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  "Description": "Modelling of population growth under static and dynamic\nenvironmental conditions. Includes functions for model fitting\nand making prediction under isothermal and dynamic conditions.\nThe methods (algorithms & models) are based on predictive\nmicrobiology (See Perez-Rodriguez and Valero (2012,\nISBN:978-1-4614-5519-6)).",
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  "Repository": "https://albgarre.r-universe.dev",
  "Date/Publication": "2025-12-18 19:41:35 UTC",
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  "Author": "Alberto Garre [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4404-3550>),\nJeroen Koomen [aut],\nHeidy den Besten [aut],\nMarcel Zwietering [aut]",
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      "date": "2020-10-22"
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      "date": "2020-11-12"
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    {
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      "date": "2020-11-26"
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      "date": "2021-07-06"
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      "date": "2021-08-23"
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    "check_growth_guess",
    "compare_growth_fits",
    "compare_secondary_fits",
    "distribution_to_logcount",
    "fit_coupled_growth",
    "fit_dynamic_growth",
    "fit_growth",
    "fit_isothermal_growth",
    "fit_MCMC_growth",
    "fit_multiple_growth",
    "fit_multiple_growth_MCMC",
    "fit_secondary_growth",
    "fit_serial_dilution",
    "get_TTDs",
    "is.DynamicGrowth",
    "is.FitDynamicGrowth",
    "is.FitDynamicGrowthMCMC",
    "is.FitIsoGrowth",
    "is.FitMultipleDynamicGrowth",
    "is.FitMultipleDynamicGrowthMCMC",
    "is.FitSecondaryGrowth",
    "is.GlobalGrowthFit",
    "is.GrowthFit",
    "is.GrowthPrediction",
    "is.GrowthUncertainty",
    "is.IsothermalGrowth",
    "is.MCMCgrowth",
    "is.StochasticGrowth",
    "lambda_to_Q0",
    "make_guess_coupled",
    "make_guess_primary",
    "make_guess_secondary",
    "predict_dynamic_growth",
    "predict_growth",
    "predict_growth_uncertainty",
    "predict_isothermal_growth",
    "predict_MCMC_growth",
    "predict_stochastic_growth",
    "predictMCMC",
    "predictMCMC_coupled",
    "primary_model_data",
    "Q0_to_lambda",
    "secondary_model_data",
    "show_guess_coupled",
    "time_to_logcount",
    "time_to_size"
  ],
  "_datasets": [
    {
      "name": "arabian_tractors",
      "title": "Number of tractors in the Arab World according to the World Bank",
      "object": "arabian_tractors",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "year",
        "tractors"
      ],
      "rows": 40,
      "table": true,
      "tojson": true
    },
    {
      "name": "conditions_pH_temperature",
      "title": "Conditions during a dynamic growth experiment",
      "object": "conditions_pH_temperature",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "time",
        "temperature",
        "pH"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_cardinal",
      "title": "Growth rates obtained for several growth experiments",
      "object": "example_cardinal",
      "class": [
        "data.frame"
      ],
      "fields": [
        "temperature",
        "pH",
        "mu"
      ],
      "rows": 64,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_coupled_onestep",
      "title": "Example data for two-steps fitting of the Baranyi-Ratkowsky model",
      "object": "example_coupled_onestep",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "time",
        "temp",
        "logN"
      ],
      "rows": 162,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_coupled_twosteps",
      "title": "Example data for two-steps fitting of the Baranyi-Ratkowsky model",
      "object": "example_coupled_twosteps",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "temp",
        "mu",
        "lambda"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_dynamic_growth",
      "title": "Microbial growth under dynamic conditions",
      "object": "example_dynamic_growth",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "time",
        "logN"
      ],
      "rows": 30,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_env_conditions",
      "title": "Environmental conditions during a dynamic experiment",
      "object": "example_env_conditions",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "time",
        "temperature",
        "aw"
      ],
      "rows": 3,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_od",
      "title": "Example data for TTD calculation and the serial-dilution method",
      "object": "example_od",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "time",
        "S/7/35/R1_0",
        "S/7/35/R2_0",
        "S/7/35/R3_0",
        "S/7/35/R1_1",
        "S/7/35/R2_1",
        "S/7/35/R3_1",
        "S/7/35/R1_2",
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        "S/7/35/R3_2",
        "S/7/35/R1_3",
        "S/7/35/R2_3",
        "S/7/35/R3_3",
        "S/7/35/R1_4",
        "S/7/35/R2_4",
        "S/7/35/R3_4",
        "S/7/35/R1_5",
        "S/7/35/R2_5",
        "S/7/35/R3_5",
        "S/7/35/R1_6",
        "S/7/35/R2_6",
        "S/7/35/R3_6",
        "S/7/35/R1_7",
        "S/7/35/R2_7",
        "S/7/35/R3_7",
        "S/7/35/R1_8",
