BayesERbook: Exposure-response analysis with Bayesian approaches

Authors

Kenta Yoshida

Danielle Navarro

François Mercier

Published

2025-06-17

Welcome

This book provides examples of exposure-response analysis with Bayesian methods.

Install necessary packages

The examples utilizes BayesERtools package.

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

You can install the package as follows:

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

Quick Example

library(BayesERtools)
library(dplyr)
ggplot2::theme_set(ggplot2::theme_bw(base_size = 12))

# Data
data(d_sim_binom_cov)
df_er_ae_hgly2 <- 
  d_sim_binom_cov |> 
  mutate(AUCss_1000 = AUCss / 1000) |> 
  filter(AETYPE == "hgly2")

# Fit a model
ermod <- dev_ermod_bin(
  data = df_er_ae_hgly2,
  var_resp = "AEFLAG",
  var_exposure = "AUCss_1000"
)

# Goodness-of-fit plot
plot_er_gof(ermod, var_group = "Dose_mg", show_coef_exp = TRUE) *
  xgxr::xgx_scale_x_log10(guide = ggplot2::guide_axis(minor.ticks = TRUE))

Model types supported by `BayesERtools`

	Binary endpoint		Continuous endpoint
	Linear (logit)	E_max (logit)	Linear	E_max
backend	`rstanarm`	`rstanemax`	`rstanarm`	`rstanemax`
reference	🔗	🔗	🔗	🔗
develop model	✅	✅	✅	✅
simulate & plot ER	✅	✅	✅	✅
exposure metrics selection	✅	✅	✅	✅
covariate selection	✅	❌	✅	❌
covariate forest plot	✅	❌	🟡	❌
✅ Available, 🟡 In plan/under development, ❌ Not in a current plan

Note for developer

Run usethis::use_tidy_style(strict = FALSE) before committing to ensure that the code is formatted appropriately.

Session info

Show the code

devtools::session_info()

