Search and retrieve toxicity records from the on-line database

Functions to search and retrieve records from the on-line 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 on-line 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())

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().

Details

The functions described here to search and retrieve records from the on-line database are experimental. This is because this feature is not formally supported by the EPA, and it may break in future iterations of the on-line 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.

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

Pepijn de Vries

Examples

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