Package: BayesianDEB 0.2.1

Branimir K. Hackenberger

BayesianDEB: Bayesian Dynamic Energy Budget Modelling

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'.

Authors:Branimir K. Hackenberger [aut, cre], Tamara Djerdj [aut], Domagoj K. Hackenberger [aut]

BayesianDEB_0.2.1.tar.gz
BayesianDEB_0.2.1.zip(r-4.7)BayesianDEB_0.2.1.zip(r-4.6)BayesianDEB_0.2.1.zip(r-4.5)
BayesianDEB_0.2.1.tgz(r-4.6-any)BayesianDEB_0.2.1.tgz(r-4.5-any)
BayesianDEB_0.2.1.tar.gz(r-4.7-any)BayesianDEB_0.2.1.tar.gz(r-4.6-any)
BayesianDEB_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BayesianDEB/json (API)

# Install 'BayesianDEB' in R:
install.packages('BayesianDEB', repos = c('https://sciom.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sciom/bayesiandeb/issues

Datasets:

On CRAN:

Conda:

4.82 score 11 scripts 441 downloads 32 exports 43 dependencies

Last updated from:06cffd795c. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK190
source / vignettesOK254
linux-release-x86_64OK190
macos-release-arm64OK128
macos-oldrel-arm64OK151
windows-develOK114
windows-releaseOK126
windows-oldrelOK130
wasm-releaseOK168

Exports:arrheniusbdeb_databdeb_derivedbdeb_diagnosebdeb_ec50bdeb_fitbdeb_loobdeb_modelbdeb_ppcbdeb_predictbdeb_prior_predictivebdeb_session_infobdeb_summarybdeb_toxdeb_fluxesdeb_simulatedebtox_simulateobs_lognormalobs_negbinomobs_normalobs_poissonobs_student_tplot_dose_responseprior_betaprior_defaultprior_exponentialprior_halfcauchyprior_halfnormalprior_lognormalprior_normalprior_speciesrepro_to_intervals

Dependencies:abindbackportsbayesplotcheckmateclicpp11deSolvedistributionaldplyrfarvergenericsggplot2ggridgesgluegtableisobandlabelinglifecyclemagrittrmatrixStatsnumDerivpillarpkgconfigplyrposteriorpurrrR6RColorBrewerRcppreshape2rlangS7scalesstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr

Bayesian DEB Modelling of Eisenia fetida Growth and DEBtox Analysis
Introduction | Prerequisites | Part 1: Eisenia fetida Growth | Data description | Individual model: single organism | Step 1: Prepare data | Step 2: Specify model and priors | Step 3: Fit via MCMC | Step 4: Convergence diagnostics | Step 5: Posterior summary | Step 6: Posterior predictive check | Step 7: Derived quantities | Step 8: Scenario analysis — reduced food | Hierarchical model: 21 individuals | Model structure | Prepare and specify | Fit | Diagnostics | Population-level results | Shrinkage of individual estimates | Prediction for a new individual | Individual vs hierarchical: comparison | Part 2: DEBtox Analysis | Background | Data exploration | Data preparation | Model specification | Parameter estimates | EC~50~ and NEC | Dose-response curve | Prior sensitivity analysis | Part 3: Practical Tools | Structural vs physical length | Prior predictive check | Observation model selection | Temperature correction | Energy flux calculator | Converting cumulative reproduction data | Validation Against Published DEB Parameters | Summary | References | Session info
Rendered fromcase_study_eisenia_folsomia.Rmdusingknitr::rmarkdown

Last update: 2026-05-12
Started: 2026-04-06

Getting Started with BayesianDEB
Overview | Installation | Example: Individual Growth Model | 1. Prepare Data | 2. Specify Model | 3. Fit Model | 4. Diagnostics | 5. Posterior Predictive Checks | 6. Derived Quantities | 7. Trajectory Plot | Example: Hierarchical Model (Multiple Individuals) | Example: DEBtox Model | Prior Specification | Observation Models | Further Reading
Rendered fromgetting_started.Rmdusingknitr::rmarkdown

