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  "Title": "Mathematical Modelling of (Dynamic) Microbial Inactivation",
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  "Authors@R": "c(person(\"Alberto\", \"Garre\", email = \"garre.alberto@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Pablo S.\", \"Fernandez\", email = \"pablo.fernandez@upct.es\", role = \"aut\"),\nperson(\"Jose A.\", \"Egea\", email = \"josea.egea@upct.es\", role = \"aut\")\n)",
  "Description": "Functions for modelling microbial inactivation under\nisothermal or dynamic conditions. The calculations are based on\nseveral mathematical models broadly used by the scientific\ncommunity and industry. Functions enable to make predictions\nfor cases where the kinetic parameters are known. It also\nimplements functions for parameter estimation for isothermal\nand dynamic conditions. The model fitting capabilities include\nan Adaptive Monte Carlo method for a Bayesian approach to\nparameter estimation.",
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  "Repository": "https://albgarre.r-universe.dev",
  "Date/Publication": "2025-11-03 16:59:10 UTC",
  "RemoteUrl": "https://github.com/albgarre/bioinactivation",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-22 09:57:26 UTC",
    "User": "root"
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  "Author": "Alberto Garre [aut, cre],\nPablo S. Fernandez [aut],\nJose A. Egea [aut]",
  "Maintainer": "Alberto Garre <garre.alberto@gmail.com>",
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  ],
  "_tags": [],
  "_topics": [
    "food",
    "food-safety",
    "inactivation-models",
    "isothermal-experiments",
    "prediction"
  ],
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    "extra/contents.json",
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    "extra/readme.md",
    "manual.pdf"
  ],
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  "_realowner": "albgarre",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2015-12-11"
    },
    {
      "version": "1.1.1",
      "date": "2016-02-04"
    },
    {
      "version": "1.1.2",
      "date": "2016-03-21"
    },
    {
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      "date": "2016-09-18"
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    {
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    },
    {
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      "date": "2017-11-23"
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    {
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      "date": "2017-12-15"
    },
    {
      "version": "1.2.2",
      "date": "2019-06-05"
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    {
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    "fit_inactivation_MCMC",
    "fit_isothermal_inactivation",
    "get_isothermal_model_data",
    "get_model_data",
    "goodness_of_fit",
    "is.FitInactivation",
    "is.FitInactivationMCMC",
    "is.IsoFitInactivation",
    "is.PredInactivationMCMC",
    "is.SimulInactivation",
    "predict_inactivation",
    "predict_inactivation_MCMC",
    "time_to_logreduction"
  ],
  "_datasets": [
    {
      "name": "dynamic_inactivation",
      "title": "Example Dynamic Inactivation of a Microorganis",
      "object": "dynamic_inactivation",
      "class": [
        "data.frame"
      ],
      "fields": [
        "time",
        "N",
        "temperature"
      ],
      "rows": 40,
      "table": true,
      "tojson": true
    },
    {
      "name": "isothermal_inactivation",
      "title": "Example Isothermal Inactivation of a Microorganis",
      "object": "isothermal_inactivation",
      "class": [
        "data.frame"
      ],
      "fields": [
        "time",
        "temp",
        "log_diff"
      ],
      "rows": 68,
      "table": true,
      "tojson": true
    },
    {
      "name": "laterosporus_dyna",
      "title": "Example Dynamic Inactivation of a Laterosporus",
      "object": "laterosporus_dyna",
      "class": [
        "data.frame"
      ],
      "fields": [
        "time",
        "temp",
        "logN"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "laterosporus_iso",
      "title": "Example Isothermal Inactivation of a Laterosporus",
      "object": "laterosporus_iso",
      "class": [
        "data.frame"
      ],
      "fields": [
        "time",
        "temp",
        "log_diff"
      ],
      "rows": 52,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Arrhenius_iso",
      "title": "Isothermal Arrhenius model",
      "topics": [
        "Arrhenius_iso"
      ]
    },
    {
      "page": "Bigelow_iso",
