This package is considered a duplicate. The official version of this package is found at:https://genentech.r-universe.dev/BayesERtools

Package: BayesERtools 0.2.7

Kenta Yoshida

BayesERtools: Bayesian Exposure-Response Analysis Tools

Suite of tools that facilitate exposure-response analysis using Bayesian methods. The package provides a streamlined workflow for fitting types of models that are commonly used in exposure-response analysis - linear and Emax for continuous endpoints, logistic linear and logistic Emax for binary endpoints, as well as performing simulation and visualization. Learn more about the workflow at <https://genentech.github.io/BayesERbook/>.

Authors:Kenta Yoshida [aut, cre], François Mercier [aut], Danielle Navarro [aut], Genentech, Inc. [cph]

BayesERtools_0.2.7.tar.gz
BayesERtools_0.2.7.tar.gz(r-4.7-any)BayesERtools_0.2.7.tar.gz(r-4.6-any)
BayesERtools_0.2.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BayesERtools/json (API)

# Install 'BayesERtools' in R:

install.packages('BayesERtools', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/genentech/bayesertools/issues

Pkgdown/docs site:https://genentech.github.io

Datasets:

d_sim_binom_cov - Sample simulated data for exposure-response with binary endpoint.
d_sim_binom_cov_hgly2 - Sample simulated data for exposure-response with binary endpoint.
d_sim_emax - Sample simulated data for Emax exposure-response models with covariates.
d_sim_lin - Sample simulated data for exposure-response with continuous endpoint using linear model.
d_sim_placebo - Sample simulated data for Emax exposure-response models with covariates and placebo

On CRAN:

4.04 score 55 scripts 638 downloads 50 exports 128 dependencies

Last updated from:d18c86ed2a. Checks:4 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	OK	360
source / vignettes	OK	297
linux-release-x86_64	OK	353
wasm-release	OK	220

Exports:.dev_ermod_refmodel .select_cov_projpred as_draws as_draws_array as_draws_df as_draws_list as_draws_matrix as_draws_rvars build_spec_coveff build_spec_coveff_one_variable calc_ersim_med_qi combine_er_components dev_ermod_bin dev_ermod_bin_cov_sel dev_ermod_bin_emax dev_ermod_bin_emax_exp_sel dev_ermod_bin_exp_sel dev_ermod_emax dev_ermod_emax_exp_sel dev_ermod_lin dev_ermod_lin_cov_sel dev_ermod_lin_exp_sel eval_ermod extract_coef_exp_ci extract_data extract_exp_sel_comp extract_exp_sel_list_model extract_kfold_loo extract_mod extract_var_cov extract_var_exposure extract_var_resp extract_var_selected kfold loo plot_coveff plot_er plot_er_exp_sel plot_er_gof plot_submod_performance plot_var_ranking print_coveff prior_summary replace_spec_coveff sim_coveff sim_er sim_er_curve sim_er_curve_marg sim_er_new_exp sim_er_new_exp_marg

Dependencies:abind backports base64enc bayesplot BH bigD bitops boot bslib cachem callr checkmate cli colourpicker commonmark cpp11 crosstalk curl desc digest distributional dplyr DT dygraphs evaluate farver fastmap fontawesome fs generics ggdist ggplot2 ggridges glue gridExtra gt gtable gtools highr htmltools htmlwidgets httpuv igraph inline isoband jquerylib jsonlite juicyjuice knitr labeling later lattice lazyeval lifecycle litedown lme4 loo magrittr markdown MASS Matrix matrixStats memoise mime miniUI minqa nlme nloptr numDeriv otel pillar pkgbuild pkgconfig plyr posterior processx promises ps purrr quadprog QuickJSR R6 rappdirs rbibutils RColorBrewer Rcpp RcppEigen RcppParallel Rdpack reactable reactR reformulas reshape2 rlang rmarkdown rstan rstanarm rstanemax rstantools S7 sass scales shiny shinyjs shinystan shinythemes sourcetools StanHeaders stringi stringr survival tensorA threejs tibble tidyr tidyselect tinytex utf8 V8 vctrs viridisLite withr xfun xml2 xtable xts yaml zoo

