R Observatory: Metrics for rtransparency version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rtransparency

1.0.0

Identifies Indicators of Transparency

0packages depend

381downloads / year

67.3%test coverage

13/13checks pass

Overview

About

Maintained by Ahmad Sofi-MahmudiFirst published 2026-07-021 releasesCRAN page ↗GitHub ↗

Use this package to identify indicators of transparency within the published literature. It can identify and extract text related to indicators of transparency from specifically formatted TXT files and from PMC XML files (i.e. XML files downloaded from the PubMed Central). It builds on the original 'rtransparent' tool of Serghiou et al. (2021) doi:10.1371/journal.pbio.3001107.

Install

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

install.packages("rtransparency", 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("choxos/rtransparency")

Development version from choxos/rtransparency. 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-rtransparency

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-rtransparency

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-rtransparency

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

Health

CRAN checks

13OK

Slowest check: 3.0 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 1.34

67.3%

Coverage · measured lines

100%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-03
9 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,041 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 13%
Documented parameters: 97%
Return-value docs: 100%
References docs: 0%

Downloads

381

CRAN downloads in the past year

Rank #23,911 · ~1/day · ~32/mo

Releases R versions

Daily download trend is not available in this view yet.

13730 days

38190 days

3811 year

Compare downloads with other packages →

Also on15 r2u6 autocran

Repository

GitHub ↗ choxos/rtransparency

1Stars

0Forks

0Open issues

0Open PRs

45Releases

192Commits

3Contributors

code-sharingconflict-of-interestdata-sharingopen-sciencer-packagetransparencyfunding-disclosureprotocol-registration

License GPL-3.0 · 192 commits · Last activity 2026-06-25 · 0% stars, 30d

Stars over time

2026-06-16 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/choxos/rtransparency on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (3)

CITATION.cffcodemeta.jsonZenodo

Show all practices

Governance and community (3)

Issue templatesPR templateSecurity policy

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

dplyr magrittr purrr readr rlang stringr tibble tidyselect utf8 xml2

LinkingTo (0)

none

Suggests (7)

furrr future ggplot2 knitr readxl rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Ahmad Sofi-Mahmudi

Maintainer, Author

Authors (2)

Ahmad Sofi-Mahmudi

Maintainer, Author

Stylianos Serghiou

Author

Package Timeline

1 release. R releases are shown for context.

1.0.0Latest
2026-07-02 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-02
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 11 KB / 2 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rtransparency")

The authors publish a CITATION.cff, so they have said how they want this cited. Run citation() and use what it gives you.

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 rtransparency version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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