getCitation: Get public-domain citation data

In pmparser: Create and Maintain a Relational Database of Data from PubMed/MEDLINE

Get public-domain citation data

Description

Get the latest version of the NIH Open Citation Collection from figshare here, and optionally write it to the database. This function requires the shell command unzip, available by default on most Unix systems. This function should not normally be called directly, as it is called by modifyPubmedDb().

Usage

getCitation(
  localDir,
  filename = "open_citation_collection.zip",
  nrows = Inf,
  tableSuffix = NULL,
  overwrite = FALSE,
  con = NULL,
  checkMd5 = TRUE
)

Arguments

localDir	String indicating path to directory containing the citation file or to which the citation file should be downloaded.
filename	String indicating name of the citation file. This should not normally be changed from the default.
nrows	Number indicating how many rows of the citation file to read. This should not normally be changed from the default.
tableSuffix	String indicating suffix, if any, to append to the table name.
overwrite	Logical indicating whether to overwrite an existing table.
con	Connection to the database, created using DBI::dbConnect().
checkMd5	Logical indicating whether to download the citation file if the MD5 sums of the local and remote versions do not match. This should not normally be changed from the default.

Value

If con is NULL, the function returns a data.table with columns citing_pmid and cited_pmid. Beware this is a large table and could swamp the machine's memory. If con is not NULL, the function returns NULL invisibly.

See Also

parsePmidStatus(), modifyPubmedDb()

Examples

## Not run: 
dCitation = getCitation('.')

## End(Not run)

pmparser documentation built on April 4, 2025, 4:55 a.m.