Type:	Package
Title:	R Interface to the Species+ Database
Version:	1.3.0
Description:	A programmatic interface to the Species+ https://speciesplus.net/ database via the Species+/CITES Checklist API https://api.speciesplus.net/.
URL:	https://docs.ropensci.org/rcites/, https://github.com/ropensci/rcites
BugReports:	https://github.com/ropensci/rcites/issues
License:	MIT + file LICENSE
Depends:	R (≥ 3.1.0)
Imports:	cli, curl, httr, jsonlite
Suggests:	knitr, testthat, tibble, rmarkdown, rworldmap (≥ 1.3.6), vcr (≥ 1.2.0)
Encoding:	UTF-8
RoxygenNote:	7.2.3
VignetteBuilder:	knitr
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2023-02-12 20:25:38 UTC; kc
Author:	Kevin Cazelles [aut, cre], Jonas Geschke [aut], Ignasi Bartomeus [aut], Jonathan Goldenberg [ctb], Marie-Bé Leduc [ctb], Yasmine Verzelen [ctb], Noam Ross [rev], Margaret Siple [rev]
Maintainer:	Kevin Cazelles <kevin.cazelles@gmail.com>
Repository:	CRAN
Date/Publication:	2023-02-12 21:50:02 UTC

rcites

Description

A programmatic interface to the Species+ https://speciesplus.net/ database via the Species+/CITES Checklist API https://api.speciesplus.net/.

Author(s)

Maintainer: Kevin Cazelles kevin.cazelles@gmail.com (ORCID)

Authors:

• Jonas Geschke jonas.e.geschke@gmail.com (ORCID)

• Ignasi Bartomeus (ORCID)

Other contributors:

• Jonathan Goldenberg [contributor]

• Marie-Bé Leduc [contributor]

• Yasmine Verzelen [contributor]

• Noam Ross [reviewer]

• Margaret Siple [reviewer]

See Also

Useful links:

• https://docs.ropensci.org/rcites/

• https://github.com/ropensci/rcites

• Report bugs at https://github.com/ropensci/rcites/issues

Print methods for objects of class ⁠spp_raw*⁠.

Description

Print the outputs of a Species+ API call.

Usage

## S3 method for class 'spp_raw'
print(x, ...)

## S3 method for class 'spp_raw_multi'
print(x, ...)

## S3 method for class 'spp_cites_leg'
print(x, ...)

## S3 method for class 'spp_cites_leg_multi'
print(x, ...)

## S3 method for class 'spp_distr'
print(x, ...)

## S3 method for class 'spp_distr_multi'
print(x, ...)

## S3 method for class 'spp_eu_leg'
print(x, ...)

## S3 method for class 'spp_eu_leg_multi'
print(x, ...)

## S3 method for class 'spp_refs'
print(x, ...)

## S3 method for class 'spp_refs_multi'
print(x, ...)

## S3 method for class 'spp_taxon'
print(x, ...)

Arguments

Value

The JSON result.

Login helper function

Description

Set and forget the authentification token for the current session.

Usage

set_token(token = NULL)

forget_token()

Arguments

Functions

• set_token(): set the environment variable SPECIESPLUS_TOKEN.

• forget_token(): forget the environment variable SPECIESPLUS_TOKEN.

References

https://api.speciesplus.net/documentation

Examples

## Not run: 
# NB: the token below is not working and should not be used
set_token("8QW6Qgh57sBG2k0gtt")

## End(Not run)

Get current CITES appendix listings and reservations

Description

Retrieve current CITES appendix listings and reservations, CITES quotas, and CITES suspensions for a given taxon concept.

Usage

spp_cites_legislation(
  taxon_id,
  scope = "current",
  language = "en",
  raw = FALSE,
  token = NULL,
  verbose = TRUE,
  pause = 1,
  ...
)

Arguments

Value

If raw is set to TRUE then an object of class spp_raw (or spp_raw_multi if length(taxon_id) > 1) is returned which is essentially a list of lists (see option as = 'parsed' in httr::content()). Otherwise, an object of class spp_cites_leg (or spp_cites_leg_multi if length(taxon_id)>1) is returned which is a list of three data frames:

1. cites_listings: lists CITES annex listings EU suspensions,

2. cites_quotas: lists CITES quotas,

3. cites_suspensions: lists CITES suspensions.

References

https://api.speciesplus.net/documentation/v1/cites_legislation/index.html

Examples

## Not run: 
# this calls will only work if a token is set and valid
res1 <- spp_cites_legislation(taxon_id = 4521)
res2 <- spp_cites_legislation(taxon_id = c('4521', '3210', '10255'))
res3 <- spp_cites_legislation(taxon_id = 4521, scope = 'all',
verbose = FALSE, config=httr::verbose())
res4 <- spp_cites_legislation(taxon_id = 4521, language = 'fr')

## End(Not run)

Get distributions data available for a given taxon concept

Description

Retrieve distributions data available for a given taxon concept for which the the taxon identifier is known.

