{
  "_id": "6ae0533c93f02b9aed9799fe",
  "Package": "BayesianDEB",
  "Title": "Bayesian Dynamic Energy Budget Modelling",
  "Version": "0.2.1",
  "Date": "2026-06-17",
  "Authors@R": "c(\nperson(\"Branimir K.\", \"Hackenberger\",\nemail = \"branimir@sciom.hr\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Tamara\", \"Djerdj\",\nrole = \"aut\"),\nperson(\"Domagoj K.\", \"Hackenberger\",\nrole = \"aut\")\n)",
  "Description": "Provides a Bayesian framework for Dynamic Energy Budget\n(DEB) modelling via 'Stan'. Implements the standard DEB model\nof Kooijman (2010, <doi:10.1017/CBO9780511805400>) as a\nstate-space model with Hamiltonian Monte Carlo inference\n(Carpenter et al., 2017, <doi:10.18637/jss.v076.i01>). Includes\nindividual-level growth models, growth-reproduction models,\nhierarchical multi-individual models with partial pooling, and\ntoxicokinetic-toxicodynamic (TKTD) models for ecotoxicology\nfollowing the DEBtox framework (Jager et al., 2006,\n<doi:10.1007/s10646-006-0060-x>). Supports prior specification\nfrom biological knowledge, convergence diagnostics (Vehtari et\nal., 2021, <doi:10.1214/20-BA1221>), posterior predictive\nchecks, derived quantity estimation, and visualisation via\n'ggplot2'.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/sciom/BayesianDEB",
  "BugReports": "https://github.com/sciom/BayesianDEB/issues",
  "Encoding": "UTF-8",
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  "Repository": "https://sciom.r-universe.dev",
  "Date/Publication": "2026-06-29 18:51:08 UTC",
  "RemoteUrl": "https://github.com/sciom/BayesianDEB",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-27 07:23:11 UTC",
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  "Author": "Branimir K. Hackenberger [aut, cre],\nTamara Djerdj [aut],\nDomagoj K. Hackenberger [aut]",
  "Maintainer": "Branimir K. Hackenberger <branimir@sciom.hr>",
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  "_expires": "2027-02-04T07:31:06.000Z",
  "_created": "2026-10-27T07:23:11.000Z",
  "_published": "2026-10-27T07:31:08.713Z",
  "_upstream": "https://github.com/sciom/BayesianDEB",
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  "_exports": [
    "arrhenius",
    "bdeb_data",
    "bdeb_derived",
    "bdeb_diagnose",
    "bdeb_ec50",
    "bdeb_fit",
    "bdeb_loo",
    "bdeb_model",
    "bdeb_ppc",
    "bdeb_predict",
    "bdeb_prior_predictive",
    "bdeb_session_info",
    "bdeb_summary",
    "bdeb_tox",
    "deb_fluxes",
    "deb_simulate",
    "debtox_simulate",
    "obs_lognormal",
    "obs_negbinom",
    "obs_normal",
    "obs_poisson",
    "obs_student_t",
    "plot_dose_response",
    "prior_beta",
    "prior_default",
    "prior_exponential",
    "prior_halfcauchy",
    "prior_halfnormal",
    "prior_lognormal",
    "prior_normal",
    "prior_species",
    "repro_to_intervals"
  ],
  "_datasets": [
    {
      "name": "debtox_growth",
      "title": "Simulated DEBtox Growth Data",
      "object": "debtox_growth",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "concentration",
        "time",
        "length"
      ],
      "rows": 280,
      "table": true,
      "tojson": true
    },
    {
      "name": "eisenia_cd",
      "title": "Eisenia andrei Cadmium Toxicity Data (Van Gestel 1991)",
      "object": "eisenia_cd",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "time",
        "length",
        "concentration"
      ],
      "rows": 35,
      "table": true,
      "tojson": true
    },
    {
      "name": "eisenia_growth",
      "title": "Simulated Eisenia fetida Growth Data",
      "object": "eisenia_growth",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "time",
        "length"
      ],
      "rows": 273,
      "table": true,
      "tojson": true
    },
    {
      "name": "eisenia_neuhauser",
      "title": "Eisenia fetida Growth Data (Neuhauser 1980)",
      "object": "eisenia_neuhauser",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "time",
        "length"
      ],
      "rows": 37,
      "table": true,
      "tojson": true
    },
    {
      "name": "folsomia_repro",
      "title": "Simulated Folsomia candida Reproduction Data",
      "object": "folsomia_repro",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "concentration",
        "t_start",
        "t_end",
        "count"
      ],
      "rows": 30,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "arrhenius",
