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BayesERtools

Bayesian Exposure-Response Analysis Tools

v0.2.6 · Jun 12, 2026 · Apache License 2.0
CRAN GitHub Mirror

Description

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/>.

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CRAN Check Status

6 ERROR
7 OK
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r-devel-linux-x86_64-debian-clang OK
r-devel-linux-x86_64-debian-gcc ERROR
r-devel-linux-x86_64-fedora-clang ERROR
r-devel-linux-x86_64-fedora-gcc ERROR
r-devel-windows-x86_64 ERROR
r-oldrel-macos-arm64 OK
r-oldrel-macos-x86_64 OK
r-oldrel-windows-x86_64 ERROR
r-patched-linux-x86_64 OK
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r-release-macos-x86_64 OK
r-release-windows-x86_64 OK
Check details (6 non-OK)
ERROR r-devel-linux-x86_64-debian-gcc

tests

Running ‘testthat.R’ [112s/143s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(BayesERtools)
  > 
  > test_check("BayesERtools")
  Loading required namespace: projpred
  Saving _problems/test-dev_ermod_lin-229.R
  
  Diagnostic flags present.
  See ?`loo-glossary` (sections `diag_diff` and `diag_elpd`)
  or https://mc-stan.org/loo/reference/loo-glossary.html.
  Loading required package: bayestestR
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dev_ermod_emax.R:150:5'): plot_e
...[truncated]...
`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1` and `2` don't exist.
  ── Error ('test-dev_ermod_lin.R:229:5'): Exposure metrics selection ────────────
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  ── Error ('test-dev_ermod_lin.R:427:5'): plot.ermod_exp_sel calls plot_er_exp_sel ──
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-linux-x86_64-fedora-clang

tests

Running ‘testthat.R’ [291s/379s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(BayesERtools)
  > 
  > test_check("BayesERtools")
  Loading required namespace: projpred
  Saving _problems/test-dev_ermod_lin-229.R
  
  Diagnostic flags present.
  See ?`loo-glossary` (sections `diag_diff` and `diag_elpd`)
  or https://mc-stan.org/loo/reference/loo-glossary.html.
  Loading required package: bayestestR
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dev_ermod_emax.R:150:5'): plot_e
...[truncated]...
`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1` and `2` don't exist.
  ── Error ('test-dev_ermod_lin.R:229:5'): Exposure metrics selection ────────────
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  ── Error ('test-dev_ermod_lin.R:427:5'): plot.ermod_exp_sel calls plot_er_exp_sel ──
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-linux-x86_64-fedora-gcc

tests

Running ‘testthat.R’ [307s/396s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(BayesERtools)
  > 
  > test_check("BayesERtools")
  Loading required namespace: projpred
  Saving _problems/test-dev_ermod_lin-229.R
  
  Diagnostic flags present.
  See ?`loo-glossary` (sections `diag_diff` and `diag_elpd`)
  or https://mc-stan.org/loo/reference/loo-glossary.html.
  Loading required package: bayestestR
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dev_ermod_emax.R:150:5'): plot_e
...[truncated]...
`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1` and `2` don't exist.
  ── Error ('test-dev_ermod_lin.R:229:5'): Exposure metrics selection ────────────
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  ── Error ('test-dev_ermod_lin.R:427:5'): plot.ermod_exp_sel calls plot_er_exp_sel ──
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-windows-x86_64

tests

Running 'testthat.R' [181s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(BayesERtools)
  > 
  > test_check("BayesERtools")
  Loading required namespace: projpred
  Saving _problems/test-dev_ermod_lin-229.R
  
  Diagnostic flags present.
  See ?`loo-glossary` (sections `diag_diff` and `diag_elpd`)
  or https://mc-stan.org/loo/reference/loo-glossary.html.
  Loading required package: bayestestR
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dev_ermod_emax.R:150:5'): plot_ermod 
...[truncated]...
`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1` and `2` don't exist.
  ── Error ('test-dev_ermod_lin.R:229:5'): Exposure metrics selection ────────────
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  ── Error ('test-dev_ermod_lin.R:427:5'): plot.ermod_exp_sel calls plot_er_exp_sel ──
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-oldrel-windows-x86_64

tests

Running 'testthat.R' [242s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(BayesERtools)
  > 
  > test_check("BayesERtools")
  Loading required namespace: projpred
  Saving _problems/test-dev_ermod_lin-229.R
  
  Diagnostic flags present.
  See ?`loo-glossary` (sections `diag_diff` and `diag_elpd`)
  or https://mc-stan.org/loo/reference/loo-glossary.html.
  Loading required package: bayestestR
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dev_ermod_emax.R:150:5'): plot_ermod 
...[truncated]...
`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1` and `2` don't exist.
  ── Error ('test-dev_ermod_lin.R:229:5'): Exposure metrics selection ────────────
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  ── Error ('test-dev_ermod_lin.R:427:5'): plot.ermod_exp_sel calls plot_er_exp_sel ──
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-release-linux-x86_64

tests

Running ‘testthat.R’ [171s/218s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(BayesERtools)
  > 
  > test_check("BayesERtools")
  Loading required namespace: projpred
  Saving _problems/test-dev_ermod_lin-229.R
  
  Diagnostic flags present.
  See ?`loo-glossary` (sections `diag_diff` and `diag_elpd`)
  or https://mc-stan.org/loo/reference/loo-glossary.html.
  Loading required package: bayestestR
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dev_ermod_emax.R:150:5'): plot_e
...[truncated]...
`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1` and `2` don't exist.
  ── Error ('test-dev_ermod_lin.R:229:5'): Exposure metrics selection ────────────
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  ── Error ('test-dev_ermod_lin.R:427:5'): plot.ermod_exp_sel calls plot_er_exp_sel ──
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  Error:
  ! Test failures.
  Execution halted

Additional Issues

donttest Details →

Check History

ERROR 10 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Jun 27, 2026
ERROR r-devel-linux-x86_64-debian-gcc

tests

Running ‘testthat.R’ [108s/129s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additiona
...[truncated]...
dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-linux-x86_64-fedora-clang

tests

Running ‘testthat.R’ [291s/379s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additiona
...[truncated]...
dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-devel-linux-x86_64-fedora-gcc

tests

Running ‘testthat.R’ [307s/396s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additiona
...[truncated]...
dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ]
  Error:
  ! Test failures.
  Execution halted
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
ERROR r-devel-linux-x86_64-debian-gcc

package dependencies

Package required but not available: ‘rstanarm’

Packages suggested but not available for checking: 'xgxr', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

Dependency Network

Dependencies Reverse dependencies dplyr tidyr purrr ggplot2 gt cli rlang rstanarm rstanemax rstantools loo ggdist posterior BayesERtools

Version History

8 tracked
updated 0.2.6 ← 0.2.5 diff Jun 13, 2026
updated 0.2.5 ← 0.2.4 diff Apr 23, 2026
new 0.2.4 Mar 10, 2026
updated 0.2.4 ← 0.2.3 diff Oct 1, 2025
updated 0.2.3 ← 0.2.2 diff Jun 15, 2025
updated 0.2.2 ← 0.2.1 diff Jun 5, 2025
updated 0.2.1 ← 0.2.0 diff Feb 11, 2025
new 0.2.0 Feb 9, 2025