Skip to contents

Search AlgaeBase for information about a species of algae

Source: R/algaebase_api_functions.R
get_algaebase_species.Rd

[Deprecated]

This function has been deprecated. Users are encouraged to use match_algaebase_species instead.

This function searches the AlgaeBase API for species based on genus and species names. It allows for flexible search parameters such as filtering by exact matches, returning the most recent results, and including higher taxonomy details.

Usage

get_algaebase_species(
  genus,
  species,
  subscription_key = Sys.getenv("ALGAEBASE_KEY"),
  higher = TRUE,
  unparsed = FALSE,
  newest_only = TRUE,
  exact_matches_only = TRUE,
  apikey = deprecated()
)

Arguments

genus

A character string specifying the genus name.

species

A character string specifying the species or specific epithet.

subscription_key

A character string containing the API key for accessing the AlgaeBase API. By default, the key is read from the environment variable ALGAEBASE_KEY.

You can provide the key in three ways:

  • Directly as a parameter: get_algaebase_species("Skeletonema", "marinoi", subscription_key = "your_key_here")

  • Temporarily for the session: Sys.setenv(ALGAEBASE_KEY = "your_key_here")

  • Permanently across sessions by adding it to your ~/.Renviron file. Use usethis::edit_r_environ() to open the file, then add: ALGAEBASE_KEY=your_key_here

higher

A logical value indicating whether to include higher taxonomy details (default is TRUE).

unparsed

A logical value indicating whether to print the full JSON response from the API (default is FALSE).

newest_only

A logical value indicating whether to return only the most recent entries (default is TRUE).

exact_matches_only

A logical value indicating whether to return only exact matches (default is TRUE).

apikey

[Deprecated] Use subscription_key instead.

Value

A data frame with details about the species, including:

  • taxonomic_status — The current status of the taxon (e.g., accepted, synonym, unverified).

  • taxon_rank — The rank of the taxon (e.g., species, genus).

  • accepted_name — The currently accepted scientific name, if applicable.

  • authorship — Author information for the scientific name (if available).

  • mod_date — Date when the taxonomic record was last modified.

  • ... — Other relevant information returned by the data source.

Details

A valid API key is requested from the AlgaeBase team.

This function queries the AlgaeBase API for species based on the genus and species names, and filters the results based on various parameters. The function handles different taxonomic ranks and formats the output for easy use. It can merge higher taxonomy data if requested.

See also

https://www.algaebase.org/ for AlgaeBase website.

Examples

if (FALSE) { # \dontrun{
# Search for a species with exact matches only, return the most recent results
result <- get_algaebase_species(
  genus = "Skeletonema", species = "marinoi", subscription_key = "your_api_key"
)

# Print result
print(result)
} # }