R Observatory: Metrics for pubmedR version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pubmedR

1.0.2

Gathering Metadata About Publications, Grants, Clinical Trials from 'PubMed' Database

1packages depend

177.6Kdownloads / year

12.2%test coverage

13/13checks pass

Overview

About

Maintained by Massimo AriaFirst published 2020-03-205 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("pubmedR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("massimoaria/pubmedR")

Development version from massimoaria/pubmedR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-pubmedr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-pubmedR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-pubmedR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.5 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.13

12.2%

Coverage · measured lines

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-08
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 20%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

177.6K

CRAN downloads in the past year

Rank #1,043 · ~487/day · ~14.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

10.6K30 days

37.7K90 days

177.6K1 year

Compare downloads with other packages →

Also on205 r2u25 autocran991 conda_forge

Repository

GitHub ↗ massimoaria/pubmedr

46Stars

13Forks

1Open issues

0Open PRs

2Releases

53Commits

2Contributors

53 commits · Last activity 2026-05-05 · 0% stars, 30d

Stars over time

2025-05-29 · 422026-07-07 · 46

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/massimoaria/pubmedr on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-04-11

claude

Most recent: claude on 2026-04-11

Evidence

claude: on 2026-04-11 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

rentrez XML

LinkingTo (0)

none

Suggests (5)

bibliometrix knitr rmarkdown testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

1indirect

bibliometrix

Code & Tests

People & History

People (1)

Maintainer (1)

Massimo Aria

Author, Maintainer

Authors (1)

Massimo Aria

Author, Maintainer

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

1.0.2Latest
2026-05-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.0
2026-04-15 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.0.3
2020-07-09 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.0.2
2020-04-03 · diff ↗
0.0.1
2020-03-20
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-20
Total releases: 5 / 6 yrs
License: GPL-3 OSI
Download size: 31 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pubmedR")

Format

Aria, M. (2026). pubmedR: Gathering Metadata About Publications, Grants, Clinical Trials from 'PubMed' Database (Version 1.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.pubmedR

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for pubmedR version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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