Fetch records from Entrez

Fetching can be slow, and Entrez will time out requests that take too long. This helper supports pagination if you specify retmax.

Usage

efetch(
  id_set,
  ...,
  retstart = 0L,
  retmax = NA,
  retmode = "xml",
  rettype = NULL,
  .method = NA,
  .cookies = NA,
  .paginate = 200L,
  .process = NA,
  .progress = "Fetching",
  .path = NULL,
  .call = rlang::current_env()
)

Arguments

id_set

ID set object.

...

additional API parameters (refer to Entrez documentation). Any set to NULL are removed.

retstart

integer: index of first result (starts from 0).

retmax

integer: maximum number of results to return. When NA this returns all results. When NULL, uses the Entrez default (typically 20). Note that when using pagination with web history, it is possible that slightly more than retmax results will be returned.

retmode

character: requested document file format.

rettype

character: requested document type.

.method

HTTP verb. If NA, a sensible default is chosen based on the request parameters.

.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.

.process

function that processes the API results. Can be a function or builtin processor as described in process. Additional builtin processors are available:

"uilist" to extract a list of IDs (suitable for rettype = "uilist"),
NA to use a sensible choice based on parameters. In particular, for "uilist" requests, it will return an id_list object.

.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().

.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

output of .process from each page of results, combined with vctrs::list_unchop().

Usage

Arguments

Value

See also