      "title": "Isothermal Bigelow's Model",
      "topics": [
        "Bigelow_iso"
      ]
    },
    {
      "page": "build_temperature_interpolator",
      "title": "Continuum Interpolation of Discrete Temperatures Values",
      "topics": [
        "build_temperature_interpolator"
      ]
    },
    {
      "page": "check_model_params",
      "title": "Correctness Check of Model Parameters",
      "topics": [
        "check_model_params"
      ]
    },
    {
      "page": "dArrhenius_model",
      "title": "First derivative of the Arrhenius model",
      "topics": [
        "dArrhenius_model"
      ]
    },
    {
      "page": "dBigelow_model",
      "title": "First Derivate of the Linear Bigelow Model",
      "topics": [
        "dBigelow_model"
      ]
    },
    {
      "page": "dGeeraerd_model",
      "title": "First Derivate of Geeraerd's Model",
      "topics": [
        "dGeeraerd_model"
      ]
    },
    {
      "page": "dMafart_model",
      "title": "First Derivate of the Weibull-Mafart Model",
      "topics": [
        "dMafart_model"
      ]
    },
    {
      "page": "dMetselaar_model",
      "title": "First Derivate of the Metselaar Model",
      "topics": [
        "dMetselaar_model"
      ]
    },
    {
      "page": "dPeleg_model",
      "title": "First Derivate of the Weibull-Peleg Model",
      "topics": [
        "dPeleg_model"
      ]
    },
    {
      "page": "dynamic_inactivation",
      "title": "Example Dynamic Inactivation of a Microorganis",
      "topics": [
        "dynamic_inactivation"
      ]
    },
    {
      "page": "fit_dynamic_inactivation",
      "title": "Fitting of Dynamic Inactivation Models",
      "topics": [
        "fit_dynamic_inactivation"
      ]
    },
    {
      "page": "fit_inactivation_MCMC",
      "title": "Fitting of dynamic inactivation with MCMC",
      "topics": [
        "fit_inactivation_MCMC"
      ]
    },
    {
      "page": "fit_isothermal_inactivation",
      "title": "Fit of Isothermal Experiments",
      "topics": [
        "fit_isothermal_inactivation"
      ]
    },
    {
      "page": "Geeraerd_iso",
      "title": "Isothermal Geeraerd Model",
      "topics": [
        "Geeraerd_iso"
      ]
    },
    {
      "page": "get_isothermal_model_data",
      "title": "Isothermal Model Data",
      "topics": [
        "get_isothermal_model_data"
      ]
    },
    {
      "page": "get_model_data",
      "title": "Mapping of Simulation Model Functions",
      "topics": [
        "get_model_data"
      ]
    },
    {
      "page": "get_prediction_cost",
      "title": "Error of the Prediction of Microbial Inactivation",
      "topics": [
        "get_prediction_cost"
      ]
    },
    {
      "page": "goodness_dyna",
      "title": "Goodness of fit for Dynamic fits",
      "topics": [
        "goodness_dyna"
      ]
    },
    {
      "page": "goodness_iso",
      "title": "Goodness of fit for Isothermal fits",
      "topics": [
        "goodness_iso"
      ]
    },
    {
      "page": "goodness_MCMC",
      "title": "Goodness of fit for MCMC fits",
      "topics": [
        "goodness_MCMC"
      ]
    },
    {
      "page": "goodness_of_fit",
      "title": "Goodness of fit for microbial inactivation models",
      "topics": [
        "goodness_of_fit"
      ]
    },
    {
      "page": "is.FitInactivation",
      "title": "Test of FitInactivation object",
      "topics": [
        "is.FitInactivation"
      ]
    },
    {
      "page": "is.FitInactivationMCMC",
      "title": "Test of FitInactivationMCMC object",
      "topics": [
        "is.FitInactivationMCMC"
      ]
    },
    {
      "page": "is.IsoFitInactivation",
      "title": "Test of IsoFitInactivation object",
      "topics": [
        "is.IsoFitInactivation"
      ]
    },
    {
      "page": "is.PredInactivationMCMC",
      "title": "Test of PredInactivationMCMC object",
      "topics": [
        "is.PredInactivationMCMC"
      ]
    },
    {
      "page": "is.SimulInactivation",
      "title": "Test of SimulInactivation object",
      "topics": [
        "is.SimulInactivation"
      ]
    },
    {
      "page": "isothermal_inactivation",
      "title": "Example Isothermal Inactivation of a Microorganis",
      "topics": [
        "isothermal_inactivation"
      ]
    },
    {
      "page": "laterosporus_dyna",
      "title": "Example Dynamic Inactivation of a Laterosporus",
      "topics": [
        "laterosporus_dyna"
      ]
    },
    {
      "page": "laterosporus_iso",
      "title": "Example Isothermal Inactivation of a Laterosporus",
      "topics": [
        "laterosporus_iso"
      ]
    },
    {
