R Observatory: Metrics for shrinkr version 0.4.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

shrinkr

0.4.5Package record

Modular Bayesian Hierarchical Shrinkage Models

0packages depend

1.2Kdownloads / year

72.6%test coverage

13/13flavors OK

Overview

About

Maintained by Jacob M. MarongeCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: GlaxoSmithKline Research & Development Limited

Implements a two-stage Bayesian hierarchical modeling framework for applying shrinkage to subgroup-specific effects. The package separates model fitting (Stage 1) from hierarchical shrinkage (Stage 2), enabling modular sensitivity analyses without refitting expensive Markov chain Monte Carlo (MCMC) chains. Supports flexible prior specifications through the 'distributional' package, mixture approximations via 'mclust', and efficient 'Stan'-based inference.

Changes in 0.4.5

Documentation

**Improved CRAN compatibility.** Updated package metadata and documentation following CRAN review comments, including expanding Markov chain Monte Carlo (MCMC) on first use in the DESCRIPTION file.
**Modernized examples.** Reworked documentation examples so lightweight examples are executable and self-contained. Replaced unnecessary \dontrun{} blocks with executable examples or \donttest{} where appropriate.
**Protected computationally intensive examples.** Kept examples that require fitting Bayesian hierarchical models with Stan inside \dontrun{} because they are not suitable for routine CRAN example checks.
**Improved method documentation examples.** Added small example objects for selected shrinkr_fit and mixture-method documentation so examples no longer depend on objects created in other help pages.

Show all changes in 0.4.5Hide the rest of the changes in 0.4.5

Vignettes

**Restored graphical parameters.** Updated the federated_learning vignette to save and restore graphical settings after calls to par(), avoiding persistent changes to the user's plotting environment.

---

From NEWS.md in the release

Install

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

install.packages("shrinkr", 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("GSK-Biostatistics/shrinkr")

Development version from GSK-Biostatistics/shrinkr. 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-shrinkr

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-shrinkr

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-shrinkr

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: 11.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK7 OK2026-07-07

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.5

READMEYes · 1,263 wordsVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 0.4.5Citation fileNoWebsiteYes · pkgdown

Help pages: 36 (6 internal)includes a package overview page
Examples that run: 88%23 run in a plain check · 3 never run
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 3%

Vignettes (5)

How these are measured

Downloads

1.2K

CRAN downloads in the past year

Rank #11,667 · ~3/day · ~102/mo

Releases R versions

Daily download trend is not available in this view yet.

30330 days

92990 days

1.2K1 year

Compare downloads with other packages →

Also on60 r2u4 autocran

How downloads are counted

Repository

gsk-biostatistics/shrinkr ↗Organization: GSK-Biostatistics

3Stars

0Forks

0Open issues

0Open PRs

1Releases

14Commits

1Commit identities

License file reads as GPL-3.0 · 14 commits · Last activity 2026-07-06 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2026-07-07 · 02026-08-08 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/gsk-biostatistics/shrinkr 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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-07-06 · The repository has a site deploy workflow

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Installing shrinkr adds 52 packages (26 with compiled code, 47 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, loo 2.7 MB.

Depends (1)

R >= 4.1

Imports (14)

rstan mclust posterior distributional cli tibble dplyr purrrstatsutilsmethodsRcpp RcppParallel rstantools

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.32.10)

Suggests (16)

testthat ggplot2 knitr rmarkdown patchwork tidybayes bayesplot tidyverse ggdist ggridges brms tidyrsurvivalMASSMatrixbeastt

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Jacob M. Maronge

Author, Maintainer since 0.4.5 (2026)

GlaxoSmithKline Research & Development Limited

Copyright holder, Funder

Trustees of Columbia University

Copyright holder

R/stanmodels.R, configure, configure.win

Listed in earlier versions (1)

Maronge

no longer listed · 0.4.5

Releases (1)

0.4.5Latest
record
2026-07-06 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-06
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1
Download size: 3.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("shrinkr")

Format

Maronge, J. M., GlaxoSmithKline Research & Development Limited, & Columbia University, T. o. (2026). shrinkr: Modular Bayesian Hierarchical Shrinkage Models (Version 0.4.5) [Computer software]. https://doi.org/10.32614/CRAN.package.shrinkr

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 shrinkr version 0.4.5 [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.

Report a problem with this page →