Welcome to the iucnr package, a comprehensive tool designed for researchers and conservationists to access and analyze data from the IUCN Red List of Threatened Species. This package allows users to retrieve and integrate taxonomic and vernacular name data, empowering them to conduct thorough assessments of species status and threats. With a strong emphasis on enhancing biodiversity research, iucnr offers a user-friendly interface for navigating the extensive datasets available through the Global Biodiversity Information Facility (GBIF).
The iucnr package enables access to Red List data on threatened species without the need for an internet connection, making it a valuable resource for evaluating the conservation status of various species. The information is sourced from the GBIF repository (https://www.gbif.org/dataset/19491596-35ae-4a91-9a98-85cf505f1bd3).
While there are other packages available for similar purposes, they typically require an API key to access the IUCN API, which can be a barrier for some users.
Spanish Version
Bienvenido al paquete iucnr, una herramienta integral diseñada para investigadores y conservacionistas que desean acceder y analizar datos de la Lista Roja de Especies Amenazadas de la IUCN. Este paquete permite a los usuarios recuperar e integrar datos taxonómicos y nombres vernáculos, empoderándolos para realizar evaluaciones exhaustivas sobre el estado y las amenazas a las especies. iucnr ofrece una interfaz amigable para navegar a través de los extensos conjuntos de datos disponibles a través de la Global Biodiversity Information Facility (GBIF) de la Lista Roja de Especies Amenazadas sin necesidad de estar conectado a internet, lo que lo convierte en un recurso valioso para evaluar el estado de conservación de diversas especies. La información se obtiene del repositorio de GBIF (https://www.gbif.org/dataset/19491596-35ae-4a91-9a98-85cf505f1bd3).
Si bien existen otros paquetes disponibles para objetivos similares, estos generalmente requieren una clave de API para acceder al API de la IUCN, lo que puede ser un obstáculo para algunos usuarios.
Installation
install.packages("iucnr")
# or
pak::pak("iucnr")Also you can install the iucnr package from GitHub using the following command:
pak::pak("PaulESantos/iucnr")Example
- Define a vector of species names
species_names <- c("Panthera uncia", "Lynx lynx", "Ara militaris", "Zonotrichia capencis")- Example usage of the get_conservation_status function This retrieves the conservation status for the specified species
library(iucnr)
#> This is iucnr 0.0.0.1
#> The iucnr package is compatible with IUCN Red List version 2024-1,
#> providing tools to access and analyze the latest conservation status data.
conservation_status <- get_conservation_status(species_names = species_names)
conservation_status
#> [1] "Vulnerable" "Least Concern" "Vulnerable" "no match found"- Example usage of the get_conservation_status function within a tibble This creates a tibble and adds a new column with the conservation status of each species
species_data <- tibble::tibble(species = species_names) |>
dplyr::mutate(iucn = get_conservation_status(species))
species_data
#> # A tibble: 4 × 2
#> species iucn
#> <chr> <chr>
#> 1 Panthera uncia Vulnerable
#> 2 Lynx lynx Least Concern
#> 3 Ara militaris Vulnerable
#> 4 Zonotrichia capencis no match found- Example usage of the get_iucn_data function This retrieves detailed IUCN data for the specified species names
iucn_data_result <- get_iucn_data(species_names)