Last update: 2026-05-12
Started: 2026-04-06

Readme and manuals

Help Manual

Help pageTopics
Arrhenius Temperature Correctionarrhenius
Prepare Data for BDEB Modelsbdeb_data
Compute Derived Biological Quantities from the Posteriorbdeb_derived bdeb_derived.bdeb_fit bdeb_derived.default
MCMC Convergence Diagnosticsbdeb_diagnose
Extract EC50 and NEC from a DEBtox Fitbdeb_ec50
Fit a BDEB Model via Hamiltonian Monte Carlobdeb_fit
LOO Cross-Validation for Model Comparisonbdeb_loo
Specify a BDEB Modelbdeb_model
Plot Methods for BDEB Objectsbdeb_plots
Posterior Predictive Checks for BDEB Modelsbdeb_ppc
Prior Predictive Checkbdeb_prior_predictive
Methods for 'bdeb_prior' Objectsbdeb_prior-methods plot.bdeb_prior print.bdeb_prior print.summary.bdeb_prior summary.bdeb_prior
Reproducibility Reportbdeb_session_info
DEBtox Model Specificationbdeb_tox
Extract Point Estimates from a BDEB Fitcoef.bdeb_fit
Posterior Credible Intervals for BDEB Model Parametersconfint.bdeb_fit
Compute DEB Energy Fluxesdeb_fluxes
Simulate DEB Growth Trajectorydeb_simulate
Simulated DEBtox Growth Datadebtox_growth
Simulate DEBtox Growth Under Toxicant Exposuredebtox_simulate
Eisenia andrei Cadmium Toxicity Data (Van Gestel 1991)eisenia_cd
Simulated Eisenia fetida Growth Dataeisenia_growth
Eisenia fetida Growth Data (Neuhauser 1980)eisenia_neuhauser
Fitted Values from a BDEB Fitfitted.bdeb_fit
Simulated Folsomia candida Reproduction Datafolsomia_repro
Log-Likelihood of a BDEB FitlogLik.bdeb_fit
Number of Observations Used in a BDEB Fitnobs.bdeb_fit
Observation Model Specificationsobservation_models obs_lognormal obs_negbinom obs_normal obs_poisson obs_student_t
Plot DEBtox Dose-Responseplot_dose_response
Plot a BDEB Data Objectplot.bdeb_data
Plot Convergence Diagnosticsplot.bdeb_diagnostics
Plot a BDEB Fitplot.bdeb_fit
Plot a BDEB Model Specificationplot.bdeb_model
Plot Posterior Predictive Checksplot.bdeb_ppc
Plot Posterior Predictive Trajectoriesplot.bdeb_prediction
Predict from a BDEB Fitbdeb_predict predict.bdeb_fit
Print a BDEB Data Objectprint.bdeb_data
Print a BDEB Diagnostics Reportprint.bdeb_diagnostics
Print a BDEB Fitprint.bdeb_fit
Print a BDEB Model Specificationprint.bdeb_model
Print a BDEB Posterior Predictive Checkprint.bdeb_ppc
Print a BDEB Predictionprint.bdeb_prediction
Default Priors for DEB Parametersprior_default
Species-Specific Priors from the AmP Collectionprior_species
Prior Distribution Specifications for BDEB Modelspriors prior_beta prior_exponential prior_halfcauchy prior_halfnormal prior_lognormal prior_normal
Convert Cumulative Reproduction to Intervalsrepro_to_intervals
Residuals from a BDEB Fitresiduals.bdeb_fit
Summary of a BDEB Data Objectprint.summary.bdeb_data summary.bdeb_data
Compact Summary of a BDEB Diagnostics Reportsummary.bdeb_diagnostics
Posterior Summary for a BDEB Fitsummary.bdeb_fit
Summary of a BDEB Model Specificationprint.summary.bdeb_model summary.bdeb_model
Tabulate Posterior Predictive Quantilessummary.bdeb_prediction
Posterior Covariance Matrix of BDEB Model Parametersvcov.bdeb_fit