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Match Species to IUCN RedList Categories

Source: R/splnr_get_IUCNRedList.R
splnr_get_IUCNRedList.Rd

The splnr_get_IUCNRedList function retrieves IUCN Red List category information for a given set of species and appends it to your input dataframe.

Usage

splnr_get_IUCNRedList(df, species_col = "Species")

Arguments

df

The input dataframe containing the species names to be matched.

species_col

A character string specifying the name of the column in df that contains the species scientific names (e.g., "Species" or "scientific_name"). Defaults to "Species".

Value

A dataframe identical to the input df, but with an additional column named IUCN_Category. If a species is not found on the IUCN Red List, its IUCN_Category will be NA.

Details

To use this function, you must first obtain an API key from IUCN. This is an alphanumeric string required for every request. You can visit the IUCN website to request a key using rl_use_iucn(). Please note that receiving your key might take 1-2 days after submitting the form.

Once you receive your API key, it is crucial to set it as an environment variable named IUCN_REDLIST_KEY. You can do this temporarily for the current R session using Sys.setenv(IUCN_REDLIST_KEY = "YOUR_API_KEY_HERE"). To set it permanently, you should add IUCN_REDLIST_KEY = "YOUR_API_KEY_HERE" to your .Renviron file. You can check if the key is set correctly using Sys.getenv("IUCN_REDLIST_KEY").

The IUCN Red List uses various categories to assess extinction risk. This function queries the Red List for the following categories:

  • DD: Data Deficient

  • LC: Least Concern

  • NT: Near Threatened

  • VU: Vulnerable

  • EN: Endangered

  • CR: Critically Endangered

  • EW: Extinct in the Wild

  • EX: Extinct

  • LRlc: Lower Risk / least concern (old category)

  • LRnt: Lower Risk / near threatened (old category)

  • LRcd: Lower Risk / conservation dependent (old category)

The function will attempt to match your species against any of these categories present in the IUCN Red List database.

Examples

if (FALSE) { # \dontrun{
# Ensure your IUCN_REDLIST_KEY is set as an environment variable before running.
# For example: Sys.setenv(IUCN_REDLIST_KEY = "YOUR_API_KEY_HERE")

# Example: Create a dataframe with species names and retrieve their IUCN Red List categories.
df_species_redlist <- data.frame(Species = c("Diomedea exulans",
                                              "Hippocampus kuda",
                                              "Squatina squatina")) %>%
  splnr_get_IUCNRedList()
print(df_species_redlist)

# Example with a different column name for species
df_alt_col <- data.frame(ScientificName = c("Panthera leo", "Orcinus orca")) %>%
  splnr_get_IUCNRedList(species_col = "ScientificName")
print(df_alt_col)
} # }