R Observatory: Metrics for hdbayes version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hdbayes

0.2.0

Bayesian Analysis of Generalized Linear Models with Historical Data

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Ethan M. AltFirst published 2024-04-083 releasesCRAN page ↗GitHub ↗

User-friendly functions for leveraging (multiple) historical data set(s) in Bayesian analysis of generalized linear models (GLMs) and survival models, along with support for Bayesian model averaging (BMA). The package provides functions for sampling from posterior distributions under various informative priors, including the prior induced by the Bayesian hierarchical model, power prior by Ibrahim and Chen (2000) doi:10.1214/ss/1009212673, normalized power prior by Duan et al. (2006) doi:10.1002/env.752, normalized asymptotic power prior by Ibrahim et al. (2015) doi:10.1002/sim.6728, commensurate prior by Hobbs et al. (2011) doi:10.1111/j.1541-0420.2011.01564.x, robust meta-analytic-predictive prior by Schmidli et al. (2014) doi:10.1111/biom.12242, latent exchangeability prior by Alt et al. (2024) doi:10.1093/biomtc/ujae083, and a normal (or half-normal) prior. The package also includes functions for computing model averaging weights, such as BMA, pseudo-BMA, pseudo-BMA with the Bayesian bootstrap, and stacking (Yao et al., 2018 doi:10.1214/17-BA1091), as well as for generating posterior samples from the ensemble distributions to reflect model uncertainty. In addition to GLMs, the package supports survival models including: (1) accelerated failure time (AFT) models, (2) piecewise exponential (PWE) models, i.e., proportional hazards models with piecewise constant baseline hazards, and (3) mixture cure rate models that assume a common probability of cure across subjects, paired with a PWE model for the non-cured population. Functions for computing marginal log-likelihoods under each implemented prior are also included. The package compiles all the 'CmdStan' models once during installation using the 'instantiate' package.

Install

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

install.packages("hdbayes", 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("ethan-alt/hdbayes")

Development version from ethan-alt/hdbayes. 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-hdbayes

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-hdbayes

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-hdbayes

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 4.2 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 86%
Documented parameters: 100%
Return-value docs: 100%
References docs: 86%

Downloads

2.6K

CRAN downloads in the past year

Rank #14,750 · ~7/day · ~219/mo

Releases R versions

Daily download trend is not available in this view yet.

16530 days

70090 days

2.6K1 year

Compare downloads with other packages →

Also on419 r2u21 autocran

Repository

GitHub ↗ ethan-alt/hdbayes

15Stars

3Forks

0Open issues

2Open PRs

2Releases

377Commits

5Contributors

377 commits · Last activity 2025-11-14 · 0% stars, 30d

Stars over time

2025-08-03 · 122026-07-07 · 15

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/ethan-alt/hdbayes on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (10)

instantiate callr fs formula.toolsstatsposterior enrichwith bridgesampling mvtnorm loo

LinkingTo (0)

none

Suggests (9)

cmdstanr ggplot2 ggthemes knitrparallelrmarkdown tibble dplyrsurvival

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Ethan M. Alt

Author, Maintainer, Copyright holder

Authors (4)

Ethan M. Alt

Author, Maintainer, Copyright holder

Luiz M. Carvalho

Author

Xinxin Chen

Author

Joseph G. Ibrahim

Author

Contributors (1)

Xiuya Chang

Contributor

Copyright holders (1)

Ethan M. Alt

Author, Maintainer, Copyright holder

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
2025-11-15 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.1
2024-08-23 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.0.3
2024-04-08
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-08
Total releases: 3 / 2 yrs
License: MIT + file LICENSE OSI
Additional repositories: mc-stan.org
Minimum R: ≥ 4.2.0
Bundled data: 27 KB / 8 files
Download size: 474 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hdbayes")

Format

Alt, E. M., Carvalho, L. M., Chang, X., Chen, X., & Ibrahim, J. G. (2025). hdbayes: Bayesian Analysis of Generalized Linear Models with Historical Data (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.hdbayes

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 hdbayes version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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