R Observatory: Metrics for baggr version 0.8.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before Nov 1 or it will be archived. See the check details

baggr

0.8.2Package record

Bayesian Aggregate Treatment Effects

0packages depend

6.1Kdownloads / year

–test coverage

8/13flavors OK

Overview

About

Maintained by Witold WiecekCRAN page ↗GitHub ↗Issues ↗

Running and comparing meta-analyses of data with hierarchical Bayesian models in Stan, including convenience functions for formatting data, plotting and pooling measures specific to meta-analysis. This implements many models from Meager (2019) doi:10.1257/app.20170299.

Changes in 0.8.2

Functionality:

Improved funnel plot function
Faster logit model via bernoulli_logit_glm
Added predict.baggr() alias

Documentation:

Added a vignette baggr_selection that has examples of how to do selection models

Fixes:

Fix to selection model: I did marginalisation of likelihood wrong and the previous results were biased towards the "uncorrected" hypermeans in presence of heterogeneity.
Fixed some inconsistencies in how predicted effects were handled in models with individual-level data (with covariates that change within study)
Fixed some bugs in predictive density calculations in cross-validation

Show all changes in 0.8.2Hide the rest of the changes in 0.8.2

Specification of prior for sigma (SD) in rubin_full model
Log-predictive density for "mu & tau" model was wrong; new version relies on multivariate

From NEWS.md in the release

Install

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

install.packages("baggr", 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("wwiecek/baggr")

Development version from wwiecek/baggr. 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-baggr

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-baggr

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-baggr

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

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  baggr/tests/testthat/test_loo.R (.Dim: 2, .Dimnames: 2)
  baggr/tests/testthat/test_ordering.R (.Label: 1)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
'.Label' should be changed to 'levels'.

Additional issues

CRAN check page ↗

Slowest check: 28.3 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE9 OK, 4 NOTE2026-07-29
ERROR9 OK, 3 NOTE, 1 ERROR2026-07-27
NOTE11 OK, 2 NOTE2026-07-16
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22

Show 2 earlier changesHide 2 earlier changes

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 0.8.2

READMENoVignettesYes · 3 · dynamicNEWSYes · 67% structured · mentions 0.8.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 48 (1 internal)includes a package overview page
Examples that run: 75%12 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 3 never run
Exported functions with examples: 62%
Documented parameters: 100%
Return-value docs: 77%
Help pages citing references: 23%

Vignettes (3)

How these are measured

Downloads

6.1K

CRAN downloads in the past year

Rank #5,207 · ~17/day · ~512/mo

Releases R versions

Daily download trend is not available in this view yet.

59930 days

1.6K90 days

6.1K1 year

Compare downloads with other packages →

Also on565 r2u44 autocran170 c2d4u

How downloads are counted

Repository

wwiecek/baggr ↗Account: wwiecek

51Stars

14Forks

17Open issues

3Open PRs

7Releases

691Commits

7Commit identities

meta-analysisstanbayesian-statisticstreatment-effectsquantile-regression

License file reads as GPL-3.0 · 691 commits · Last activity 2026-06-16 · +2% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 73%
Median days to close, 50 most recently updated closed issues: 1,093
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-01-08 · 492026-09-22 · 51

How these are measured

PracticesBeta

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

Checks run against github.com/wwiecek/baggr on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

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)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Codexfirst seen 2025-11-19
Pull request it wrote: opened by a project member

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing baggr adds 69 packages (35 with compiled code, 70 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (2)

R >= 3.5.0Rcpp

Imports (12)

rstan rstantools bayesplot crayon forestplot ggplot2 ggplotify ggrepel gridExtrautilsstatsmethods

LinkingTo (6)

StanHeaders rstan BH (>= 1.66.0-1)Rcpp RcppParallel RcppEigen

Suggests (5)

knitr covr mvtnorm rmarkdown testthat

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 (5)

Witold Wiecek

Maintainer since 0.1.0 (2019), Author

Rachael Meager

Author

Brice Green

Contributor · added in 0.3.0

loo_compare, many visuals

Danny Toomey

Contributor · added in 0.7.8

many bug fixes

Trustees of Columbia University

Copyright holder

package skeleton

Releases (14)

Pick two releases to compare their code metrics.

0.8.2Latest
record
2026-06-16 · current release · diff ↗ ·
added 1 export
funnel
R
R 4.6.0 released · 2026-04-24
0.8
record
2026-02-10 · diff ↗ ·
added 2 exports
funnel_plot, selection
0.7.11
record
2025-06-19 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.7.8
record
2024-02-12 · diff ↗ ·
added 4 exports
bubble, hypermean, hypersd, study_effects
R
R 4.3.0 released · 2023-04-21
0.7.6
record
2023-03-22 · diff ↗
0.7.4
record
2023-01-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.6.21
record
2022-03-15 · diff ↗ ·
added 1 export
student_t
0.6.18
record
2022-01-04 · diff ↗ ·
removed 1 export
summarise_quantiles_data

added 1 export
lognormal
0.6.9
record
2021-09-02 · diff ↗ ·
added 2 exports
mutau_cor, single_comp_plot
R
R 4.1.0 released · 2021-05-18
0.6.4
record
2021-05-12 · diff ↗ ·
removed 1 export
show_model

added 5 exports
binary_to_individual, labbe, plot_quantiles, random_effects, summarise_quantiles_data

Show 6 earlier eventsHide 6 earlier events

R
R 4.0.0 released · 2020-04-24
0.4.0
record
2020-02-28 · diff ↗ ·
added 1 export
fixed_effects
0.3.0
record
2020-01-08 · diff ↗ ·
added 8 exports
baggr_theme_get, baggr_theme_replace, baggr_theme_set, baggr_theme_update, forest_plot, heterogeneity, loo_compare, mint
0.2.0
record
2019-10-29 · diff ↗ ·
added 8 exports
cauchy, effect_draw, effect_plot, lkj, multinormal, normal, pooling, uniform
0.1.0
record
2019-08-01
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-01
Total releases: 14 / 7 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 558 KB / 7 files
Download size: 3.0 MB

Appears in task views

Bayesian Inference Meta-Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("baggr")

Format

Wiecek, W., Columbia University, T. o., Green, B., Meager, R., & Toomey, D. (2026). baggr: Bayesian Aggregate Treatment Effects (Version 0.8.2) [Computer software]. https://doi.org/10.32614/CRAN.package.baggr

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 baggr version 0.8.2 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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