websearch: Search and retrieve toxicity records from the online database

In ECOTOXr: Download and Extract Data from US EPA's ECOTOX Database

Search and retrieve toxicity records from the online database

Description

Functions to search and retrieve records from the online database at https://cfpub.epa.gov/ecotox/search.cfm.

Usage

websearch_ecotox(
  fields = list_ecotox_web_fields(),
  habitat = c("aquire", "terrestrial"),
  verify_ssl = getOption("ECOTOXr_verify_ssl"),
  ...
)

list_ecotox_web_fields(...)

Arguments

fields	A named list of characters, used to build a search for for the online search query of https://cfpub.epa.gov/ecotox/search.cfm. Use list_ecotox_web_fields() to construct a valid list.
habitat	Use aquire (default) to retrieve aquatic data, terrestrial for, you've guessed it, terrestrial data.
verify_ssl	When set to FALSE the SSL certificate of the host (EPA) is not verified. Can also be set as option: options(ECOTOXr_verify_ssl = TRUE). Default is TRUE.
...	In case of list_ecotox_web_fields() the dots can be used as search field values used to update the returned list of fields. In case of websearch_ecotox() the dots can be used to pass custom options to the underlying httr2::req_options() call. For available field names, use names(list_ecotox_web_fields())

Details

The functions described here to search and retrieve records from the online database are experimental. This is because this feature is not formally supported by the EPA, and it may break in future iterations of the online database. The functions form an interface between R and the ECOTOX website and is therefore limited by its restrictions as described in the package documentation: ECOTOXr. The functions should therefore be used with caution.

Value

Returns named list of dplyr::tibbles with search results. Results are unpolished and ‘as is’ returned by EPA's web service.

list_ecotox_web_fields() returns a named list with fields that can be used in a web search of EPA's ECOTOX database, using websearch_ecotox().

Note

IMPORTANT: when you plan to perform multiple adjacent searches (for instance in a loop), please insert a call to Sys.sleep(). This to avoid overloading the server and getting your IP address banned from the server.

Author(s)

Pepijn de Vries

See Also

Other online-functions: download_ecotox_data(), get_ecotox_url()

Other search-functions: search_ecotox()

Examples

if (interactive()) {
  search_fields <-
    list_ecotox_web_fields(
      txAdvancedSpecEntries     = "daphnia magna",
      RBSPECSEARCHTYPE          = "EXACT",
      txAdvancedChemicalEntries = "benzene",
      RBCHEMSEARCHTYPE          = "EXACT")
  search_results <- websearch_ecotox(search_fields)
}

ECOTOXr documentation built on April 12, 2025, 1:27 a.m.