R Observatory: Metrics for pema version 0.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pema

0.1.5Package record

Penalized Meta-Analysis

0packages depend

8.8Kdownloads / year

18.4%test coverage

13/13flavors OK

Overview

About

Maintained by Caspar J van LissaCRAN page ↗GitHub ↗Website ↗

Conduct penalized meta-analysis, see Van Lissa, Van Erp, & Clapper (2023) doi:10.31234/osf.io/6phs5. In meta-analysis, there are often between-study differences. These can be coded as moderator variables, and controlled for using meta-regression. However, if the number of moderators is large relative to the number of studies, such an analysis may be overfit. Penalized meta-regression is useful in these cases, because it shrinks the regression slopes of irrelevant moderators towards zero.

Install

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

install.packages("pema", 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("cjvanlissa/pema")

Development version from cjvanlissa/pema. 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-pema

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-pema

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-pema

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: 41.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK13 OK2026-06-08

Show 5 earlier changesHide 5 earlier changes

NOTE12 OK, 1 NOTE2026-06-07
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.5

READMEYes · 326 wordsVignettesYes · 2 · evaluation depends on the environmentNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 12includes a package overview page
Examples that run: 89%8 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 79%
Return-value docs: 100%
Help pages citing references: 33%

Vignettes (2)

How these are measured

Downloads

8.8K

CRAN downloads in the past year

Rank #6,564 · ~24/day · ~731/mo

Releases R versions

Daily download trend is not available in this view yet.

48130 days

1.3K90 days

8.8K1 year

Compare downloads with other packages →

Also on391 r2u8 autocran147 c2d4u

How downloads are counted

Repository

cjvanlissa/pema ↗Account: cjvanlissa

0Stars

1Forks

0Open issues

0Open PRs

1Releases

205Commits

7Commit identities

205 commits · Last activity 2025-08-08

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 414
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

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

Checks run against github.com/cjvanlissa/pema on 2026-10-18.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-08-08 · The repository has a site deploy workflow

pkgdown site last built 2025-08-08, before release 0.1.5 (2025-10-06)

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing pema adds 74 packages (39 with compiled code, 67 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 3.4.0

Imports (9)

methodsrstan Rcpp RcppParallel (>= 5.0.1)rstantools sn shiny ggplot2 cli

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.26.0)

Suggests (8)

rmarkdown knitr mice testthat webexercises bain metaforest metafor

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Caspar J van Lissa

Author, Maintainer since 0.1.0 (2021)

Sara J van Erp

Author

Listed in earlier versions (2)

Caspar J

no longer listed · 0.1.0 to 0.1.5

Sara J

no longer listed · 0.1.0 to 0.1.5

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-10-06
0.1.5Latest
record
2025-10-06 · current release · diff ↗
archivedRemoved from CRAN
2025-08-25
errors were not corrected in time
R
R 4.5.0 released · 2025-04-11
0.1.4
record
2025-03-30 · diff ↗ ·
added 1 export
check_workshop_data
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.1.3
record
2023-03-16 · diff ↗ ·
added 1 export
plot_sensitivity
0.1.2
record
2022-07-17 · diff ↗
0.1.1
record
2022-04-25 · diff ↗ ·
added 3 exports
I2, sample_prior, shiny_prior
R
R 4.2.0 released · 2022-04-22
0.1.0
record
2021-12-15
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-15
Total releases: 6 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.4.0
Bundled data: 46 KB / 2 files
Download size: 1.0 MB

Appears in task views

Meta-Analysis

Cite

Cite this package

Run in R for the authors' entry:

citation("pema")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.31234/osf.io/6phs5.

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 pema version 0.1.5 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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