R Observatory: Metrics for PublicationBiasBenchmark version 0.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PublicationBiasBenchmark

0.3.0Package record

Benchmark for Publication Bias Correction Methods

0packages depend

4.4Kdownloads / year

48.8%test coverage

13/13flavors OK

Overview

About

Maintained by František BartošCRAN page ↗GitHub ↗Website ↗Issues ↗

Implements a unified interface for benchmarking meta-analytic publication bias correction methods through simulation studies (see Bartoš et al., 2025, doi:10.48550/arXiv.2510.19489). It provides 1) predefined data-generating mechanisms from the literature, 2) functions for running meta-analytic methods on simulated data, 3) pre-simulated datasets and pre-computed results for reproducible benchmarks, 4) tools for visualizing and comparing method performance.

Changes in 0.3.0

Features

Added RTMA method
Added MAN method
Added MMPH method
Added fit_limit argument to run_method() that aborts a fit exceeding the given number of minutes and returns a standard failure result with note = "time limit exceeded with <fit_limit> minutes". The fit runs in a reused background R process so that methods sitting in compiled sampling code (RoBMA, RTMA, MMPH) can be stopped as well.

From NEWS.md in the release

Install

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

install.packages("PublicationBiasBenchmark", 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("FBartos/PublicationBiasBenchmark")

Development version from FBartos/PublicationBiasBenchmark. 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-publicationbiasbenchmark

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-PublicationBiasBenchmark

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-PublicationBiasBenchmark

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: 3.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-31

Show 2 earlier changesHide 2 earlier changes

WARNING11 OK, 2 WARNING2026-05-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.0

READMEYes · 1,407 wordsVignettesYes · 7 · dynamicNEWSYes · 100% structured · mentions 0.3.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 54 (6 internal)includes a package overview page
Examples that run: 71%24 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran) · 6 never run
Exported functions with examples: 67%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 48% with a bibliography file

Vignettes (7)

Adding New Data-Generating Mechanisms HTML
Adding New Methods HTML
Computing Method Measures HTML
Computing Method Results HTML
Using Precomputed Measures HTML
Using Precomputed Results HTML
Using Presimulated Datasets HTML

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #8,383 · ~12/day · ~363/mo

Releases R versions

Daily download trend is not available in this view yet.

49430 days

1.1K90 days

4.4K1 year

Compare downloads with other packages →

Also on136 r2u9 autocran

How downloads are counted

Repository

fbartos/publicationbiasbenchmark ↗Account: FBartos

2Stars

1Forks

0Open issues

1Open PRs

6Releases

167Commits

3Commit identities

benchmarkmeta-analysispublication-biassimulation

167 commits · Last activity 2026-09-30 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 89%
Median days to close, 50 most recently updated closed issues: 5
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-09-19 · 22026-07-07 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/fbartos/publicationbiasbenchmark 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 (2)

PR template (inherited from fbartos)

The repository owner accepts GitHub Sponsors

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-09-30 · The repository has a site deploy workflow

pkgdown site last built 2026-09-30

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-11-27
Pull request: opened by its own account
Claude Codefirst seen 2026-05-23
Named in .Rbuildignore: .claude
Pull request it wrote: opened by a project member

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

29 external dependencies (excludes base and recommended)

Installing PublicationBiasBenchmark adds 89 packages (46 with compiled code, 76 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 3.5.0

Imports (17)

statscallr metafor osfrMASSnumDeriv pwr sandwich clubSandwich lmtest puniform MAIVE phacking robumeta publipha rstan Rdpack

LinkingTo (0)

none

Suggests (14)

RoBMA pkgload BayesTools testthat withr rmarkdown knitr kableExtra DT ggplot2 scales ggdist rprojroot desc

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (4)

František Bartoš

Author, Maintainer since 0.1.0 (2025)

Samuel Pawel

Author

Björn S. Siepe

Author

Petr Čala

Author

Releases (7)

Pick two releases to compare their code metrics.

0.3.0Latest
record
2026-09-30 · current release · diff ↗
0.2.1
record
2026-05-23 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.2.0
record
2026-03-16 · diff ↗
0.1.3
record
2025-12-05 · diff ↗ ·
added 2 exports
measure, measure_mcse
0.1.2
record
2025-11-26 · diff ↗
0.1.1
record
2025-11-17 · diff ↗
0.1.0
record
2025-11-05
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-11-05
Total releases: 7 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 856 KB

Appears in task views

Meta-Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PublicationBiasBenchmark")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 PublicationBiasBenchmark version 0.3.0 [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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