An R-package to gather bibliographic data from PubMed. | Installation | Load the package | NCBI API key | A brief example | One-step workflow: pmCollect() | Step-by-step workflow | Step 1: Build the query | Step 2: Check the effectiveness of the query | Step 3: Download the collection of document metadata | Step 4: Convert the XML object into a data frame | Fetching records by PMID | Citation enrichment | An overview of the collection using bibliometrix
Package: pubmedR 1.0.2.9000
pubmedR: Gathering Metadata About Publications, Grants, Clinical Trials from 'PubMed' Database
A set of tools to extract bibliographic content from 'PubMed' database using 'NCBI' REST API <https://www.ncbi.nlm.nih.gov/home/develop/api/>. It includes functions to search, download, and convert 'PubMed' bibliographic records into data frames compatible with the 'bibliometrix' package. Features include programmatic query building, batch downloading by PMID, citation enrichment via 'NCBI' E-Link, and robust error handling with automatic retry logic.
Authors:
pubmedR_1.0.2.9000.tar.gz
pubmedR_1.0.2.9000.zip(r-4.7)pubmedR_1.0.2.9000.zip(r-4.6)pubmedR_1.0.2.9000.zip(r-4.5)
pubmedR_1.0.2.9000.tgz(r-4.6-any)pubmedR_1.0.2.9000.tgz(r-4.5-any)
pubmedR_1.0.2.9000.tar.gz(r-4.7-any)pubmedR_1.0.2.9000.tar.gz(r-4.6-any)
pubmedR_1.0.2.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pubmedR/json (API)
| # Install 'pubmedR' in R: |
| install.packages('pubmedR', repos = c('https://massimoaria.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/massimoaria/pubmedr/issues
Last updated from:add34a2fbf. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 155 | ||
| source / vignettes | OK | 216 | ||
| linux-release-x86_64 | OK | 134 | ||
| macos-release-arm64 | OK | 102 | ||
| macos-oldrel-arm64 | OK | 80 | ||
| windows-devel | OK | 79 | ||
| windows-release | OK | 92 | ||
| windows-oldrel | OK | 86 | ||
| wasm-release | OK | 155 |
Exports:pmApi2dfpmApiRequestpmCitedBypmCollectpmEnrichCitationspmExtractReferencespmFetchByIdpmQueryBuildpmQueryTotalCountpmReferences
Dependencies:askpasscurlhttrjsonlitemimeopensslR6rentrezsysXML
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert xml PubMed bibliographic data into a dataframe | pmApi2df |
| Gather bibliographic content from PubMed database using NCBI entrez APIs | pmApiRequest |
| Find articles that cite a given PubMed article | pmCitedBy |
| Collect and process PubMed bibliographic data in one step | pmCollect |
| Enrich a PubMed dataframe with citation data | pmEnrichCitations |
| Extract references from PubMed XML records | pmExtractReferences |
| Fetch PubMed records by PMID | pmFetchById |
| Build a PubMed search query programmatically | pmQueryBuild |
| Count the number of documents returned by a query | pmQueryTotalCount |
| Find references cited by a given PubMed article | pmReferences |
