bayesnec

2.1.3.1

A Bayesian No-Effect- Concentration (NEC) Algorithm

0packages depend

4.9Kdownloads / year

53.9%test coverage

12/13checks pass

Overview

About

Maintained by Rebecca FisherFirst published 2021-07-0215 releasesCRAN page ↗GitHub ↗

Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)doi:10.18637/jss.v080.i01; Burkner (2018)doi:10.32614/RJ-2018-017; Carpenter 'et al.' (2017)doi:10.18637/jss.v076.i01 to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)doi:10.1016/j.ecoenv.2009.09.012), 'NSEC' (see Fisher and Fox (2023)doi:10.1002/etc.5610), and 'N(S)EC (see Fisher et al. 2023doi:10.1002/ieam.4809). A full description of this package can be found in Fisher 'et al.' (2024)doi:10.18637/jss.v110.i05. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)https://CRAN.R-project.org/package=R2jags; Fisher et al. (2020)doi:10.5281/ZENODO.3966864).

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("bayesnec", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("open-aims/bayesnec")

Development version from open-aims/bayesnec. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bayesnec

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-bayesnec

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-bayesnec

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 7.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.20

53.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 207 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 32%
Documented parameters: 99%
Return-value docs: 100%
References docs: 21%

Downloads

4.9K

CRAN downloads in the past year

Rank #9,728 · ~13/day · ~407/mo

Releases R versions

Daily download trend is not available in this view yet.

36830 days

1.1K90 days

4.9K1 year

Compare downloads with other packages →

Also on254 r2u4 autocran21 c2d4u

Repository

GitHub ↗ open-aims/bayesnec

15Stars

8Forks

29Open issues

4Open PRs

1Releases

1,187Commits

23Contributors

concentration-responseno-effect-concentrationthreshold-derivationecotoxicologytoxicologynon-linear-decaybayesian-inference

1,187 commits · Last activity 2026-07-31 · 0% stars, 30d

Stars over time

2025-03-02 · 132026-07-07 · 15

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/open-aims/bayesnec on 2026-07-31.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Coverage (1)

Codecov

Show all practices

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.1brms ggplot2

Imports (10)

formula.tools loo dplyr tidyr purrr tibble tidyselect evaluate rlang chk

LinkingTo (0)

none

Suggests (4)

rstan knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Rebecca Fisher

Author, Maintainer

Authors (4)

Rebecca Fisher

Author, Maintainer

Diego R. Barneche

Author · added in 2.1.3.0

David R. Fox

Author · added in 2.1.3.0

Gerard F. Ricardo

Author · added in 2.1.3.0

Listed in earlier versions (3)

Diego Barneche

no longer listed · 1.0.1 to 2.1.2.0

David Fox

no longer listed · 1.0.1 to 2.1.2.0

Gerard Ricardo

no longer listed · 1.0.1 to 2.1.2.0

Package Timeline

15 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.1.3.1Latest
2025-08-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
2.1.3.0
2024-08-19 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.1.2.0
2024-03-28 · diff ↗
2.1.1.0
2023-09-26 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.0.3
2023-03-29 · diff ↗
2.1.0.2
2023-02-21 · diff ↗
2.1.0.1
2023-02-07 · diff ↗
2.1.0.0
2022-12-15 · diff ↗
2.0.2.5
2022-10-31 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.0.2.4
2022-04-21 · diff ↗
2.0.2.3
2022-03-28 · diff ↗

Show 5 earlier events

2.0.2
2021-10-17 · diff ↗
2.0.1
2021-09-20 · diff ↗
2.0
2021-09-16 · diff ↗
1.0.1
2021-07-02
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-02
Total releases: 15 / 5 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.1
Bundled data: 3.1 MB / 3 files
Download size: 4.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Analysis of Pharmacokinetic Data

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