easyPubMed (version 3.1.6)

epm_fetch: 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
)

Value

an easyPubMed object.

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.

Author

Damiano Fantini,

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)