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.3 (2024-02-29)
 os       macOS Sonoma 14.7.6
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Zurich
 date     2025-06-17
 pandoc   3.4 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package        * version    date (UTC) lib source
 abind            1.4-8      2024-09-12 [1] CRAN (R 4.3.3)
 arrayhelpers     1.1-0      2020-02-04 [1] CRAN (R 4.3.0)
 backports        1.5.0      2024-05-23 [1] CRAN (R 4.3.3)
 base64enc        0.1-3      2015-07-28 [1] RSPM (R 4.3.0)
 BayesERtools   * 0.2.2      2025-06-06 [1] CRAN (R 4.3.3)
 bayesplot      * 1.11.1     2024-02-15 [1] CRAN (R 4.3.1)
 boot             1.3-28.1   2022-11-22 [1] RSPM (R 4.3.0)
 cachem           1.1.0      2024-05-16 [1] CRAN (R 4.3.3)
 checkmate        2.3.2      2024-07-29 [1] CRAN (R 4.3.3)
 cli              3.6.4      2025-02-13 [1] CRAN (R 4.3.3)
 coda             0.19-4.1   2024-01-31 [1] CRAN (R 4.3.1)
 codetools        0.2-19     2023-02-01 [1] CRAN (R 4.3.3)
 colorspace       2.1-1      2024-07-26 [1] CRAN (R 4.3.3)
 colourpicker     1.3.0      2023-08-21 [1] CRAN (R 4.3.0)
 crosstalk        1.2.1      2023-11-23 [1] RSPM (R 4.3.0)
 curl             5.2.0      2023-12-08 [1] RSPM (R 4.3.0)
 devtools         2.4.5      2022-10-11 [1] CRAN (R 4.3.0)
 digest           0.6.37     2024-08-19 [1] CRAN (R 4.3.3)
 distributional   0.5.0      2024-09-17 [1] CRAN (R 4.3.3)
 dplyr          * 1.1.4      2023-11-17 [1] CRAN (R 4.3.1)
 DT               0.31       2023-12-09 [1] RSPM (R 4.3.0)
 dygraphs         1.1.1.6    2018-07-11 [1] CRAN (R 4.3.0)
 ellipsis         0.3.2      2021-04-29 [1] RSPM (R 4.3.0)
 evaluate         0.24.0     2024-06-10 [1] CRAN (R 4.3.3)
 farver           2.1.2      2024-05-13 [1] CRAN (R 4.3.3)
 fastmap          1.2.0      2024-05-15 [1] CRAN (R 4.3.3)
 forcats        * 1.0.0      2023-01-29 [1] RSPM (R 4.3.0)
 fs               1.6.5      2024-10-30 [1] CRAN (R 4.3.3)
 generics         0.1.3      2022-07-05 [1] RSPM (R 4.3.0)
 ggdist           3.3.2      2024-03-05 [1] CRAN (R 4.3.1)
 ggplot2        * 3.5.2.9001 2025-06-16 [1] Github (tidyverse/ggplot2@a2d0181)
 glue             1.8.0      2024-09-30 [1] CRAN (R 4.3.3)
 gridExtra        2.3        2017-09-09 [1] CRAN (R 4.3.0)
 gt             * 1.0.0      2025-04-05 [1] CRAN (R 4.3.3)
 gtable           0.3.6      2024-10-25 [1] CRAN (R 4.3.3)
 gtools           3.9.5      2023-11-20 [1] CRAN (R 4.3.1)
 here           * 1.0.1      2020-12-13 [1] RSPM (R 4.3.0)
 hms              1.1.3      2023-03-21 [1] RSPM (R 4.3.0)
 htmltools        0.5.8.1    2024-04-04 [1] CRAN (R 4.3.1)
 htmlwidgets      1.6.4      2023-12-06 [1] RSPM (R 4.3.0)
 httpuv           1.6.15     2024-03-26 [1] CRAN (R 4.3.1)
 igraph           2.0.3      2024-03-13 [1] CRAN (R 4.3.1)
 inline           0.3.19     2021-05-31 [1] CRAN (R 4.3.0)
 jsonlite         1.9.0      2025-02-19 [1] CRAN (R 4.3.3)
 knitr            1.48       2024-07-07 [1] CRAN (R 4.3.3)
 later            1.3.2      2023-12-06 [1] RSPM (R 4.3.0)
 lattice          0.22-5     2023-10-24 [1] CRAN (R 4.3.3)
 lifecycle        1.0.4      2023-11-07 [1] RSPM (R 4.3.0)
 lme4             1.1-35.5   2024-07-03 [1] CRAN (R 4.3.3)
 loo            * 2.7.0      2024-02-24 [1] CRAN (R 4.3.1)
 lubridate      * 1.9.4      2024-12-08 [1] CRAN (R 4.3.3)
 magrittr         2.0.3      2022-03-30 [1] RSPM (R 4.3.0)
 markdown         1.13       2024-06-04 [1] CRAN (R 4.3.3)
 MASS             7.3-60.0.1 2024-01-13 [1] RSPM (R 4.3.0)
 Matrix           1.6-5      2024-01-11 [1] CRAN (R 4.3.3)
 matrixStats      1.5.0      2025-01-07 [1] CRAN (R 4.3.3)
 memoise          2.0.1      2021-11-26 [1] RSPM (R 4.3.0)
 mime             0.12       2021-09-28 [1] RSPM (R 4.3.0)