Overview of the package

0. Analysis workflow & supported model types | 1. ER model development | 2. Simulation from developed ER model | 3. Plot simulated ER curve | Acknowledgement

Rendered fromoverview_of_the_package.Rmdusingknitr::rmarkdown

Last update: 2026-06-13
Started: 2025-02-10

Help page	Topics
Transform to 'draws' objects	as_draws as_draws.ermod as_draws_array as_draws_array.ermod as_draws_df as_draws_df.ermod as_draws_list as_draws_list.ermod as_draws_matrix as_draws_matrix.ermod as_draws_rvars as_draws_rvars.ermod
Build specifications for covariate effect simulation/visualization	build_spec_coveff
Calculate median and quantile intervals from ersim object	calc_ersim_med_qi
Combine ER plot components	combine_er_components
Sample simulated data for exposure-response with binary endpoint.	d_sim_binom_cov d_sim_binom_cov_hgly2
Sample simulated data for Emax exposure-response models with covariates.	d_sim_emax
Sample simulated data for exposure-response with continuous endpoint using linear model.	d_sim_lin
Sample simulated data for Emax exposure-response models with covariates and placebo	d_sim_placebo
Develop linear ER model for binary or continuous endpoint	dev_ermod_bin dev_ermod_lin
Perform covariate selection for linear ER model	dev_ermod_bin_cov_sel dev_ermod_lin_cov_sel
Exposure metrics selection for linear ER models	dev_ermod_bin_exp_sel dev_ermod_lin_exp_sel
Develop Emax model for continuous and binary endpoint	dev_ermod_bin_emax dev_ermod_emax
Exposure metrics selection for Emax models	dev_ermod_bin_emax_exp_sel dev_ermod_emax_exp_sel
Customize specifications for covariate effect simulations/visualizations	build_spec_coveff_one_variable edit_spec_coveff replace_spec_coveff
S3 methods for the classes 'ermod_bin_cov_sel'	ermod_cov_sel_method plot.ermod_cov_sel print.ermod_cov_sel
S3 methods for the classes 'ermod_exp_sel'	ermod_exp_sel_method plot.ermod_exp_sel print.ermod_exp_sel
S3 methods for the classes 'ermod_*'	coef.ermod ermod_method plot.ermod_bin print.ermod summary.ermod
S3 methods for the classes ersim_* and ersim_med_qi_*	ersim_method plot.ersim plot.ersim_med_qi
Evaluate exposure-response model prediction performance	eval_ermod
Extract credible interval of the exposure coefficient	extract_coef_exp_ci
Extract elements from S3 objects	extract_data extract_exp_sel_comp extract_exp_sel_list_model extract_method extract_mod extract_var_cov extract_var_exposure extract_var_resp extract_var_selected
Run k-fold cross-validation	extract_kfold_loo kfold kfold.ermod
Efficient approximate leave-one-out cross-validation (LOO)	loo loo.ermod loo.ermod_bin_emax loo.ermod_emax
Probability of Direction (pd)	p_direction p_direction.ermod_bin
Plot variable selection performance	plot_cov_sel plot_submod_performance plot_var_ranking
Visualize the covariate effects for ER model	plot_coveff plot_coveff.coveffsim plot_coveff.ermod
Plot ER model simulations	plot_er plot_er.ermod plot_er.ersim plot_er.ersim_med_qi
Plot exposure metric selection comparison	plot_er_exp_sel
Default GOF plot for ER model	plot_er_gof
Format the covariate effect simulation results for printing	print_coveff
Summarize the priors used for linear or linear logistic regression models	prior_summary prior_summary.ermod
Perform simulation of covariate effects for ER model	sim_coveff
Simulate from ER model	sim_er
Simulate from ER model at specified exposure values	sim_er_curve sim_er_new_exp
Calculate marginal expected response for specified exposure values	sim_er_curve_marg sim_er_new_exp_marg

Package: BayesERtools 0.2.7

BayesERtools: Bayesian Exposure-Response Analysis Tools

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Help Manual

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