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

Provides a simple interface for extracting various elements from the publicly available PubMed XML files, incorporating PubMed's regular updates, and combining the data with the NIH Open Citation Collection. See Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.

Version: 1.0.13
Depends: R (≥ 3.6)
Imports: curl (≥ 4.3.2), data.table (≥ 1.12.2), DBI (≥ 1.1.0), foreach (≥ 1.5.0), glue (≥ 1.4.2), iterators (≥ 1.0.12), jsonlite (≥ 1.7.0), R.utils (≥ 2.10.1), RCurl (≥ 1.98), withr (≥ 2.3.0), xml2 (≥ 1.3.3)
Suggests: bigrquery (≥ 1.3.2), doParallel (≥ 1.0.16), RMariaDB (≥ 1.0.9), RPostgres (≥ 1.2.0), RSQLite (≥ 2.2.0), testthat (≥ 2.3.2), knitr, rmarkdown
Published: 2022-11-24
Author: Jake Hughey [aut, cre], Josh Schoenbachler [aut], Elliot Outland [aut]
Maintainer: Jake Hughey <jakejhughey at gmail.com>
License: GPL-2
URL: https://pmparser.hugheylab.org, https://github.com/hugheylab/pmparser
NeedsCompilation: no
SystemRequirements: head, unzip, sqlite
Materials: NEWS
CRAN checks: pmparser results

Documentation:

Reference manual: pmparser.pdf
Vignettes: Data Dictionary

Downloads:

Package source: pmparser_1.0.13.tar.gz
Windows binaries: r-devel: pmparser_1.0.13.zip, r-release: pmparser_1.0.11.zip, r-oldrel: not available
macOS binaries: r-release (arm64): pmparser_1.0.11.tgz, r-oldrel (arm64): pmparser_1.0.11.tgz, r-release (x86_64): pmparser_1.0.13.tgz, r-oldrel (x86_64): pmparser_1.0.13.tgz
Old sources: pmparser archive

Linking:

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