 miniUI           0.1.1.1    2018-05-18 [1] RSPM (R 4.3.0)
 minqa            1.2.7      2024-05-20 [1] CRAN (R 4.3.3)
 nlme             3.1-164    2023-11-27 [1] CRAN (R 4.3.3)
 nloptr           2.1.1      2024-06-25 [1] CRAN (R 4.3.3)
 pillar           1.10.1     2025-01-07 [1] CRAN (R 4.3.3)
 pkgbuild         1.4.3      2023-12-10 [1] RSPM (R 4.3.0)
 pkgconfig        2.0.3      2019-09-22 [1] RSPM (R 4.3.0)
 pkgload          1.3.4      2024-01-16 [1] RSPM (R 4.3.0)
 plyr             1.8.9      2023-10-02 [1] RSPM (R 4.3.0)
 posterior      * 1.6.1      2025-02-27 [1] https://stan-dev.r-universe.dev (R 4.3.3)
 profvis          0.3.8      2023-05-02 [1] CRAN (R 4.3.0)
 promises         1.3.0      2024-04-05 [1] CRAN (R 4.3.1)
 purrr          * 1.0.4      2025-02-05 [1] CRAN (R 4.3.3)
 QuickJSR         1.3.1      2024-07-14 [1] CRAN (R 4.3.3)
 R6               2.6.1      2025-02-15 [1] CRAN (R 4.3.3)
 RColorBrewer     1.1-3      2022-04-03 [1] RSPM (R 4.3.0)
 Rcpp           * 1.0.13     2024-07-17 [1] CRAN (R 4.3.3)
 RcppParallel     5.1.9      2024-08-19 [1] CRAN (R 4.3.3)
 readr          * 2.1.5      2024-01-10 [1] RSPM (R 4.3.0)
 remotes          2.5.0      2024-03-17 [1] CRAN (R 4.3.1)
 reshape2         1.4.4      2020-04-09 [1] RSPM (R 4.3.0)
 rlang            1.1.5      2025-01-17 [1] CRAN (R 4.3.3)
 rmarkdown        2.27       2024-05-17 [1] CRAN (R 4.3.3)
 rprojroot        2.0.4      2023-11-05 [1] RSPM (R 4.3.0)
 rstan            2.32.6     2024-03-05 [1] CRAN (R 4.3.1)
 rstanarm         2.32.1     2024-01-18 [1] CRAN (R 4.3.1)
 rstanemax      * 0.1.9.1001 2025-02-17 [1] local
 rstantools       2.4.0      2024-01-31 [1] CRAN (R 4.3.1)
 rstudioapi       0.16.0     2024-03-24 [1] CRAN (R 4.3.1)
 S7               0.2.0      2024-11-07 [1] CRAN (R 4.3.3)
 scales           1.4.0      2025-04-24 [1] CRAN (R 4.3.3)
 sessioninfo      1.2.2      2021-12-06 [1] CRAN (R 4.3.0)
 shiny            1.9.1      2024-08-01 [1] CRAN (R 4.3.3)
 shinyjs          2.1.0      2021-12-23 [1] RSPM (R 4.3.0)
 shinystan        2.6.0      2022-03-03 [1] CRAN (R 4.3.0)
 shinythemes      1.2.0      2021-01-25 [1] CRAN (R 4.3.0)
 StanHeaders      2.32.9     2024-05-29 [1] CRAN (R 4.3.3)
 stringi          1.8.4      2024-05-06 [1] CRAN (R 4.3.1)
 stringr        * 1.5.1      2023-11-14 [1] RSPM (R 4.3.0)
 survival         3.7-0      2024-06-05 [1] CRAN (R 4.3.3)
 svUnit           1.0.6      2021-04-19 [1] CRAN (R 4.3.0)
 tensorA          0.36.2.1   2023-12-13 [1] CRAN (R 4.3.1)
 threejs          0.3.3      2020-01-21 [1] CRAN (R 4.3.0)
 tibble         * 3.2.1      2023-03-20 [1] RSPM (R 4.3.0)
 tidybayes      * 3.0.6      2023-08-12 [1] CRAN (R 4.3.0)
 tidyr          * 1.3.1      2024-01-24 [1] RSPM (R 4.3.0)
 tidyselect       1.2.1      2024-03-11 [1] CRAN (R 4.3.1)
 tidyverse      * 2.0.0      2023-02-22 [1] RSPM (R 4.3.0)
 timechange       0.3.0      2024-01-18 [1] RSPM (R 4.3.0)
 tzdb             0.4.0      2023-05-12 [1] RSPM (R 4.3.0)
 urlchecker       1.0.1      2021-11-30 [1] CRAN (R 4.3.0)
 usethis          2.2.3      2024-02-19 [1] CRAN (R 4.3.1)
 V8               5.0.0      2024-08-16 [1] CRAN (R 4.3.3)
 vctrs            0.6.5      2023-12-01 [1] RSPM (R 4.3.0)
 withr            3.0.2      2024-10-28 [1] CRAN (R 4.3.3)
 xfun             0.46       2024-07-18 [1] CRAN (R 4.3.3)
 xml2             1.3.6      2023-12-04 [1] RSPM (R 4.3.0)
 xtable           1.8-4      2019-04-21 [1] RSPM (R 4.3.0)
 xts              0.14.1     2024-10-15 [1] CRAN (R 4.3.3)
 yaml             2.3.10     2024-07-26 [1] CRAN (R 4.3.3)
 zoo              1.8-13     2025-02-22 [1] CRAN (R 4.3.3)

 [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

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