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.

Last updated 2 days ago

6.34 score 5 stars 7 scripts 131 downloads

bmabasket - Bayesian Model Averaging for Basket Trials

An implementation of the Bayesian model averaging method of Psioda and others (2019) <doi:10.1093/biostatistics/kxz014> for basket trials. Contains a user-friendly wrapper for simulating basket trials under conditions and analyzing them with a Bayesian model averaging approach.

Last updated 2 years ago

openblascppopenmp

3.18 score 1 stars 1 dependents 1 scripts 371 downloads

bayescopulareg - Bayesian Copula Regression

Tools for Bayesian copula generalized linear models (GLMs). The sampling scheme is based on Pitt, Chan, and Kohn (2006) <doi:10.1093/biomet/93.3.537>. Regression parameters (including coefficients and dispersion parameters) are estimated via the adaptive random walk Metropolis approach developed by Haario, Saksman, and Tamminen (1999) <doi:10.1007/s001800050022>. The prior for the correlation matrix is based on Hoff (2007) <doi:10.1214/07-AOAS107>.

Last updated 4 years ago

openblascppopenmp

2.70 score 239 downloads

surbayes - Bayesian Analysis of Seemingly Unrelated Regression Models

Implementation of the direct Monte Carlo approach of Zellner and Ando (2010) <doi:10.1016/j.jeconom.2010.04.005> to sample from posterior of Seemingly Unrelated Regression (SUR) models. In addition, a Gibbs sampler is implemented that allows the user to analyze SUR models using the power prior.

Last updated 5 years ago

openblascppopenmp

2.70 score 1 scripts 151 downloads