R Observatory: Metrics for europepmc version 0.4.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

europepmc

0.4.3Package record

R Interface to the Europe PubMed Central RESTful Web Service

1packages depend

19.2Kdownloads / year

82.8%test coverage

13/13flavors OK

Overview

About

Maintained by Najko JahnCRAN page ↗GitHub ↗Website ↗Issues ↗

An R Client for the Europe PubMed Central RESTful Web Service (see https://europepmc.org/RestfulWebService for more information). It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible. No registration or API key is required. See the vignettes for usage examples.

Changes in 0.4.3

Skip test on CRAN

From NEWS.md in the release

Install

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

install.packages("europepmc", 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("ropensci/europepmc")

Development version from ropensci/europepmc. 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-europepmc

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-europepmc

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-europepmc

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.3

READMEYes · 602 wordsVignettesYes · 2 · staticNEWSYes · 100% structured · mentions 0.4.3Citation fileNoWebsiteYes · pkgdown

Help pages: 18includes a package overview page
Examples that run: 0%16 never run
Exported functions with examples: 94%
Documented parameters: 91%
Return-value docs: 71%
Help pages citing references: 0%

Vignettes (2)

Making trend graphs HTML
Overview HTML

How these are measured

Downloads

19.2K

CRAN downloads in the past year

Rank #3,293 · ~53/day · ~1.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.2K30 days

3.4K90 days

19.2K1 year

Compare downloads with other packages →

Also on157 r2u12 autocran2K conda_forge137 c2d4u

How downloads are counted

Repository

ropensci/europepmc ↗Organization: ropensci

32Stars

9Forks

12Open issues

1Open PRs

8Releases

253Commits

6Commit identities

europe-pmcrrstatsbibliometricsscientific-literaturescientific-publicationsr-packagepubmed

253 commits · Last activity 2023-11-20 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 36
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-14 · 272026-09-14 · 32

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/ropensci/europepmc on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2019-06-05

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing europepmc adds 36 packages (23 with compiled code, 23 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, openssl 1.1 MB.

Depends (1)

R >= 3.00

Imports (11)

httr jsonlite plyr dplyr progress urltools purrr xml2 tibble tidyr rlang

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

genekitr

How these are counted

Code & Tests

People & History

People (2)

Najko Jahn

Maëlle Salmon

Contributor · added in 0.2

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.4.3Latest
record
2023-09-20 · current release · diff ↗
0.4.2
record
2023-08-21 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.4.1
record
2021-09-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.4
record
2020-05-31 · diff ↗ ·
removed 2 exports
epmc_tm, epmc_tm_count

added 3 exports
epmc_annotations_by_id, epmc_search_by_doi, epmc_search_by_doi_
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.3
record
2018-04-20 · diff ↗
0.2
record
2017-12-11 · diff ↗ ·
added 1 export
epmc_hits_trend
R
R 3.4.0 released · 2017-04-21

Show 6 earlier eventsHide 6 earlier events

0.1.4
record
2017-03-20 · diff ↗
0.1.3
record
2017-02-23 · diff ↗
0.1.2
record
2017-01-08 · diff ↗ ·
added 1 export
epmc_profile
0.1.1
record
2017-01-06 · diff ↗ ·
added 1 export
epmc_search_
0.1.0
record
2016-07-13
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-07-13
Total releases: 11 / 10 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.00
Download size: 683 KB

Appears in task views

Web Technologies and Services

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("europepmc")

Format

Jahn, N., & Salmon, M. (2023). europepmc: R Interface to the Europe PubMed Central RESTful Web Service (Version 0.4.3) [Computer software]. https://doi.org/10.32614/CRAN.package.europepmc

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 europepmc version 0.4.3 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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