Package: hdbayes 0.1.1.9000

Ethan M. Alt

hdbayes: Bayesian Analysis of Generalized Linear Models with Historical Data

User-friendly functions for leveraging (multiple) historical data set(s) for generalized linear models (GLMs) and survival models. The package provides functions for sampling from the posterior distribution 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. 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 the marginal log-likelihood under each implemented prior are also included. The package compiles all the 'CmdStan' models once during installation using the 'instantiate' package.

Authors:Ethan M. Alt [aut, cre, cph], Xinxin Chen [aut], Luiz M. Carvalho [aut], Joseph G. Ibrahim [aut], Xiuya Chang [ctb]

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NEWS

# Install 'hdbayes' in R:
install.packages('hdbayes', repos = c('https://ethan-alt.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ethan-alt/hdbayes/issues

Datasets:
  • E1684 - ECOG E1684 Trial
  • E1690 - ECOG E1690 Trial
  • E1694 - ECOG E1694 Trial
  • E2696 - ECOG E2696 Trial
  • IBCSG_curr - International Breast Cancer Study Group (IBCSG) Trial VI Data
  • IBCSG_hist - International Breast Cancer Study Group (IBCSG) Trial VI Data
  • actg019 - AIDS Clinical Trial ACTG019
  • actg036 - AIDS Clinical Trial ACTG036

On CRAN:

Conda:

6.34 score 5 stars 7 scripts 131 downloads 62 exports 44 dependencies

Last updated 16 hours agofrom:4f21a7ee57. Checks:12 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 31 2025
R-4.5-win-x86_64OKMar 31 2025
R-4.5-mac-x86_64OKMar 31 2025
R-4.5-mac-aarch64OKMar 31 2025
R-4.5-linux-x86_64OKMar 31 2025
R-4.4-win-x86_64OKMar 31 2025
R-4.4-mac-x86_64OKMar 31 2025
R-4.4-mac-aarch64OKMar 31 2025
R-4.4-linux-x86_64OKMar 31 2025
R-4.3-win-x86_64OKMar 31 2025
R-4.3-mac-x86_64OKMar 31 2025
R-4.3-mac-aarch64OKMar 31 2025

Exports:aft.bhmaft.commensurateaft.leapaft.logml.commensurateaft.logml.leapaft.logml.mapaft.logml.nppaft.logml.postaft.logml.ppaft.logml.stratified.ppaft.nppaft.npp.logncaft.postaft.ppaft.stratified.ppcurepwe.bhmcurepwe.commensuratecurepwe.leapcurepwe.logml.commensuratecurepwe.logml.leapcurepwe.logml.mapcurepwe.logml.nppcurepwe.logml.postcurepwe.logml.ppcurepwe.logml.stratified.ppcurepwe.nppcurepwe.npp.lognccurepwe.postcurepwe.ppcurepwe.stratified.ppglm.bhmglm.commensurateglm.leapglm.logml.commensurateglm.logml.leapglm.logml.mapglm.logml.nappglm.logml.nppglm.logml.postglm.logml.ppglm.nappglm.nppglm.npp.logncglm.postglm.ppglm.rmaplm.npppwe.bhmpwe.commensuratepwe.leappwe.logml.commensuratepwe.logml.leappwe.logml.mappwe.logml.npppwe.logml.postpwe.logml.pppwe.logml.stratified.pppwe.npppwe.npp.logncpwe.postpwe.pppwe.stratified.pp

Dependencies:abindbackportsbridgesamplingBrobdingnagcallrcheckmateclicodacolorspacedistributionalenrichwithfansifarverformula.toolsfsgenericsglueinstantiatelabelinglatticelifecyclemagrittrMatrixmatrixStatsmunsellmvtnormnumDerivoperator.toolspillarpkgconfigposteriorprocessxpsR6RColorBrewerrlangscalesstringistringrtensorAtibbleutf8vctrsviridisLite

AIDS-Progression

Rendered fromAIDS-Progression.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2024-08-20
Started: 2024-08-17

