Notes | New features of easyPubMed version r this_epm_ver | Installation | Stable Version | Dev Version(s) | Tutorial | Overview | Advanced Operations | Non-standard PubMed Queries | Retrieve non-XML Records | Queries Returning Large Numbers of Records | Save Raw Records Locally | Alternative Approaches for Record Parsing | Software Maintenance and Life Cycle | Additional Information | More info, other examples and vignettes, and Advanced Guides | References | Feedback, Citations and Collaborations | SessionInfo
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:
easyPubMed_3.1.3.tar.gz
easyPubMed_3.1.3.zip(r-4.7)easyPubMed_3.1.3.zip(r-4.6)easyPubMed_3.1.3.zip(r-4.5)
easyPubMed_3.1.3.tgz(r-4.6-any)easyPubMed_3.1.3.tgz(r-4.5-any)
easyPubMed_3.1.3.tar.gz(r-4.7-any)easyPubMed_3.1.3.tar.gz(r-4.6-any)
easyPubMed_3.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
easyPubMed/json (API)
| # Install 'easyPubMed' in R: |
| install.packages('easyPubMed', repos = c('https://dami82.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dami82/easypubmed/issues
Datasets:
- epm_samples - Preprocessed PubMed Records and Data
- epm_stopwords - PubMed Query Stopwords
Last updated from:6affef0e1a. Checks:8 OK, 1 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 134 | ||
| source / vignettes | ERROR | 207 | ||
| linux-release-x86_64 | OK | 153 | ||
| macos-release-arm64 | OK | 134 | ||
| macos-oldrel-arm64 | OK | 104 | ||
| windows-devel | OK | 125 | ||
| windows-release | OK | 117 | ||
| windows-oldrel | OK | 135 | ||
| wasm-release | OK | 113 |
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
Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.
Retrieving and Processing PubMed Records using easyPubMed
Last update: 2024-01-03
Started: 2023-11-23
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 Data | epm_samples |
| PubMed Query Stopwords | epm_stopwords |
| Retrieve PubMed Data in XML or TXT Format | fetch_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 Search | get_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 Records | table_articles_byAuth |