      "page": "Metselaar_iso",
      "title": "Isothermal Metselaar model",
      "topics": [
        "Metselaar_iso"
      ]
    },
    {
      "page": "plot.FitInactivation",
      "title": "Plot of FitInactivation Object",
      "topics": [
        "plot.FitInactivation"
      ]
    },
    {
      "page": "plot.FitInactivationMCMC",
      "title": "Plot of FitInactivationMCMC Object",
      "topics": [
        "plot.FitInactivationMCMC"
      ]
    },
    {
      "page": "plot.IsoFitInactivation",
      "title": "Plot of IsoFitInactivation Object",
      "topics": [
        "plot.IsoFitInactivation"
      ]
    },
    {
      "page": "plot.PredInactivationMCMC",
      "title": "Plot of PredInactivationMCMC Object",
      "topics": [
        "plot.PredInactivationMCMC"
      ]
    },
    {
      "page": "plot.SimulInactivation",
      "title": "Plot of SimulInactivation Object",
      "topics": [
        "plot.SimulInactivation"
      ]
    },
    {
      "page": "predict_inactivation",
      "title": "Prediction of Dynamic Inactivation",
      "topics": [
        "predict_inactivation"
      ]
    },
    {
      "page": "predict_inactivation_MCMC",
      "title": "Dynamic Prediction Intervals from a Monte Carlo Adjustment",
      "topics": [
        "predict_inactivation_MCMC"
      ]
    },
    {
      "page": "sample_dynaFit",
      "title": "Random sample of the parameters of a FitInactivation object",
      "topics": [
        "sample_dynaFit"
      ]
    },
    {
      "page": "sample_IsoFit",
      "title": "Random sample of the parameters of a IsoFitInactivation object",
      "topics": [
        "sample_IsoFit"
      ]
    },
    {
      "page": "sample_MCMCfit",
      "title": "Random sample of the parameters of a FitInactivationMCMC object",
      "topics": [
        "sample_MCMCfit"
      ]
    },
    {
      "page": "summary.FitInactivation",
      "title": "Summary of a FitInactivation object",
      "topics": [
        "summary.FitInactivation"
      ]
    },
    {
      "page": "summary.FitInactivationMCMC",
      "title": "Summary of a FitInactivationMCMC object",
      "topics": [
        "summary.FitInactivationMCMC"
      ]
    },
    {
      "page": "summary.IsoFitInactivation",
      "title": "Summary of a IsoFitInactivation object",
      "topics": [
        "summary.IsoFitInactivation"
      ]
    },
    {
      "page": "time_to_logreduction",
      "title": "Time to reach X log reductions",
      "topics": [
        "time_to_logreduction"
      ]
    },
    {
      "page": "WeibullMafart_iso",
      "title": "Isothermal Weibull-Mafart Model",
      "topics": [
        "WeibullMafart_iso"
      ]
    },
    {
      "page": "WeibullPeleg_iso",
      "title": "Isothermal Weibull-Peleg Model",
      "topics": [
        "WeibullPeleg_iso"
      ]
    }
  ],
  "_readme": "https://github.com/albgarre/bioinactivation/raw/HEAD/README.md",
  "_rundeps": [
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    "scales",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "inactivation.Rmd",
      "filename": "inactivation.html",
      "title": "bioinactivation: Software for modelling microbial inactivation",
      "author": "Alberto Garre, Pablo S. Fernandez, Jose A. Egea",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Example data sets included in the package",
        "The example data set of an isothermal experiment",
        "The example data set of a dynamic experiment",
        "The example data set of an isothermal study of Bacillus laterosporus",
        "The example data set of a non-isothermal study of laterosporus",
        "Inactivation models implemented",
        "Bigelow model for isothermal data",
        "Bigelow model for nonisothermal data",
        "Weibullian models",
        "Weibull-Peleg model for isothermal inactivation",
        "Weibull-Peleg model for non-isothermal inactivation",
        "Weibull-Mafart model for isothermal inactivation",
        "Weibull-Mafart model for nonisothermal inactivation",
        "Geeraerd model",
        "Arrhenius inactivation model",
        "Prediction of microbial inactivation",
        "Fitting of isothermal data",
        "Fitting of dynamic experiments using non-linear regression",
        "Fitting of dynamic experiments using Markov Chain Monte Carlo methods",
        "References"
      ],
      "created": "2015-10-16 15:40:42",
      "modified": "2025-04-07 05:57:28",
      "commits": 25
    }
  ],
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  "_nocasepkg": "bioinactivation",
  "_universes": [
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