Readme and manuals

Help Manual

Help pageTopics
AIDS Clinical Trial ACTG019actg019
AIDS Clinical Trial ACTG036actg036
Posterior of Bayesian hierarchical model (BHM)aft.bhm
Posterior of commensurate prior (CP)aft.commensurate
Posterior of latent exchangeability prior (LEAP)aft.leap
Log marginal likelihood of an accelerated failure time (AFT) model under the commensurate prior (CP)aft.logml.commensurate
Log marginal likelihood of an accelerated failure time (AFT) model under latent exchangeability prior (LEAP)aft.logml.leap
Log marginal likelihood of an accelerated failure time (AFT) model under the meta-analytic predictive (MAP) prioraft.logml.map
Log marginal likelihood of an accelerated failure time (AFT) model under normalized power prior (NPP)aft.logml.npp
Log marginal likelihood of an accelerated failure time (AFT) model under a normal/half-normal prioraft.logml.post
Log marginal likelihood of an accelerated failure time (AFT) model under the power prior (PP)aft.logml.pp
Log marginal likelihood of an accelerated failure time (AFT) model under the stratified power prior (PP)aft.logml.stratified.pp
Posterior of normalized power prior (NPP)aft.npp
Estimate the logarithm of the normalizing constant for normalized power prior (NPP) for one data setaft.npp.lognc
Posterior of a normal/half-normal prioraft.post
Posterior of power prior (PP) with fixed a_0aft.pp
Posterior of stratified power prior (PP) with fixed a_0aft.stratified.pp
Posterior of Bayesian hierarchical model (BHM)curepwe.bhm
Posterior of commensurate prior (CP)curepwe.commensurate
Posterior of latent exchangeability prior (LEAP)curepwe.leap
Log marginal likelihood of a mixture cure rate (CurePWE) under the commensurate prior (CP)curepwe.logml.commensurate
Log marginal likelihood of a mixture cure rate (CurePWE) model under latent exchangeability prior (LEAP)curepwe.logml.leap
Log marginal likelihood of a mixture cure rate (CurePWE) model under the meta-analytic predictive (MAP) priorcurepwe.logml.map
Log marginal likelihood of a mixture cure rate (CurePWE) model under normalized power prior (NPP)curepwe.logml.npp
Log marginal likelihood of a mixture cure rate (CurePWE) model under a normal/half-normal priorcurepwe.logml.post
Log marginal likelihood of a standard cure rate (CurePWE) model under the power prior (PP)curepwe.logml.pp
Log marginal likelihood of a mixture cure rate (CurePWE) model under the stratified power prior (PP)curepwe.logml.stratified.pp
Posterior of normalized power prior (NPP)curepwe.npp
Estimate the logarithm of the normalizing constant for normalized power prior (NPP) for one data setcurepwe.npp.lognc
Posterior of a normal/half-normal priorcurepwe.post
Posterior of power prior (PP) with fixed a_0curepwe.pp
Posterior of stratified power prior (PP) with fixed a_0curepwe.stratified.pp
ECOG E1684 TrialE1684
ECOG E1690 TrialE1690
ECOG E1694 TrialE1694
ECOG E2696 TrialE2696
Posterior of Bayesian hierarchical model (BHM)glm.bhm
Posterior of commensurate prior (CP)glm.commensurate
Posterior of latent exchangeability prior (LEAP)glm.leap
Log marginal likelihood of a GLM under commensurate prior (CP)glm.logml.commensurate
Log marginal likelihood of a GLM under latent exchangeability prior (LEAP)glm.logml.leap
Log marginal likelihood of a GLM under meta-analytic predictive (MAP) priorglm.logml.map
Log marginal likelihood of a GLM under normalized asymptotic power prior (NAPP)glm.logml.napp
Log marginal likelihood of a GLM under normalized power prior (NPP)glm.logml.npp
Log marginal likelihood of a GLM under a normal/half-normal priorglm.logml.post
Log marginal likelihood of a GLM under power prior (PP)glm.logml.pp
Posterior of normalized asymptotic power prior (NAPP)glm.napp
Posterior of normalized power prior (NPP)glm.npp
Estimate the logarithm of the normalizing constant for normalized power prior (NPP) for one data setglm.npp.lognc
Posterior of a normal/half-normal priorglm.post
Posterior of power prior (PP) with fixed a_0glm.pp
Posterior of robust meta-analytic predictive prior (RMAP)glm.rmap
International Breast Cancer Study Group (IBCSG) Trial VI DataIBCSG_curr
International Breast Cancer Study Group (IBCSG) Trial VI DataIBCSG_hist
Posterior of normalized power prior (NPP) for normal linear modelslm.npp
Posterior of Bayesian hierarchical model (BHM)pwe.bhm
Posterior of commensurate prior (CP)pwe.commensurate
Posterior of latent exchangeability prior (LEAP)pwe.leap
Log marginal likelihood of a piecewise exponential (PWE) model under the commensurate prior (CP)pwe.logml.commensurate
Log marginal likelihood of a piecewise exponential (PWE) model under latent exchangeability prior (LEAP)pwe.logml.leap
Log marginal likelihood of a piecewise exponential (PWE) model under the meta-analytic predictive (MAP) priorpwe.logml.map
Log marginal likelihood of a piecewise exponential (PWE) model under normalized power prior (NPP)pwe.logml.npp
Log marginal likelihood of a piecewise exponential (PWE) model under a normal/half-normal priorpwe.logml.post
Log marginal likelihood of a piecewise exponential (PWE) model under the power prior (PP)pwe.logml.pp
Log marginal likelihood of a piecewise exponential (PWE) model under the stratified power prior (PP)pwe.logml.stratified.pp
Posterior of normalized power prior (NPP)pwe.npp
Estimate the logarithm of the normalizing constant for normalized power prior (NPP) for one data setpwe.npp.lognc
Posterior of a normal/half-normal priorpwe.post
Posterior of power prior (PP) with fixed a_0pwe.pp
Posterior of stratified power prior (PP) with fixed a_0pwe.stratified.pp