      "title": "Arrhenius Temperature Correction",
      "topics": [
        "arrhenius"
      ]
    },
    {
      "page": "bdeb_data",
      "title": "Prepare Data for BDEB Models",
      "topics": [
        "bdeb_data"
      ]
    },
    {
      "page": "bdeb_derived",
      "title": "Compute Derived Biological Quantities from the Posterior",
      "topics": [
        "bdeb_derived",
        "bdeb_derived.bdeb_fit",
        "bdeb_derived.default"
      ]
    },
    {
      "page": "bdeb_diagnose",
      "title": "MCMC Convergence Diagnostics",
      "topics": [
        "bdeb_diagnose"
      ]
    },
    {
      "page": "bdeb_ec50",
      "title": "Extract EC50 and NEC from a DEBtox Fit",
      "topics": [
        "bdeb_ec50"
      ]
    },
    {
      "page": "bdeb_fit",
      "title": "Fit a BDEB Model via Hamiltonian Monte Carlo",
      "topics": [
        "bdeb_fit"
      ]
    },
    {
      "page": "bdeb_loo",
      "title": "LOO Cross-Validation for Model Comparison",
      "topics": [
        "bdeb_loo"
      ]
    },
    {
      "page": "bdeb_model",
      "title": "Specify a BDEB Model",
      "topics": [
        "bdeb_model"
      ]
    },
    {
      "page": "bdeb_plots",
      "title": "Plot Methods for BDEB Objects",
      "topics": [
        "bdeb_plots"
      ]
    },
    {
      "page": "bdeb_ppc",
      "title": "Posterior Predictive Checks for BDEB Models",
      "topics": [
        "bdeb_ppc"
      ]
    },
    {
      "page": "bdeb_prior_predictive",
      "title": "Prior Predictive Check",
      "topics": [
        "bdeb_prior_predictive"
      ]
    },
    {
      "page": "bdeb_prior-methods",
      "title": "Methods for 'bdeb_prior' Objects",
      "topics": [
        "bdeb_prior-methods",
        "plot.bdeb_prior",
        "print.bdeb_prior",
        "print.summary.bdeb_prior",
        "summary.bdeb_prior"
      ]
    },
    {
      "page": "bdeb_session_info",
      "title": "Reproducibility Report",
      "topics": [
        "bdeb_session_info"
      ]
    },
    {
      "page": "bdeb_tox",
      "title": "DEBtox Model Specification",
      "topics": [
        "bdeb_tox"
      ]
    },
    {
      "page": "coef.bdeb_fit",
      "title": "Extract Point Estimates from a BDEB Fit",
      "topics": [
        "coef.bdeb_fit"
      ]
    },
    {
      "page": "confint.bdeb_fit",
      "title": "Posterior Credible Intervals for BDEB Model Parameters",
      "topics": [
        "confint.bdeb_fit"
      ]
    },
    {
      "page": "deb_fluxes",
      "title": "Compute DEB Energy Fluxes",
      "topics": [
        "deb_fluxes"
      ]
    },
    {
      "page": "deb_simulate",
      "title": "Simulate DEB Growth Trajectory",
      "topics": [
        "deb_simulate"
      ]
    },
    {
      "page": "debtox_growth",
      "title": "Simulated DEBtox Growth Data",
      "topics": [
        "debtox_growth"
      ]
    },
    {
      "page": "debtox_simulate",
      "title": "Simulate DEBtox Growth Under Toxicant Exposure",
      "topics": [
        "debtox_simulate"
      ]
    },
    {
      "page": "eisenia_cd",
      "title": "Eisenia andrei Cadmium Toxicity Data (Van Gestel 1991)",
      "topics": [
        "eisenia_cd"
      ]
    },
    {
      "page": "eisenia_growth",
      "title": "Simulated Eisenia fetida Growth Data",
      "topics": [
        "eisenia_growth"
      ]
    },
    {
      "page": "eisenia_neuhauser",
      "title": "Eisenia fetida Growth Data (Neuhauser 1980)",
      "topics": [
        "eisenia_neuhauser"
      ]
    },
    {
      "page": "fitted.bdeb_fit",
      "title": "Fitted Values from a BDEB Fit",
      "topics": [
        "fitted.bdeb_fit"
      ]
    },
    {
      "page": "folsomia_repro",
      "title": "Simulated Folsomia candida Reproduction Data",
      "topics": [
        "folsomia_repro"
      ]
    },
    {
      "page": "logLik.bdeb_fit",
      "title": "Log-Likelihood of a BDEB Fit",
      "topics": [
        "logLik.bdeb_fit"
      ]
    },
    {
      "page": "nobs.bdeb_fit",
      "title": "Number of Observations Used in a BDEB Fit",
      "topics": [
        "nobs.bdeb_fit"
      ]
    },
    {
      "page": "observation_models",
      "title": "Observation Model Specifications",
      "topics": [
        "observation_models",
        "obs_lognormal",
        "obs_negbinom",
        "obs_normal",
        "obs_poisson",
