Package: easyPubMed 3.1.3

easyPubMed: Search and Retrieve Scientific Publication Records from PubMed

Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.

Authors:Damiano Fantini

easyPubMed_3.1.3.tar.gz
easyPubMed_3.1.3.zip(r-4.5)easyPubMed_3.1.3.zip(r-4.4)easyPubMed_3.1.3.zip(r-4.3)
easyPubMed_3.1.3.tgz(r-4.4-any)easyPubMed_3.1.3.tgz(r-4.3-any)
easyPubMed_3.1.3.tar.gz(r-4.5-noble)easyPubMed_3.1.3.tar.gz(r-4.4-noble)
easyPubMed_3.1.3.tgz(r-4.4-emscripten)easyPubMed_3.1.3.tgz(r-4.3-emscripten)
easyPubMed.pdf |easyPubMed.html✨
easyPubMed/json (API)

# Install 'easyPubMed' in R:
install.packages('easyPubMed', repos = c('https://dami82.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dami82/easypubmed/issues

Datasets:

On CRAN:

7.80 score 21 stars 4 packages 167 scripts 670 downloads 30 exports 1 dependencies

Last updated 11 months agofrom:6affef0e1a. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 29 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:epm_fetchepm_import_xmlepm_parseepm_parse_recordepm_queryepm_query_by_fulltitleepm_query_by_pmidfetch_pubmed_datafetchEPMDataget_epm_dataget_epm_metaget_epm_rawget_epm_uilistget_pubmed_idsgetEPMDatagetEPMJobListgetEPMMetagetEPMMiscgetEPMQuerygetEPMRawgetEPMUilistparseEPMDatasetEPMDatasetEPMJobListsetEPMMetasetEPMMiscsetEPMQuerysetEPMRawsetEPMUilisttable_articles_byAuth

Dependencies:rlang

Retrieving and Processing PubMed Records using easyPubMed

Damiano Fantini

Rendered fromeasyPubMed_demo.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-01-03
Started: 2023-11-23

Readme and manuals

Help Manual

Help pageTopics
Class easyPubMed.easyPubMed-class initialize,easyPubMed-method
Fetch Raw Records from Pubmed.epm_fetch
Import PubMed Records from Local Files.epm_import_xml
Extract Information from a Raw PubMed Record.epm_parse
Extract Information from a Raw PubMed Record.epm_parse_record
Search for PubMed Records.epm_query
Query PubMed by Full-length Title.epm_query_by_fulltitle
Query PubMed by PMIDs.epm_query_by_pmid
Preprocessed PubMed Records and Dataepm_samples
PubMed Query Stopwordsepm_stopwords
Retrieve PubMed Data in XML or TXT Formatfetch_pubmed_data
Method fetchEPMData.fetchEPMData fetchEPMData,easyPubMed,list-method
Get Processed Data from an easyPubMed Object.get_epm_data
Get Meta Data from an easyPubMed Object.get_epm_meta
Get Raw Data from an easyPubMed Object.get_epm_raw
Get PubMed Record Identifiers from an easyPubMed Object.get_epm_uilist
Simple PubMed Record Searchget_pubmed_ids
Method getEPMData.getEPMData getEPMData,easyPubMed-method
Method getEPMJobList.getEPMJobList getEPMJobList,easyPubMed-method
Method getEPMMeta.getEPMMeta getEPMMeta,easyPubMed-method
Method getEPMMisc.getEPMMisc getEPMMisc,easyPubMed-method
Method getEPMQuery.getEPMQuery getEPMQuery,easyPubMed-method
Method getEPMRaw.getEPMRaw getEPMRaw,easyPubMed-method
Method getEPMUilist.getEPMUilist getEPMUilist,easyPubMed-method
Method parseEPMData.parseEPMData parseEPMData,easyPubMed,list-method
Print method of the easyPubMed Class.print,easyPubMed-method
Method setEPMData.setEPMData setEPMData,easyPubMed,data.frame-method
Method setEPMJobList.setEPMJobList setEPMJobList,easyPubMed,data.frame-method
Method setEPMMeta.setEPMMeta setEPMMeta,easyPubMed,list-method
Method setEPMMisc.setEPMMisc setEPMMisc,easyPubMed,list-method
Method setEPMQuery.setEPMQuery setEPMQuery,easyPubMed,character-method
Method setEPMRaw.setEPMRaw setEPMRaw,easyPubMed,list-method
Method setEPMUilist.setEPMUilist setEPMUilist,easyPubMed,list-method
Show method of the easyPubMed Class.show,easyPubMed-method
Extract Publication and Affiliation Data from PubMed Recordstable_articles_byAuth