R Observatory: Metrics for BayesianDEB version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BayesianDEB

0.2.1Package record

Bayesian Dynamic Energy Budget Modelling

0packages depend

2.2Kdownloads / year

80.6%test coverage

13/13flavors OK

Overview

About

Maintained by Branimir K. HackenbergerCRAN page ↗GitHub ↗Issues ↗

Provides a Bayesian framework for Dynamic Energy Budget (DEB) modelling via 'Stan'. Implements the standard DEB model of Kooijman (2010, doi:10.1017/CBO9780511805400) as a state-space model with Hamiltonian Monte Carlo inference (Carpenter et al., 2017, doi:10.18637/jss.v076.i01). Includes individual-level growth models, growth-reproduction models, hierarchical multi-individual models with partial pooling, and toxicokinetic-toxicodynamic (TKTD) models for ecotoxicology following the DEBtox framework (Jager et al., 2006, doi:10.1007/s10646-006-0060-x). Supports prior specification from biological knowledge, convergence diagnostics (Vehtari et al., 2021, doi:10.1214/20-BA1221), posterior predictive checks, derived quantity estimation, and visualisation via 'ggplot2'.

Changes in 0.2.1

Second-round JSS revision: diagnostics display polish, fully runnable

(toolchain-gated) examples, and replication / manuscript reproducibility

fixes.

print.bdeb_diagnostics() now prints a compact table by default, hiding the per-time-point latent states (x_sol[i,j], L_hat[i]); the new full = TRUE argument restores the complete table (also available via summary(x)$table).
plot.bdeb_diagnostics() likewise hides the per-time-point latent states by default for a shorter, more readable R-hat / ESS plot; the new full = TRUE argument plots every monitored quantity. The subtitle notes how many latent rows were hidden.
bdeb_diagnose() and the bdeb_diagnostics print/summary/plot methods, plus bdeb_loo(), bdeb_derived() and bdeb_summary(), moved their examples from \dontrun{} to a cmdstanr-gated \donttest{} block, so example() runs them when a CmdStan toolchain is available (mirroring bdeb_fit()).

Show all changes in 0.2.1Hide the rest of the changes in 0.2.1

plot_dose_response() now draws posterior-median EC50 (dashed red) and NEC (dotted green) reference lines, drops non-finite draws, and clips the view with coord_cartesian() so degenerate draws no longer appear as vertical artefacts.
Replication material: a single-command replicate_all.R reproduces every manuscript figure, table and printed number in ~1 min from cached draws; every manuscript code listing is now executed and printed; outputs use a fixed seed for bit-identical reproduction; and the README maps every figure to the script that produces it.

From NEWS.md in the release

Install

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

install.packages("BayesianDEB", 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("sciom/BayesianDEB")

Development version from sciom/BayesianDEB. 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-bayesiandeb

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-BayesianDEB

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-BayesianDEB

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK11 OK2026-04-25
NOTE6 OK, 2 NOTE2026-04-22

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.1

READMEYes · 875 wordsVignettesYes · 2 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 0.2.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Description cites a JSS article

Help pages: 65 (12 internal)includes a package overview page
Examples that run: 48%23 run in a plain check · 25 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 32%

Vignettes (2)

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #17,088 · ~6/day · ~182/mo

Releases R versions

Daily download trend is not available in this view yet.

24330 days

74890 days

2.2K1 year

Compare downloads with other packages →

Also on95 r2u35 autocran

How downloads are counted

Repository

sciom/bayesiandeb ↗Organization: sciom

0Stars

1Forks

0Open issues

0Open PRs

4Releases

42Commits

1Commit identities

42 commits · Last activity 2026-06-29

Responsiveness

not measured

Forks over time

2026-05-28 · 12026-07-07 · 1

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/sciom/bayesiandeb on 2026-10-22.

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (2)

CITATION.cffZenodo

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing BayesianDEB adds 45 packages (25 with compiled code, 42 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bayesplot 5.0 MB.

Depends (1)

R >= 4.1.0

Imports (8)

posterior rlang cli ggplot2 bayesplot deSolvestatsutils

LinkingTo (0)

none

Suggests (10)

cmdstanr testthat loo digest dplyr tidyr gridExtra knitr rmarkdown withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Branimir K. Hackenberger

Author, Maintainer since 0.1.4 (2026)

Tamara Djerdj

Author

Domagoj K. Hackenberger

Author

Releases (2)

Pick two releases to compare their code metrics.

0.2.1Latest
record
2026-06-17 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.1.4
record
2026-04-21
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-21
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Additional repositories: stan-dev.r-universe.dev
Minimum R: ≥ 4.1.0
Bundled data: 4.9 KB / 5 files
Download size: 2.0 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("BayesianDEB")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.5281/zenodo.19443804, 10.1017/cbo9780511805400.

The repository also keeps a CITATION.cff.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for BayesianDEB version 0.2.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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