iucn_data_result
#> submitted_name core_id scientific_name kingdom
#> 1 Ara militaris 22685548 Ara militaris (Linnaeus, 1766) ANIMALIA
#> 2 Lynx lynx 12519 Lynx lynx (Linnaeus, 1758) ANIMALIA
#> 3 Panthera uncia 22732 Panthera uncia (Schreber, 1775) ANIMALIA
#> 4 Zonotrichia capencis <NA> <NA> <NA>
#> phylum class order family genus specific_epithet
#> 1 CHORDATA AVES PSITTACIFORMES PSITTACIDAE Ara militaris
#> 2 CHORDATA MAMMALIA CARNIVORA FELIDAE Lynx lynx
#> 3 CHORDATA MAMMALIA CARNIVORA FELIDAE Panthera uncia
#> 4 <NA> <NA> <NA> <NA> <NA> <NA>
#> scientific_name_authorship taxon_rank infraspecific_epithet taxonomic_status
#> 1 (Linnaeus, 1766) species <NA> accepted
#> 2 (Linnaeus, 1758) species <NA> accepted
#> 3 (Schreber, 1775) species <NA> accepted
#> 4 <NA> <NA> <NA> <NA>
#> accepted_name_usage_id
#> 1 22685548
#> 2 12519
#> 3 22732
#> 4 NA
#> bibliographic_citation
#> 1 BirdLife International 2020. Ara militaris (Linnaeus, 1766). The IUCN Red List of Threatened Species 2020: https://doi.org/10.2305/IUCN.UK.2020-3.RLTS.T22685548A179407584.en
#> 2 Breitenmoser, U., Breitenmoser-Würsten, C., Lanz, T., von Arx, M., Antonevich, A., Bao, W. & Avgan, B. 2015. Lynx lynx (Linnaeus, 1758). The IUCN Red List of Threatened Species 2015:
#> 3 McCarthy, T., Mallon, D., Jackson, R., Zahler, P. & McCarthy, K. 2017. Panthera uncia (Schreber, 1775). The IUCN Red List of Threatened Species 2017: https://doi.org/10.2305/IUCN.UK.2017-2.RLTS.T22732A50664030.en
#> 4 <NA>
#> references
#> 1 https://apiv3.iucnredlist.org/api/v3/taxonredirect/22685548
#> 2 https://apiv3.iucnredlist.org/api/v3/taxonredirect/12519
#> 3 https://apiv3.iucnredlist.org/api/v3/taxonredirect/22732
#> 4 <NA>
#> source
#> 1 BirdLife International 2020. Ara militaris (Linnaeus, 1766). The IUCN Red List of Threatened Species 2020: https://doi.org/10.2305/IUCN.UK.2020-3.RLTS.T22685548A179407584.en
#> 2 Breitenmoser, U., Breitenmoser-Würsten, C., Lanz, T., von Arx, M., Antonevich, A., Bao, W. & Avgan, B. 2015. Lynx lynx (Linnaeus, 1758). The IUCN Red List of Threatened Species 2015:
#> 3 McCarthy, T., Mallon, D., Jackson, R., Zahler, P. & McCarthy, K. 2017. Panthera uncia (Schreber, 1775). The IUCN Red List of Threatened Species 2017: https://doi.org/10.2305/IUCN.UK.2017-2.RLTS.T22732A50664030.en
#> 4 <NA>
#> threat_status occurrence_status infrasp_tag
#> 1 Vulnerable Present <NA>
#> 2 Least concern Present <NA>
#> 3 Vulnerable Present <NA>
#> 4 <NA> <NA> <NA>- Example usage of the get_vernacular_name function This retrieves the vernacular names for the specified species
vernacular_names_result <- get_vernacular_name(species = species_names)
vernacular_names_result
#> submitted_name
#> 1 Lynx lynx
#> 2 Ara militaris
#> 3 Panthera uncia
#> 4 Zonotrichia capencis
#> vernacular_name
#> 1 Lynx, Evroasiin Shiluus, Eurasian Lynx, Lince, Shiluus Mii, Lince Boreal, Lynx Boréal
#> 2 Guacamaya Verde, Guacamayo Militar, Military Macaw, Guacamayo Verde
#> 3 Léopard des neiges, Irvis, Ilbirs, Snow Leopard, Hiun chituwa, Pantera de la Nieves, Akilbirs, Sah, Babri barfi, Baral he, Snezhniy bars, Xue bào, Barfani chita, Schneeleopard, Ounce, Irbis, Irbis, Once, Panthère des neiges
#> 4 <NA>Citation
IUCN (2022). The IUCN Red List of Threatened Species. Version 2022-2. https://www.iucnredlist.org. Downloaded on 2023-05-09. https://doi.org/10.15468/0qnb58 accessed via GBIF.org on 2023-11-17. accessed via GBIF.org on 2024-10-08.
IUCN. 2024. The IUCN Red List of Threatened Species. Version 2024-1. https://www.iucnredlist.org.