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  "Package": "predmicror",
  "Title": "Fitting Predictive Microbiology Models",
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  "Date": "2026-06-05",
  "Authors@R": "c(\nperson(given = \"Vasco\", family = \"Cadavez\", role = c(\"aut\", \"cre\"),\nemail = \"vcadavez@ipb.pt\",\ncomment = c(ORCID = \"0000-0002-3077-7414\")),\nperson(given = \"Ursula\", family = \"Gonzales-Barron\", role = \"aut\",\nemail = \"ubarron@ipb.pt\",\ncomment = c(ORCID = \"0000-0002-8462-9775\"))\n)",
  "Description": "Provides predictive microbiology model functions and\nconvenience wrappers for fitting primary growth, microbial\ninactivation, dynamic, omnibus, and cardinal parameter models\nto experimental data using nonlinear least squares and related\nmixed-effects or time-varying workflows. Includes helper\nfunctions for extracting fitted values, calculating model\ndiagnostics, and comparing fitted models. Implemented model\nfamilies include those described by: Zwietering et al. (1990)\n<doi:10.1128/AEM.56.6.1875-1881.1990>, Baranyi and Roberts\n(1994) <doi:10.1016/0168-1605(94)90157-0>, Baranyi and Roberts\n(1995) <doi:10.1016/0168-1605(94)00121-L>, Buchanan et al.\n(1997) <doi:10.1006/fmic.1997.0125>, Richards (1959)\n<doi:10.1093/jxb/10.2.290>, Fang et al. (2012)\n<doi:10.1111/j.1750-3841.2012.02873.x>, Fang et al. (2013)\n<doi:10.1016/j.fm.2012.12.005>, Huang (2008)\n<doi:10.1111/j.1750-3841.2008.00785.x>, Huang (2009)\n<doi:10.1016/j.jfoodeng.2008.07.011>, Huang (2013)\n<doi:10.1016/j.foodcont.2012.11.019>, Geeraerd et al. (2005)\n<doi:10.1016/j.ijfoodmicro.2004.11.038>, van Boekel (2002)\n<doi:10.1016/S0168-1605(01)00742-5>, Peleg (1999)\n<doi:10.1016/S0963-9969(99)00081-2>, Mafart et al. (2002)\n<doi:10.1016/S0168-1605(01)00624-9>, Albert and Mafart (2005)\n<doi:10.1016/j.ijfoodmicro.2004.10.016>, Rosso et al. (1993)\n<doi:10.1006/jtbi.1993.1099>, Rosso et al. (1995)\n<doi:10.1128/AEM.61.2.610-616.1995>, and Rosso et al. (1996)\n<doi:10.4315/0362-028X-59.9.944>.",
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  "URL": "https://fsqanalytics.github.io/predmicror/,\nhttps://github.com/fsqanalytics/predmicror",
  "BugReports": "https://github.com/fsqanalytics/predmicror/issues",
  "Config/testthat/edition": "3",
  "Packaged": {
    "Date": "2026-06-19 18:41:05 UTC",
    "User": "root"
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  "Author": "Vasco Cadavez [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3077-7414>), Ursula\nGonzales-Barron [aut] (ORCID:\n<https://orcid.org/0000-0002-8462-9775>)",
  "Maintainer": "Vasco Cadavez <vcadavez@ipb.pt>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-06-19 18:11:58 UTC",
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    "predict_dynamic_inactivation",
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    "WeibullM",
    "WeibullMM",
    "WeibullPH",
    "ZwieteringFM"
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      "table": true,
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      "title": "Data of a reduced curve of microbial growth",
      "object": "growthred",
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        "logN",
        "lnN"
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      "title": "Data of INH antimicrobials",
      "object": "inh",
      "class": [
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        "Conce",
        "sqrtGR",
        "GR"
      ],
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      "table": true,
      "tojson": true
    },
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      "title": "Data of microbial inactivation Albert and Mafart (2005)",
      "object": "mafart2005Li11",
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      ],
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        "logN"
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      "title": "Data pH",
      "object": "ph",
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      ],
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        "sqrtGR",
        "GR"
      ],
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      "table": true,
      "tojson": true
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      "name": "salmonella",
      "title": "Potential growth of _Salmonella typhimurium_ on cooked chicken",
      "object": "salmonella",
      "class": [
        "data.frame"
      ],
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        "GR",
        "sqrtGR"
      ],
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      "table": true,
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    {
