonconcept(query_taxon = "Loxodonta africana")

Note that if you have decide to set your token using the third option, then the code should look like the one below:

res1 <- spp_taxonconcept(query_taxon = "Loxodonta africana", token = "8QW6Qgh57sBG2k0gtt")

Object spp_taxonconcept

res1 is an S3 object of class spp_taxon:

attributes(res1)

that contains information sorted into several data frames (see ?spp_taxonconcept for further details):

res1

For some taxa, there are more than one taxon identifier available. In general only active identifiers are listed, but the full list of identifiers are available in all_id:

res3 <- spp_taxonconcept(query = "Amazilia versicolor")
res3$general res3$all_id

Also, if the taxon is not listed, a warning message should come up.

res4 <- spp_taxonconcept(query = "Homo Sapiens")

Custom calls to spp_taxonconcept()

spp_taxonconcept() includes several arguments to retrieve a specific subset of information (see ?spp_taxonconcept for more details):

args('spp_taxonconcept')

Most importantly, the argument taxonomy allows a selection between the two databases (CITES or CMS):

spp_taxonconcept(query = "Amazilia versicolor", taxonomy = "CMS")
spp_taxonconcept(query = "Loxodonta africana", taxonomy = "CMS")

language and updated_since are convenient filters for the written language of common names (must be a two-letters code, see ISO 3166-1 alpha-2) and the last update of the entries, respectively:

spp_taxonconcept(query_taxon = "Loxodonta africana", language = 'EN',
updated_since = "2016-01-01")

Retrieve a taxon identifiers available data

In order to use the four spp_* functions, one needs to use the active taxon identifier of a given species. For instance, for the two species we used as examples above we use the value indicated in the table below:

name taxon identifier
Loxodonta africana 4521
Amazilia versicolor 3210

CITES legislation data

First, we can retrieve current CITES appendix listings and reservations, CITES quotas, and CITES suspensions for a given taxon concept.

spp_cites_legislation(taxon_id = "4521", verbose = FALSE)

EU legislation data

Similarly, we can also retrieve current EU annex listings, SRG opinions, and EU suspensions with spp_eu_legislation. Both legislation functions have a scope argument that sets the time scope of legislation and take one value among current, historic and all (default is set to current). For instance, one can get all information pertaining to EU annex listing for Amazilia versicolor with the following command line:

spp_eu_legislation(taxon_id = "3210", scope = "all", verbose = FALSE)

Distribution data

Distribution data at the country level is also available for a given taxon concept:

spp_distributions("4521", verbose = FALSE)

References

Finally, we can retrieve all available references for a given taxa.

spp_references("4521", verbose = FALSE)