Package: BayesERtools 0.2.1.1001

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], Genentech, Inc. [cph]

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BayesERtools.pdf |BayesERtools.html✨
BayesERtools/json (API)
NEWS

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

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

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

On CRAN:

Conda:

4.78 score 2 stars 20 scripts 610 downloads 49 exports 134 dependencies

Last updated 1 months agofrom:c441db486a. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 23 2025
R-4.5-winOKMar 23 2025
R-4.5-macOKMar 23 2025
R-4.5-linuxOKFeb 21 2025
R-4.4-winOKMar 23 2025
R-4.4-macOKMar 23 2025
R-4.4-linuxOKMar 23 2025
R-4.3-winOKMar 23 2025
R-4.3-macOKMar 23 2025

Exports:.dev_ermod_refmodel.select_cov_projpredas_drawsas_draws_arrayas_draws_dfas_draws_listas_draws_matrixas_draws_rvarsbuild_spec_coveffbuild_spec_coveff_one_variablecalc_ersim_med_qidev_ermod_bindev_ermod_bin_cov_seldev_ermod_bin_emaxdev_ermod_bin_emax_exp_seldev_ermod_bin_exp_seldev_ermod_emaxdev_ermod_emax_exp_seldev_ermod_lindev_ermod_lin_cov_seldev_ermod_lin_exp_seleval_ermodextract_coef_exp_ciextract_dataextract_exp_sel_compextract_exp_sel_list_modelextract_kfold_looextract_modextract_var_covextract_var_exposureextract_var_respextract_var_selectedkfoldlooplot_coveffplot_erplot_er_exp_selplot_er_gofplot_submod_performanceplot_var_rankingprint_coveffprior_summaryreplace_spec_coveffsim_coveffsim_ersim_er_curvesim_er_curve_margsim_er_new_expsim_er_new_exp_marg

Dependencies:abindarrayhelpersbackportsbase64encbayesplotBHbigDbitopsbootbslibcachemcallrcheckmateclicodacolorspacecolourpickercommonmarkcpp11crayoncrosstalkcurldescdigestdistributionaldplyrDTdygraphsevaluatefansifarverfastmapfontawesomefsgenericsggdistggplot2ggridgesgluegridExtragtgtablegtoolshighrhtmltoolshtmlwidgetshttpuvigraphinlineisobandjquerylibjsonlitejuicyjuiceknitrlabelinglaterlatticelazyevallifecyclelme4loomagrittrmarkdownMASSMatrixmatrixStatsmemoisemgcvmimeminiUIminqamunsellnlmenloptrnumDerivpillarpkgbuildpkgconfigplyrposteriorprocessxpromisespspurrrquadprogQuickJSRR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRcppParallelRdpackreactablereactRreformulasreshape2rlangrmarkdownrstanrstanarmrstanemaxrstantoolssassscalesshinyshinyjsshinystanshinythemessourcetoolsStanHeadersstringistringrsurvivalsvUnittensorAthreejstibbletidybayestidyrtidyselecttinytexutf8V8vctrsviridisLitewithrxfunxml2xtablextsyamlzoo

Overview of the package

Rendered fromoverview_of_the_package.Rmdusingknitr::rmarkdownon Mar 23 2025.

Last update: 2025-02-16
Started: 2025-02-07

Readme and manuals

Help Manual

Help pageTopics
Transform to 'draws' objectsas_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/visualizationbuild_spec_coveff
Calculate median and quantile intervals from ersim objectcalc_ersim_med_qi
Sample simulated data for exposure-response with binary endpoint.d_sim_binom_cov d_sim_binom_cov_hgly2
Sample simulated data for exposure-response with continuous endpoint using linear model.d_sim_lin
Develop linear ER model for binary or continuous endpointdev_ermod_bin dev_ermod_lin
Perform covariate selection for linear ER modeldev_ermod_bin_cov_sel dev_ermod_lin_cov_sel
Exposure metrics selection for linear ER modelsdev_ermod_bin_exp_sel dev_ermod_lin_exp_sel
Develop Emax model for continuous and binary endpointdev_ermod_bin_emax dev_ermod_emax
Exposure metrics selection for Emax modelsdev_ermod_bin_emax_exp_sel dev_ermod_emax_exp_sel
Customize specifications for covariate effect simulations/visualizationsbuild_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 performanceeval_ermod
Extract credible interval of the exposure coefficientextract_coef_exp_ci
Extract elements from S3 objectsextract_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-validationextract_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 performanceplot_cov_sel plot_submod_performance plot_var_ranking
Visualize the covariate effects for ER modelplot_coveff plot_coveff.coveffsim plot_coveff.ermod
Plot ER model simulationsplot_er plot_er.ermod plot_er.ersim plot_er.ersim_med_qi
Plot exposure metric selection comparisonplot_er_exp_sel
Default GOF plot for ER modelplot_er_gof
Format the covariate effect simulation results for printingprint_coveff
Summarize the priors used for linear or linear logistic regression modelsprior_summary prior_summary.ermod
Perform simulation of covariate effects for ER modelsim_coveff
Simulate from ER modelsim_er
Simulate from ER model at specified exposure valuessim_er_curve sim_er_new_exp
Calculate marginal expected response for specified exposure valuessim_er_curve_marg sim_er_new_exp_marg