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BayesERtools

BayesERtools provides a suite of tools that facilitate exposure-response analysis using Bayesian methods.

Tutorial (BayesERbook): https://genentech.github.io/BayesERbook/
Package documentation: https://genentech.github.io/BayesERtools/
GitHub repo of the package: https://github.com/genentech/BayesERtools/

Installation

You can install the BayesERtools with:

# install.packages('BayesERtools') # Once on CRAN
devtools::install_github("genentech/BayesERtools") # development version

You also need latest version of rstanemax (>= 0.1.7) to use Emax model.

install.packages('rstanemax', repos = c(ppm = 'https://packagemanager.posit.co/cran/latest'))

Supported model types

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Version

Install

install.packages('BayesERtools')

Monthly Downloads

634

Version

0.2.0

License

Apache License 2.0

Homepage

https://genentech.github.io/BayesERtools/

Maintainer

Kenta Yoshida

Last Published

February 12th, 2025

Functions in BayesERtools (0.2.0)

edit_spec_coveff

Customize specifications for covariate effect simulations/visualizations

dev_ermod_emax_exp_sel

Exposure metrics selection for Emax models

ermod_exp_sel_method

S3 methods for the classes ermod_exp_sel

Evaluate exposure-response model prediction performance

extract_coef_exp_ci

Extract credible interval of the exposure coefficient

Extract elements from objects of the classes ersim_* and `ersim_med_qi_*``

Format the covariate effect simulation results for printing

Plot ER model simulations

S3 methods for the classes ermod_*

Efficient approximate leave-one-out cross-validation (LOO)

Probability of Direction (pd)

plot_er_exp_sel

Plot exposure metric selection comparison

Default GOF plot for ER model

Perform simulation of covariate effects for ER model

Run k-fold cross-validation

Extract elements from S3 objects

sim_er_new_exp_marg

Calculate marginal expected response for specified exposure values

Simulate from ER model

Visualize the covariate effects for ER model

Plot variable selection performance

Simulate from ER model at specified exposure values

dev_ermod_bin_cov_sel

Perform covariate selection for linear ER model

dev_ermod_bin_exp_sel

Exposure metrics selection for linear ER models

BayesERtools-package

BayesERtools: Bayesian Exposure-Response Analysis Tools

Transform to draws objects

Develop linear ER model for binary or continuous endpoint

dev_ermod_bin_cov_functions

Internal functions for developing an ER model with covariates for binary endpoint

ermod_cov_sel_method

S3 methods for the classes ermod_bin_cov_sel

build_spec_coveff

Build specifications for covariate effect simulation/visualization

Develop Emax model for continuous and binary endpoint

calc_ersim_med_qi

Calculate median and quantile intervals from ersim object

Extract elements from an object of class ermod_*

Sample simulated data for exposure-response with continuous endpoint using linear model.

S3 methods for the classes ersim_* and ersim_med_qi_*

d_sim_binom_cov

Sample simulated data for exposure-response with binary endpoint.