R Observatory: Metrics for puniform version 0.2.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

puniform

0.2.8Package record

Meta-Analysis Methods Correcting for Publication Bias

1packages dependsuggested by 1

5.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Robbie C.M. van AertCRAN page ↗GitHub ↗Issues ↗

Provides meta-analysis methods that correct for publication bias and outcome reporting bias. Four methods and a visual tool are currently included in the package. The p-uniform method as described in van Assen, van Aert, and Wicherts (2015) doi:10.1037/met0000025 can be used for estimating the average effect size, testing the null hypothesis of no effect, and testing for publication bias using only the statistically significant effect sizes of primary studies. The second method in the package is the p-uniform* method as described in van Aert and van Assen (2023) doi:10.31222/osf.io/zqjr9. This method is an extension of the p-uniform method that allows for estimation of the average effect size and the between-study variance in a meta-analysis, and uses both the statistically significant and nonsignificant effect sizes. The third method in the package is the hybrid method as described in van Aert and van Assen (2018) doi:10.3758/s13428-017-0967-6. The hybrid method is a meta-analysis method for combining a conventional study and replication/preregistered study while taking into account statistical significance of the conventional study. This method was extended in van Aert (2025) doi:10.1037/met0000719 such that it allows for the inclusion of multiple conventional and replication/preregistered studies. The p-uniform and hybrid method are based on the statistical theory that the distribution of p-values is uniform conditional on the population effect size. The fourth method in the package is the Snapshot Bayesian Hybrid Meta-Analysis Method as described in van Aert and van Assen (2018) doi:10.1371/journal.pone.0175302. This method computes posterior probabilities for four true effect sizes (no, small, medium, and large) based on an original study and replication while taking into account publication bias in the original study. The method can also be used for computing the required sample size of the replication akin to power analysis in null-hypothesis significance testing. The meta-plot is a visual tool for meta-analysis that provides information on the primary studies in the meta-analysis, the results of the meta-analysis, and characteristics of the research on the effect under study (van Assen et al., 2023). Helper functions to apply the Correcting for Outcome Reporting Bias (CORB) method to correct for outcome reporting bias in a meta-analysis (van Aert & Wicherts, 2023).

Changes in 0.2.8

If raw correlations are provided in hybrid(), the output of fixed-effect

meta-analysis is reported as Fisher's z transformed correlations

Optimization information is now returned when puni_star() is applied and both

parameters are estimated at the same time with method = "ML"

Fix a bug in repl() that transformed the correlations to Fisher's z transformed

correlations

Added the functionality in hybrid() to also specify "yi" and "vi" as arguments

if implementation = "two"

Implemented the snapshot method on the log scale to avoid numerical underflow

From NEWS.md in the release

Install

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

install.packages("puniform", 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("RobbievanAert/puniform")

Development version from RobbievanAert/puniform. 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-puniform

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-puniform

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-puniform

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: 3.6 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.8

READMEYes · 188 wordsVignettesNoNEWSYes · 100% structured · mentions 0.2.8Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 17
Examples that run: 100%13 run in a plain check
Exported functions with examples: 81%
Documented parameters: 100%
Return-value docs: 94%
Help pages citing references: 76%

How these are measured

Downloads

5.3K

CRAN downloads in the past year

Rank #5,720 · ~14/day · ~440/mo

Releases R versions

Daily download trend is not available in this view yet.

62630 days

1.5K90 days

5.3K1 year

Compare downloads with other packages →

Also on428 r2u3 autocran2.7K conda_forge138 c2d4u

How downloads are counted

Repository

robbievanaert/puniform ↗Account: RobbievanAert

3Stars

0Forks

0Open issues

0Open PRs

3Releases

222Commits

3Commit identities

222 commits · Last activity 2025-09-02

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2018-12-04 · 32026-07-07 · 3

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/robbievanaert/puniform on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (1)

README.Rmd

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing puniform adds 9 packages (3 with compiled code, 12 MB of source tarballs). Heaviest: metafor 4.8 MB, mathjaxr 3.0 MB, Rcpp 1.8 MB.

Depends (0)

none

Imports (5)

Rcpp ADGofTeststatsmetafor numDeriv

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (1)

metadat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

PublicationBiasBenchmark

Suggests, most downloaded first

artma

How these are counted

Code & Tests

Datasets

People & History

People (1)

Robbie C.M. van Aert

Author, Maintainer since 0.1.0 (2018)

Listed in earlier versions (1)

van Aert

no longer listed · 0.2.8

Releases (10)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.8Latest
record
2025-09-02 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.2.7
record
2023-09-19 · diff ↗
0.2.6
record
2023-07-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.2.5
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2022-03-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.4
record
2021-01-06 · diff ↗
0.2.3
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2020-10-26 · diff ↗
0.2.2
record
2020-06-20 · diff ↗ ·
added 5 exports
var_dif_fis, var_boot_fis, var_dif_rmd, var_boot_rmd, var_pop
R
R 4.0.0 released · 2020-04-24
0.2.1
record
2019-08-27 · diff ↗ ·
added 1 export
meta_plot
R
R 3.6.0 released · 2019-04-26

Show 3 earlier eventsHide 3 earlier events

0.1.1
record
2019-03-06 · diff ↗
0.1.0
record
2018-07-05
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-07-05
Total releases: 10 / 8 yrs
License: GPL (>= 2) OSI
Bundled data: 0.2 KB / 1 file
Download size: 76 KB

Appears in task views

Meta-Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("puniform")

Format

van Aert, R. C. M. (2025). puniform: Meta-Analysis Methods Correcting for Publication Bias (Version 0.2.8) [Computer software]. https://doi.org/10.32614/CRAN.package.puniform

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 puniform version 0.2.8 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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