Introduction to rredlist

rredlist is an R client for the IUCN Red List API (https://api.iucnredlist.org/). The IUCN Red List is the world’s most comprehensive information source on the global extinction risk status of animal, fungus and plant species. This package provides access via R to the various data contained within this database which span range details, population size, habitat and ecology, use and/or trade, threats, and conservation actions.

Documentation for the IUCN Red List API are available at https://api.iucnredlist.org/api-docs. Note that use of the web API, and therefore this package, requires authentication.

What `rredlist` is not:

redlistr is a different package for contributors to the IUCN Red List - not working with the IUCN Red List API.
rredlist does not include support for the spatial API, described at https://apiv3.iucnredlist.org/spatial.

Installation

CRAN

install.packages("rredlist")

Development version

# From GitHub
remotes::install_github("ropensci/rredlist")

# From r-universe
install.packages("rredlist", repos = "https://ropensci.r-universe.dev/")

API Versioning

rredlist versions ≤ 0.7.1 tracked version 3 of the IUCN Red List API. rredlist versions ≥ 1.0.0 track version 4 of the IUCN Red List API. If you need to use version 3 of the API–and it is still functioning–you can install an old version of rredlist using the remotes package:

# From CRAN archive
remotes::install_version("rredlist", version = "0.7.1")

# From r-universe
remotes::install_version("rredlist", version = "0.7.1",
                         repos = "https://ropensci.r-universe.dev/")

Authentication

IUCN requires you to get your own API key, an alphanumeric string that you need to send in every request. There’s a helper function in the package helping you getting it at https://api.iucnredlist.org/users/sign_up and storing it. Once you store this key, the functions in rredlist will always default to using this key.

rredlist::rl_use_iucn()

Keep this key private. You can pass the key in to each function via the key parameter, but it’s better to store the key either as a environment variable (IUCN_REDLIST_KEY) or an R option (iucn_redlist_key) - we recommend using the former option.

Note that you can no longer generate a new API key for version 3 of the API.

Overview of available functions

Query assessments by taxa (e.g., rl_species() and rl_family())
Query assessments by habitats (e.g., rl_habitats() and rl_systems())
Query assessments by geography (e.g., rl_countries() and rl_realms())
Query assessments by actions needed (e.g., rl_actions() and rl_research())
Query assessments by threat details (e.g., rl_threats() and rl_pop_trends())
Query assessments for specific sets of taxa (e.g., rl_extinct() and rl_growth_forms())
Get all details for a single assessment (e.g., rl_species_latest() and rl_assessment())
Red List information and statistics (e.g., rl_sp_count() and rl_version())

High level interface

library("rredlist")

High level functions do the HTTP request and parse data to a list for ease of downstream use. The high level functions have no underscore on the end of the function name, e.g., rl_species(). Most of them return long lists containing lots of different information:

rl_species("Fratercula", "arctica")
#> $taxon
#> $taxon$sis_id
#> [1] 22694927
#> 
#> $taxon$scientific_name
#> [1] "Fratercula arctica"
#> 
#> $taxon$species_taxa
#> list()
#> 
...

By default, these high level functions will also parse the data to a data.frame, when possible:

rl_species("Fratercula", "arctica")$assessments
#>    year_published latest sis_taxon_id                                                    url assessment_id
#> 1            2021   TRUE     22694927 https://www.iucnredlist.org/species/22694927/166290968     166290968
#> 2            2018   TRUE     22694927 https://www.iucnredlist.org/species/22694927/132581443     132581443
#> 3            2017  FALSE     22694927 https://www.iucnredlist.org/species/22694927/117606911     117606911
#> 4            2016  FALSE     22694927  https://www.iucnredlist.org/species/22694927/93477427      93477427
#> 5            2017  FALSE     22694927 https://www.iucnredlist.org/species/22694927/110638141     110638141
#> 6            2015  FALSE     22694927  https://www.iucnredlist.org/species/22694927/82593109      82593109
#> 7            2015  FALSE     22694927  https://www.iucnredlist.org/species/22694927/60110592      60110592
#> 8            2012  FALSE     22694927  https://www.iucnredlist.org/species/22694927/38908739      38908739
#> 9            2009  FALSE     22694927  https://www.iucnredlist.org/species/22694927/28178290      28178290
...

Likely a bit faster is to parse to a list only, and not take the extra data.frame parsing time:

rl_species("Fratercula", "arctica", parse = FALSE)$assessments
#> [[1]]
#> [[1]]$year_published
#> [1] "2021"
#> 
#> [[1]]$latest
#> [1] TRUE
#> 
#> [[1]]$sis_taxon_id
#> [1] 22694927
#> 
...

For even more speed, use the low level package interface.

