Package: pmparser 1.0.20

Jake Hughey

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>.

Authors:Jake Hughey [aut, cre], Josh Schoenbachler [aut], Elliot Outland [aut]

pmparser_1.0.20.tar.gz
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pmparser_1.0.20.tgz(r-4.4-any)pmparser_1.0.20.tgz(r-4.3-any)
pmparser_1.0.20.tar.gz(r-4.5-noble)pmparser_1.0.20.tar.gz(r-4.4-noble)
pmparser_1.0.20.tgz(r-4.4-emscripten)pmparser_1.0.20.tgz(r-4.3-emscripten)
pmparser.pdf |pmparser.html✨
pmparser/json (API)
NEWS

# Install 'pmparser' in R:
install.packages('pmparser', repos = c('https://hugheylab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/hugheylab/pmparser/issues

On CRAN:

5.68 score 16 stars 1 scripts 352 downloads 19 exports 17 dependencies

Last updated 11 months agofrom:fe86e9355b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:getCitationgetPgParamsmodifyPubmedDbparseAbstractparseArticleparseArticleIdparseAuthorparseChemicalparseCommentparseDataBankparseGrantparseInvestigatorparseJournalparseKeywordparseMeshparseOtherparsePmidStatusparsePubHistoryparsePubType

Dependencies:bitopsclicodetoolscurldata.tableDBIforeachglueiteratorsjsonliteR.methodsS3R.ooR.utilsRCurlrlangwithrxml2

Data Dictionary

Rendered fromdata_dictionary.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-04-13
Started: 2020-11-16

Readme and manuals

Help Manual

Help pageTopics
Get public-domain citation datagetCitation
Get Postgres connection parametersgetPgParams
Create or update a PubMed databasemodifyPubmedDb
Parse elements from a PubMed XML fileparseAbstract parseArticle parseArticleId parseAuthor parseChemical parseComment parseDataBank parseElement parseGrant parseInvestigator parseJournal parseKeyword parseMesh parseOther parsePmidStatus parsePubHistory parsePubType