Usage

spp_distributions(
  taxon_id,
  language = "en",
  raw = FALSE,
  token = NULL,
  verbose = TRUE,
  pause = 1,
  ...
)

Arguments

Value

If raw is set to TRUE then an object of class spp_raw (or spp_raw_multi if length(taxon_id)>1) is returned which is essentially a list of lists (see option as = 'parsed' in httr::content()). Otherwise, an object of class spp_distr (or spp_distr_multi if length(taxon_id) > 1) is returned which is a list of two data frames:

1. distributions: lists distributions for a given taxon concept,

2. references: lists the corresponding references. In case taxon_id includes several elements

References

https://api.speciesplus.net/documentation/v1/distributions/index.html

Examples

## Not run: 
 # this calls will only work if a token is set and valid
 res1 <- spp_distributions(taxon_id = '4521')
 res2 <- spp_distributions(taxon_id = c('4521', '3210', '10255'))
 res3 <- spp_distributions(taxon_id = '4521', raw = TRUE)
 res4 <- spp_distributions(taxon_id = '4521', language = 'fr',
 verbose = FALSE, config = httr::progress())

## End(Not run)

Get current EU annex listings, SRG opinions, and EU suspensions

Description

Retrieve current EU annex listings, SRG opinions, and EU suspensions for a given taxon concept (identifier must be known).

Usage

spp_eu_legislation(
  taxon_id,
  scope = "current",
  language = "en",
  raw = FALSE,
  token = NULL,
  verbose = TRUE,
  pause = 1,
  ...
)

Arguments

Value

If raw is set to TRUE then an object of class spp_raw (or spp_raw_multi if length(taxon_id)>1) is returned which is essentially a list of lists (see option as = 'parsed' in httr::content()). Otherwise, an object of class spp_eu_leg (or spp_eu_leg_multi if length(taxon_id)>1) is returned which is a list of two data frames:

1. eu_listings: lists EU annex listings EU suspensions,

2. eu_decisions: lists EU decisions

References

https://api.speciesplus.net/documentation/v1/eu_legislation/index.html

Examples

## Not run: 
# this calls will only work if a token is set and valid
res1 <- spp_eu_legislation(taxon_id = '4521')
res2 <- spp_eu_legislation(taxon_id = c('4521', '3210', '10255'))
res3 <- spp_eu_legislation(taxon_id = '4521', scope = 'historic')
res4 <- spp_eu_legislation(taxon_id = '4521', scope = 'all', language='fr',
 verbose = FALSE, config=httr::verbose())

## End(Not run)

Get references for a given taxon concept

Description

Retrieve available references for a given taxon concept.

Usage

spp_references(
  taxon_id,
  raw = FALSE,
  token = NULL,
  verbose = TRUE,
  pause = 1,
  ...
)

Arguments

Value

If raw is set to TRUE then an object of class spp_raw (or spp_raw_multi if length(taxon_id) > 1) is returned which is essentially a list of lists (see option as = 'parsed' in httr::content()). Otherwise, an object of class spp_refs (or spp_refs_multi if length(taxon_id) > 1) is returned which is a list of one data frame:

• references that includes the identifier of the reference and the corresponding citation.

References

https://api.speciesplus.net/documentation/v1/references/index.html

Examples

## Not run: 
# this calls will only work if a token is set and valid
res1 <- spp_references(taxon_id = '4521')
res2 <- spp_references(c('4521', '3210', '10255'))
res3 <- spp_references(taxon_id = '4521', raw = TRUE, verbose = FALSE,
 config = httr::progress())

## End(Not run)

Get taxon concepts for a search term

Description

Retrieve the taxon concept of a specific taxon (scientific name).

Usage

spp_taxonconcept(
  query_taxon,
  taxonomy = "CITES",
  with_descendants = FALSE,
  language = NULL,
  updated_since = NULL,
  per_page = 500,
  pages = NULL,
  raw = FALSE,
  token = NULL,
  verbose = TRUE,
  pause = 1,
  ...
)

Arguments

Value

If raw = TRUE, then a object of class spp_raw is returned, which is a list of lists. If raw = FALSE, then an object of class spp_taxon is returned, it is a collection of seven data frames:

1. all_id: general information for all entries, including non-active taxon concepts,

2. general: includes general information for active taxon concepts,

3. higher_taxa: includes taxonomy information,

4. accepted_names: list of accepted names (only for synonyms),

5. common_names: list of common names (only for accepted names),

6. synonyms: list of synonyms (only for accepted names),

7. cites_listing: list of current CITES listings with annotations (missing if taxonomy == 'CMS').

References

https://api.speciesplus.net/documentation/v1/taxon_concepts/index.html

Examples

## Not run: 
# this calls will only work if a token is set and valid
res1 <- spp_taxonconcept(query_taxon = 'Loxodonta africana')
res2 <- spp_taxonconcept(query_taxon = 'Amazilia versicolor', raw = TRUE)
res3 <- spp_taxonconcept(query_taxon = '', taxonomy = 'CMS', pages = c(1, 3),
 language = 'EN', config = httr::progress())
res4 <- spp_taxonconcept(query_taxon = '', per_page = 20, pages = 44)

## End(Not run)