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. The package contains functions for sampling from the posterior distribution of a generalized linear model using 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>, the latent exchangeability prior by Alt et al. (2023) <doi:10.48550/arXiv.2303.05223>, and a normal (or half-normal) prior. Functions for computing the marginal log-likelihood under each of the implemented priors 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]

hdbayes_0.1.1.9000.tar.gz
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hdbayes.pdf |hdbayes.html
hdbayes/json (API)
NEWS

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

Peer review:

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:

6.14 score 3 stars 7 scripts 139 downloads 25 exports 45 dependencies

Last updated 3 days agofrom:3e8bf749c9. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-win-x86_64OKNov 20 2024
R-4.5-linux-x86_64OKNov 20 2024
R-4.4-win-x86_64OKNov 20 2024
R-4.4-mac-x86_64OKNov 20 2024
R-4.4-mac-aarch64OKNov 20 2024
R-4.3-win-x86_64OKNov 20 2024
R-4.3-mac-x86_64OKNov 20 2024
R-4.3-mac-aarch64OKNov 20 2024

Exports:aft.bhmaft.leapaft.logml.leapaft.logml.mapaft.logml.postaft.logml.ppaft.postaft.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.npp

Dependencies:abindbackportsbridgesamplingBrobdingnagcallrcheckmateclicodacolorspacedistributionalenrichwithfansifarverformula.toolsfsgenericsglueinstantiatelabelinglatticelifecyclemagrittrMatrixmatrixStatsmclustmunsellmvtnormnumDerivoperator.toolspillarpkgconfigposteriorprocessxpsR6RColorBrewerrlangscalesstringistringrtensorAtibbleutf8vctrsviridisLite

AIDS-Progression

Rendered fromAIDS-Progression.Rmdusingknitr::rmarkdownon Nov 20 2024.

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 latent exchangeability prior (LEAP)aft.leap
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 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
Posterior of a normal/half-normal prioraft.post
Posterior of power prior (PP) with fixed a_0aft.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