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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'.
| Version: | 0.1.4 |
| Depends: | R (≥ 4.1.0) |
| Imports: | posterior (≥ 1.5.0), rlang (≥ 1.1.0), cli (≥ 3.6.0), ggplot2 (≥ 3.4.0), bayesplot (≥ 1.10.0), deSolve (≥ 1.40), stats, utils |
| Suggests: | cmdstanr (≥ 0.8.0), testthat (≥ 3.0.0), loo (≥ 2.6.0), digest, dplyr (≥ 1.1.0), tidyr (≥ 1.3.0), knitr, rmarkdown, withr |
| Published: | 2026-04-21 |
| DOI: | 10.32614/CRAN.package.BayesianDEB |
| Author: | Branimir K. Hackenberger [aut, cre], Tamara Djerdj [aut], Domagoj K. Hackenberger [aut] |
| Maintainer: | Branimir K. Hackenberger <branimir at sciom.hr> |
| BugReports: | https://github.com/sciom/BayesianDEB/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/sciom/BayesianDEB |
| NeedsCompilation: | no |
| SystemRequirements: | CmdStan (https://mc-stan.org/users/interfaces/cmdstan) |
| Additional_repositories: | https://stan-dev.r-universe.dev |
| Citation: | BayesianDEB citation info |
| Materials: | README, NEWS |
| CRAN checks: | BayesianDEB results |
| Reference manual: | BayesianDEB.html , BayesianDEB.pdf |
| Vignettes: |
Bayesian DEB Modelling of Eisenia fetida Growth and DEBtox Analysis (source, R code) Getting Started with BayesianDEB (source, R code) |
| Package source: | BayesianDEB_0.1.4.tar.gz |
| Windows binaries: | r-release: BayesianDEB_0.1.4.zip, r-oldrel: BayesianDEB_0.1.4.zip |
| macOS binaries: | r-release (arm64): BayesianDEB_0.1.4.tgz, r-oldrel (arm64): BayesianDEB_0.1.4.tgz, r-release (x86_64): BayesianDEB_0.1.4.tgz, r-oldrel (x86_64): BayesianDEB_0.1.4.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.