epm_fetch: Fetch Raw Records from Pubmed.

In dami82/easyPubMed: Search and Retrieve Scientific Publication Records from PubMed

Fetch Raw Records from Pubmed.

Description

Fetch raw PubMed records from PubMed. Records can be downloaded in text or xml format and stored into a local object or written to local files.

Usage

epm_fetch(
  x,
  format = "xml",
  api_key = NULL,
  write_to_file = FALSE,
  outfile_path = NULL,
  outfile_prefix = NULL,
  store_contents = TRUE,
  encoding = "UTF-8",
  verbose = TRUE
)

Arguments

x	An 'easyPubMed' object.
format	String, the desired format for the raw records. This argument must take one of the following values: 'c("uilist", "medline", "xml")' and defaults to '"xml"'.
api_key	String, corresponding to the NCBI API token (if available). NCBI token strings can be requested from NCBI. Record download will be faster if a valid NCBI token is used. This argument can be 'NULL'.
write_to_file	Logical of length 1. Shall raw records be written to a file on the local machine. It defaults to 'FALSE'.
outfile_path	Path to the folder on the local machine where files will be saved (if 'write_to_file' is 'TRUE'). It must point to an already existing directory. If 'NULL', the working directory will be used.
outfile_prefix	String, prefix that will be added to the name of each file written to the local machine. This argument is parsed only when 'write_to_file' is 'TRUE'. If 'NULL', an arbitrary prefix will be added (easypubmed_job_YYYYMMDDHHMM).
store_contents	Logical of length 1. Shall raw records be stored in the 'easyPubMed' object. It defaults to 'TRUE'. It may convenient to switch this to 'FALSE' when downloading large number of records. If 'store_contents' is 'FALSE', 'write_to_file' must be 'TRUE'.
encoding	String, the encoding of the records retrieved from PubMed. Typically, this is 'UTF-8'.
verbose	Logical, shall details about the progress of the operation be printed to console.

Value

an easyPubMed object.

Author(s)

Damiano Fantini, [e-mail]

References

https://www.data-pulse.com/dev_site/easypubmed/

Examples

# Note: a time limit can be set in order to kill the operation when/if 
# the NCBI/Entrez server becomes unresponsive.
setTimeLimit(elapsed = 4.9)
try({
  x <- epm_query(query_string = 'Damiano Fantini[AU] AND "2018"[PDAT]')
  x <- epm_fetch(x = x, format = 'uilist')
  x
}, silent = TRUE)
setTimeLimit(elapsed = Inf)

dami82/easyPubMed documentation built on Jan. 4, 2024, 6:21 a.m.