        "obs_student_t"
      ]
    },
    {
      "page": "plot_dose_response",
      "title": "Plot DEBtox Dose-Response",
      "topics": [
        "plot_dose_response"
      ]
    },
    {
      "page": "plot.bdeb_data",
      "title": "Plot a BDEB Data Object",
      "topics": [
        "plot.bdeb_data"
      ]
    },
    {
      "page": "plot.bdeb_diagnostics",
      "title": "Plot Convergence Diagnostics",
      "topics": [
        "plot.bdeb_diagnostics"
      ]
    },
    {
      "page": "plot.bdeb_fit",
      "title": "Plot a BDEB Fit",
      "topics": [
        "plot.bdeb_fit"
      ]
    },
    {
      "page": "plot.bdeb_model",
      "title": "Plot a BDEB Model Specification",
      "topics": [
        "plot.bdeb_model"
      ]
    },
    {
      "page": "plot.bdeb_ppc",
      "title": "Plot Posterior Predictive Checks",
      "topics": [
        "plot.bdeb_ppc"
      ]
    },
    {
      "page": "plot.bdeb_prediction",
      "title": "Plot Posterior Predictive Trajectories",
      "topics": [
        "plot.bdeb_prediction"
      ]
    },
    {
      "page": "predict.bdeb_fit",
      "title": "Predict from a BDEB Fit",
      "topics": [
        "bdeb_predict",
        "predict.bdeb_fit"
      ]
    },
    {
      "page": "print.bdeb_data",
      "title": "Print a BDEB Data Object",
      "topics": [
        "print.bdeb_data"
      ]
    },
    {
      "page": "print.bdeb_diagnostics",
      "title": "Print a BDEB Diagnostics Report",
      "topics": [
        "print.bdeb_diagnostics"
      ]
    },
    {
      "page": "print.bdeb_fit",
      "title": "Print a BDEB Fit",
      "topics": [
        "print.bdeb_fit"
      ]
    },
    {
      "page": "print.bdeb_model",
      "title": "Print a BDEB Model Specification",
      "topics": [
        "print.bdeb_model"
      ]
    },
    {
      "page": "print.bdeb_ppc",
      "title": "Print a BDEB Posterior Predictive Check",
      "topics": [
        "print.bdeb_ppc"
      ]
    },
    {
      "page": "print.bdeb_prediction",
      "title": "Print a BDEB Prediction",
      "topics": [
        "print.bdeb_prediction"
      ]
    },
    {
      "page": "prior_default",
      "title": "Default Priors for DEB Parameters",
      "topics": [
        "prior_default"
      ]
    },
    {
      "page": "prior_species",
      "title": "Species-Specific Priors from the AmP Collection",
      "topics": [
        "prior_species"
      ]
    },
    {
      "page": "priors",
      "title": "Prior Distribution Specifications for BDEB Models",
      "topics": [
        "priors",
        "prior_beta",
        "prior_exponential",
        "prior_halfcauchy",
        "prior_halfnormal",
        "prior_lognormal",
        "prior_normal"
      ]
    },
    {
      "page": "repro_to_intervals",
      "title": "Convert Cumulative Reproduction to Intervals",
      "topics": [
        "repro_to_intervals"
      ]
    },
    {
      "page": "residuals.bdeb_fit",
      "title": "Residuals from a BDEB Fit",
      "topics": [
        "residuals.bdeb_fit"
      ]
    },
    {
      "page": "summary.bdeb_data",
      "title": "Summary of a BDEB Data Object",
      "topics": [
        "print.summary.bdeb_data",
        "summary.bdeb_data"
      ]
    },
    {
      "page": "summary.bdeb_diagnostics",
      "title": "Compact Summary of a BDEB Diagnostics Report",
      "topics": [
        "summary.bdeb_diagnostics"
      ]
    },
    {
      "page": "summary.bdeb_fit",
      "title": "Posterior Summary for a BDEB Fit",
      "topics": [
        "summary.bdeb_fit"
      ]
    },
    {
      "page": "summary.bdeb_model",
      "title": "Summary of a BDEB Model Specification",
      "topics": [
        "print.summary.bdeb_model",
        "summary.bdeb_model"
      ]
    },
    {
      "page": "summary.bdeb_prediction",
      "title": "Tabulate Posterior Predictive Quantiles",
      "topics": [
        "summary.bdeb_prediction"
      ]
    },
    {
      "page": "vcov.bdeb_fit",
      "title": "Posterior Covariance Matrix of BDEB Model Parameters",
      "topics": [
        "vcov.bdeb_fit"
      ]
    }
  ],
  "_readme": "https://github.com/sciom/BayesianDEB/raw/HEAD/README.md",
  "_rundeps": [
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    "backports",
    "bayesplot",
    "checkmate",
    "cli",
    "cpp11",
    "deSolve",
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