hdbayes
Bayesian Analysis of Generalized Linear Models with Historical Data
Description
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.
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All-time
autoCRAN-only: this name is served only by autoCRAN, so the count is exact.
CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: ‘cmdstanr’
package dependencies
Package suggested but not available for checking: 'cmdstanr'
Code
Structure
Lines of code
27,821
Files
259
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
64
Internal functions
78
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
14.1%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
1
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2024-04-08
Latest release
2025-11-15
Avg cadence
293 days
Cold removal rate
100%
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.