Low level interface

The parsing to data.frame in the high level functions does take extra time. The low level functions only do the HTTP request, and give back JSON without doing any more parsing. The low level functions DO have an underscore on the end of the function name, e.g., rl_species_():

rl_species_("Fratercula", "arctica")
#> [1] "{\"taxon\":{\"sis_id\":22694927,\"scientific_name\":\"Fratercula arctica\",\"species_taxa\":[],\"subpopulation_taxa\":[],\"infrarank_taxa\":[],\"kingdom_name\":\"ANIMALIA\",\"phylum_name\":\"CHORDATA\",\"class_name\":\"AVES\",\"order_name\":\"CHARADRIIFORMES\",\"family_name\":\"ALCIDAE\",\"genus_name\":\"Fratercula\",\"species_name\":\"arctica\",\"subpopulation_name\":null,\"infra_name\":null,\"authority\":\"(Linnaeus, 1758)\",\"species\":true,\"subpopulation\":false,\"infrarank\":false,\"ssc_groups\":[{\"name\":\"IUCN SSC Bird Red List Authority (BirdLife International)\",\"url\":\"https://www.birdlife.org/\",\"description\":\"Red List Authority Coordinator: Ian Burfield (ian.burfield@birdlife.org)\"}],\"common_names\":[{\"main\":false,\"name\":\"Puffin\",\"language\":{\"code\":\"eng\",\"description\":{\"en\":\"English\"}}},{\"main\":true,\"name\":\"Atlantic Puffin\",\"language\":{\"code\":\"eng\",\"description\":{\"en\":\"English\"}}}],\"synonyms\":[]},\"assessments\":[{\"year_published\":\"2021\",\"latest\":true,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/166290968\",\"assessment_id\":166290968,\"scopes\":[{\"description\":{\"en\":\"Europe\"},\"code\":\"2\"}]},{\"year_published\":\"2018\",\"latest\":true,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/132581443\",\"assessment_id\":132581443,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"2017\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/117606911\",\"assessment_id\":117606911,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"2016\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/93477427\",\"assessment_id\":93477427,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"2017\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/110638141\",\"assessment_id\":110638141,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"2015\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/82593109\",\"assessment_id\":82593109,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"2015\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/60110592\",\"assessment_id\":60110592,\"scopes\":[{\"description\":{\"en\":\"Europe\"},\"code\":\"2\"}]},{\"year_published\":\"2012\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/38908739\",\"assessment_id\":38908739,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"2009\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/28178290\",\"assessment_id\":28178290,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"2008\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/28179292\",\"assessment_id\":28179292,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"2004\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/28180639\",\"assessment_id\":28180639,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"2000\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/28181882\",\"assessment_id\":28181882,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"1994\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/28183212\",\"assessment_id\":28183212,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]},{\"year_published\":\"1988\",\"latest\":false,\"sis_taxon_id\":22694927,\"url\":\"https://www.iucnredlist.org/species/22694927/28184380\",\"assessment_id\":28184380,\"scopes\":[{\"description\":{\"en\":\"Global\"},\"code\":\"1\"}]}],\"params\":{\"genus_name\":\"Fratercula\",\"species_name\":\"arctica\"}}"

To consume this JSON, you can use jsonlite:

library("jsonlite")
fromJSON(rl_species_("Fratercula", "arctica"))
#> $taxon
#> $taxon$sis_id
#> [1] 22694927
#> 
#> $taxon$scientific_name
#> [1] "Fratercula arctica"
#> 
#> $taxon$species_taxa
#> list()
#> 
...

Usage best practice

Citing the IUCN Red List API

Use the function rl_citation():

rl_citation()
#> [1] "IUCN 2024. IUCN Red List of Threatened Species. Version 2024-1 <www.iucnredlist.org>"

We’d also really appreciate it if you could cite your use of this package:

citation("rredlist")
#> To cite package 'rredlist' in publications use:
#> 
#>   Gearty W, Chamberlain S (2024). _rredlist: 'IUCN' Red List Client_.
#>   doi:10.32614/CRAN.package.rredlist <https://doi.org/10.32614/CRAN.package.rredlist>, R package
#>   version 0.7.1.9000, <https://docs.ropensci.org/rredlist/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{rredlist,
#>     title = {rredlist: 'IUCN' Red List Client},
#>     author = {William Gearty and Scott Chamberlain},
#>     year = {2024},
#>     note = {R package version 0.7.1.9000},
#>     doi = {10.32614/CRAN.package.rredlist},
#>     url = {https://docs.ropensci.org/rredlist/},
#>   }

Rate Limiting

From the IUCN folks: “Too many frequent calls, or too many calls per day might get your access blocked temporarily. If you’re a heavy API user, the Red List Unit asked that you contact them, as there might be better options. They suggest a 2-second delay between your calls if you plan to make a lot of calls.”

William Gearty

2024-10-23

What `rredlist` is not:

Installation

API Versioning

Authentication

Overview of available functions

High level interface

Low level interface

Usage best practice

Citing the IUCN Red List API

Rate Limiting

About

Community

Resources

Introduction to rredlist

William Gearty

2024-10-23

What rredlist is not:

Installation

API Versioning

Authentication

Overview of available functions

High level interface

Low level interface

Usage best practice

Citing the IUCN Red List API

Rate Limiting

What `rredlist` is not: