Search Entrez databases

The search term field names are documented in the EInfo API endpoint: see einfo().

Usage

esearch(
  term,
  db,
  ...,
  retstart = 0L,
  retmax = NA,
  retmode = "xml",
  rettype = "uilist",
  usehistory = is.null(retmax) || is.na(retmax),
  WebEnv = NULL,
  query_key = NULL,
  .cookies = NA,
  .paginate = 10000L,
  .progress = "ESearch",
  .path = NULL,
  .verbose = getOption("jentre.verbose", default = TRUE),
  .call = current_env()
)

Arguments

term: search query.
db: Entrez database name.
...: additional API parameters (refer to Entrez documentation). Any set to NULL are removed.
retstart: integer: index of first result (starts from 0). Ignored when usehistory is TRUE.
retmax: integer: maximum number of results to return. When NA this returns all results. When NULL, uses the Entrez default (typically 20). Note that it is possible that slightly more than retmax results will be returned when paginating. Ignored when usehistory is TRUE.
retmode: character: currently only "xml" is supported.
rettype: character: currently only "uilist" is supported.
usehistory: logical: when TRUE use the history server to return the result.
WebEnv, query_key: either characters to pass on as-is, or web_history objects.
.cookies: path to persist cookies. If NULL, cookies are not added to the request. For helper functions: when NA, a temporary file is created (in this case only, the temporary file will be cleaned up once all requests are performed).
.paginate: controls how multiple API requests are used to complete the call. Pagination is performed using the retstart and retmax API parameters. When set to an integer, no more than .pagniate items will be requested per API call. When FALSE or 0, only one API request is sent. Ignored when usehistory is TRUE.
.progress: controls progress bar; see the progress argument of httr2::req_perform_iterative().
.path: path specification for saving raw responses. See path argument of httr2::req_perform_iterative().
.verbose: logical: when TRUE logs all API requests as messages in a compact format. This uses a summarised format that does not include the request body for POST. Use normal httr verbosity controls (e.g. httr2::local_verbosity()) to override this behaviour and see more details.
.call: call environment to use in error messages/traces. See rlang::topic-error-call and the call argument of cli::cli_abort(). You only need to specify this in internal helper functions that don't need to be mentioned in error messages.

Value

id set object (either a web_history or an id_list).

Usage

Arguments

Value

See also