      "page": "aw",
      "title": "Data of aw",
      "topics": [
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      ]
    },
    {
      "page": "BaranyiFM",
      "title": "Baranyi and Roberts full growth model",
      "topics": [
        "BaranyiFM"
      ]
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    {
      "page": "BaranyiRM",
      "title": "Baranyi and Roberts reduced growth model",
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    {
      "page": "bias_factor",
      "title": "Bias and accuracy factors",
      "topics": [
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        "bias_factor"
      ]
    },
    {
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      "title": "Data concerning _Staphylococcus aureus_ microbial inactivation in beef",
      "topics": [
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    },
    {
      "page": "BuchananRM",
      "title": "Buchanan reduced growth model",
      "topics": [
        "BuchananRM"
      ]
    },
    {
      "page": "CMAW",
      "title": "Cardinal model for water activity",
      "topics": [
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    },
    {
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      "title": "Cardinal model for growth inhibitors",
      "topics": [
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    {
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      "title": "Cardinal model for pH",
      "topics": [
        "CMPH"
      ]
    },
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      "title": "Cardinal model for temperature",
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      ]
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      "title": "Compare fitted predmicror models",
      "topics": [
        "compare_models"
      ]
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      "page": "dynamic_profile",
      "title": "Create a dynamic environmental profile",
      "topics": [
        "dynamic_profile"
      ]
    },
    {
      "page": "dynamic_sensitivity",
      "title": "Finite-difference sensitivity for dynamic predictions",
      "topics": [
        "dynamic_sensitivity"
      ]
    },
    {
      "page": "FangNLM",
      "title": "Fang no lag growth model",
      "topics": [
        "FangNLM"
      ]
    },
    {
      "page": "fit_cardinal",
      "title": "Fit a cardinal parameter model",
      "topics": [
        "fit_cardinal"
      ]
    },
    {
      "page": "fit_dynamic_growth",
      "title": "Fit dynamic microbial growth models",
      "topics": [
        "fit_dynamic_growth"
      ]
    },
    {
      "page": "fit_dynamic_inactivation",
      "title": "Fit dynamic microbial inactivation models",
      "topics": [
        "fit_dynamic_inactivation"
      ]
    },
    {
      "page": "fit_growth",
      "title": "Fit a primary growth model",
      "topics": [
        "fit_growth"
      ]
    },
    {
      "page": "fit_inactivation",
      "title": "Fit a microbial inactivation model",
      "topics": [
        "fit_inactivation"
      ]
    },
    {
      "page": "fit_metrics",
      "title": "Calculate model diagnostics for a fitted predmicror model",
      "topics": [
        "fit_metrics",
        "fit_metrics.default",
        "fit_metrics.predmicror_fit"
      ]
    },
    {
      "page": "fit_omnibus",
      "title": "Fit omnibus predictive microbiology models",
      "topics": [
        "fit_omnibus",
        "fit_omnibus_growth",
        "fit_omnibus_inactivation"
      ]
    },
    {
      "page": "GeeraerdST",
      "title": "Geeraerd inactivation model",
      "topics": [
        "GeeraerdST"
      ]
    },
    {
      "page": "growthfull",
      "title": "Data of a complete curve of microbial growth",
      "topics": [
        "growthfull"
      ]
    },
    {
      "page": "growthnolag",
      "title": "Data of a no lag curve of microbial growth",
      "topics": [
        "growthnolag"
      ]
    },
    {
      "page": "growthred",
      "title": "Data of a reduced curve of microbial growth",
      "topics": [
        "growthred"
      ]
    },
    {
      "page": "HuangFM",
      "title": "Huang full growth model",
      "topics": [
        "HuangFM"
      ]
    },
    {
      "page": "HuangNLM",
      "title": "Huang no lag growth model",
      "topics": [
        "HuangNLM"
      ]
    },
    {
      "page": "HuangRGS",
      "title": "Huang reparameterized Gompertz survival model",
      "topics": [
        "HuangRGS"
      ]
    },
    {
      "page": "HuangRM",
      "title": "Huang reduced growth model",
      "topics": [
        "HuangRM"
      ]
    },
    {
      "page": "inh",
      "title": "Data of INH antimicrobials",
      "topics": [
        "inh"
      ]
    },
    {
      "page": "mafart2005Li11",
      "title": "Data of microbial inactivation Albert and Mafart (2005)",
      "topics": [
        "mafart2005Li11"
      ]
    },
    {
      "page": "omnibus_secondary",
      "title": "Define an omnibus secondary model",
      "topics": [
        "omnibus_secondary"
      ]
    },
    {
      "page": "ph",
      "title": "Data pH",
      "topics": [
        "ph"
      ]
    },
    {
      "page": "predict_dynamic_growth",
      "title": "Predict microbial growth under dynamic environmental conditions",
      "topics": [
        "predict_dynamic_growth"
      ]
    },
    {
      "page": "predict_dynamic_inactivation",
      "title": "Predict microbial inactivation under dynamic environmental conditions",
      "topics": [
        "predict_dynamic_inactivation"
      ]
    },
    {
      "page": "predmicror_assistant",
      "title": "Assistant for predmicror",
      "topics": [
        "predmicror_assistant"
      ]
    },
    {
      "page": "predmicror_assistant_app",
      "title": "Launch the predmicror assistant Shiny app",
      "topics": [
        "predmicror_assistant_app"
      ]
    },
    {
      "page": "predmicror_augment",
      "title": "Extract fitted values and residuals from a predmicror fit",
      "topics": [
        "as.data.frame.predmicror_fit",
        "predmicror_augment",
        "predmicror_augment.default",
        "predmicror_augment.predmicror_fit"
      ]
    },
    {
      "page": "predmicror_fit_methods",
      "title": "Methods for 'predmicror_fit' objects",
      "topics": [
        "AIC.predmicror_fit",
        "BIC.predmicror_fit",
        "coef.predmicror_fit",
        "fitted.predmicror_fit",
        "logLik.predmicror_fit",
        "plot.predmicror_fit",
        "predict.predmicror_fit",
        "predmicror_fit_methods",
        "print.predmicror_fit",
        "residuals.predmicror_fit",
        "summary.predmicror_fit",
        "vcov.predmicror_fit"
      ]
    },
    {
      "page": "predmicror_models",
      "title": "List models available through the fitting wrappers",
      "topics": [
        "predmicror_models"
      ]
    },
    {
      "page": "predmicror_omnibus_methods",
      "title": "Methods for omnibus fits",
      "topics": [
        "AIC.predmicror_omnibus_fit",
        "BIC.predmicror_omnibus_fit",
        "coef.predmicror_omnibus_fit",
        "fitted.predmicror_omnibus_fit",
        "logLik.predmicror_omnibus_fit",
        "predict.predmicror_omnibus_fit",
        "predmicror_omnibus_methods",
        "print.predmicror_omnibus_fit",
        "residuals.predmicror_omnibus_fit",
        "summary.predmicror_omnibus_fit"
      ]
    },
    {
      "page": "RichardsNLM",
      "title": "Richards no lag growth model",
      "topics": [
        "RichardsNLM"
      ]
    },
    {
      "page": "RossoFM",
      "title": "Rosso full growth model",
      "topics": [
        "RossoFM"
      ]
    },
    {
      "page": "salmonella",
      "title": "Potential growth of _Salmonella typhimurium_ on cooked chicken",
      "topics": [
        "salmonella"
      ]
    },
    {
      "page": "validate_omnibus_leave_one_out",
      "title": "Validate an omnibus fit by leaving out one group",
      "topics": [
        "validate_omnibus_leave_one_out"
      ]
    },
    {
      "page": "WeibullM",
      "title": "Weibull inactivation model Mafart",
      "topics": [
        "WeibullM"
      ]
    },
    {
      "page": "WeibullMM",
      "title": "Weibull inactivation modified model Mafart",
      "topics": [
        "WeibullMM"
      ]
    },
    {
      "page": "WeibullPH",
      "title": "Weibull inactivation model Peleg and Huang",
      "topics": [
        "WeibullPH"
      ]
    },
    {
      "page": "ZwieteringFM",
      "title": "Zwietering full growth model",
      "topics": [
        "ZwieteringFM"
      ]
    }
  ],
  "_pkglogo": "https://github.com/cran/predmicror/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/cran/predmicror/raw/HEAD/README.md",
  "_rundeps": [
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    {
      "source": "cardinal-models.Rmd",
      "filename": "cardinal-models.html",
      "title": "Cardinal parameter models",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Available cardinal models",
        "Robust fitting helper",
        "Temperature model",
        "pH model",
        "Water activity model",
        "Inhibitor model",
        "Collecting diagnostics",
        "Practical notes"
      ],
      "created": "2026-06-19 18:11:58",
      "modified": "2026-06-19 18:11:58",
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