        "S/7/35/R2_8",
        "S/7/35/R3_8",
        "S/7/35/R1_9",
        "S/7/35/R2_9",
        "S/7/35/R3_9",
        "S/6,5/35/R1_0",
        "S/6,5/35/R2_0",
        "S/6,5/35/R3_0",
        "S/6,5/35/R1_1",
        "S/6,5/35/R2_1",
        "S/6,5/35/R3_1",
        "S/6,5/35/R1_2",
        "S/6,5/35/R2_2",
        "S/6,5/35/R3_2",
        "S/6,5/35/R1_3",
        "S/6,5/35/R2_3",
        "S/6,5/35/R3_3",
        "S/6,5/35/R1_4",
        "S/6,5/35/R2_4",
        "S/6,5/35/R3_4",
        "S/6,5/35/R1_5",
        "S/6,5/35/R2_5",
        "S/6,5/35/R3_5",
        "S/6,5/35/R1_6",
        "S/6,5/35/R2_6",
        "S/6,5/35/R3_6",
        "S/6,5/35/R1_7",
        "S/6,5/35/R2_7",
        "S/6,5/35/R3_7",
        "S/6,5/35/R1_8",
        "S/6,5/35/R2_8",
        "S/6,5/35/R3_8",
        "S/6,5/35/R1_9",
        "S/6,5/35/R2_9",
        "S/6,5/35/R3_9"
      ],
      "rows": 97,
      "table": true,
      "tojson": true
    },
    {
      "name": "greek_tractors",
      "title": "Number of tractors in Greece according to the World Bank",
      "object": "greek_tractors",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Domain Code",
        "Domain",
        "Country Code",
        "Country",
        "Element Code",
        "Element",
        "Item Code",
        "Item",
        "Year Code",
        "Year",
        "Unit",
        "Value",
        "Flag",
        "Flag Description"
      ],
      "rows": 46,
      "table": true,
      "tojson": true
    },
    {
      "name": "growth_pH_temperature",
      "title": "Example of dynamic growth",
      "object": "growth_pH_temperature",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "time",
        "logN"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "growth_salmonella",
      "title": "Growth of Salmonella spp in broth",
      "object": "growth_salmonella",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "time",
        "logN"
      ],
      "rows": 21,
      "table": true,
      "tojson": true
    },
    {
      "name": "multiple_conditions",
      "title": "Environmental conditions during several dynamic experiments",
      "object": "multiple_conditions",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "multiple_counts",
      "title": "Population growth observed in several dynamic experiments",
      "object": "multiple_counts",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "multiple_experiments",
      "title": "A set of growth experiments under dynamic conditions",
      "object": "multiple_experiments",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "refrigeratorSpain",
      "title": "Temperature recorded in refrigerators",
      "object": "refrigeratorSpain",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "time",
        "A1",
        "A2"
      ],
      "rows": 145,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "approx_env",
      "title": "Generates functions for linear interpolation of environmental conditions",
      "topics": [
        "approx_env"
      ]
    },
    {
      "page": "arabian_tractors",
      "title": "Number of tractors in the Arab World according to the World Bank",
      "topics": [
        "arabian_tractors"
      ]
    },
    {
      "page": "Aryani_model",
      "title": "Secondary Aryani model",
      "topics": [
        "Aryani_model"
      ]
    },
    {
      "page": "bilinear_lag",
      "title": "Bilinear model with lag phase",
      "topics": [
        "bilinear_lag"
      ]
    },
    {
      "page": "bilinear_stationary",
      "title": "Bilinear model with stationary phase",
      "topics": [
        "bilinear_stationary"
      ]
    },
    {
      "page": "calculate_gammas",
      "title": "Calculates every gamma factor",
      "topics": [
        "calculate_gammas"
      ]
    },
    {
      "page": "calculate_gammas_secondary",
      "title": "Gamma factors for fitting secondary models",
      "topics": [
        "calculate_gammas_secondary"
      ]
    },
    {
      "page": "check_growth_guess",
      "title": "Visual check of an initial guess of the model parameters",
      "topics": [
        "check_growth_guess"
      ]
    },
    {
      "page": "check_primary_pars",
      "title": "Basic check of parameters for primary models",
      "topics": [
        "check_primary_pars"
      ]
    },
    {
      "page": "check_secondary_pars",
      "title": "Basic checks of secondary parameters",
      "topics": [
        "check_secondary_pars"
      ]
    },
    {
      "page": "check_stochastic_pars",
      "title": "Model definition checks for predict_stochastic_growth",
      "topics": [
        "check_stochastic_pars"
      ]
    },
    {
      "page": "compare_growth_fits",
      "title": "Model comparison and selection for growth models",
      "topics": [
        "compare_growth_fits"
      ]
    },
    {
      "page": "compare_secondary_fits",
      "title": "Model comparison and selection for secondary growth models",
      "topics": [
        "compare_secondary_fits"
      ]
    },
    {
      "page": "conditions_pH_temperature",
      "title": "Conditions during a dynamic growth experiment",
      "topics": [
        "conditions_pH_temperature"
      ]
    },
    {
      "page": "cost_coupled_onestep",
      "title": "Residuals of the coupled Baranyi model",
      "topics": [
        "cost_coupled_onestep"
      ]
    },
    {
      "page": "cost_coupled_twosteps",
      "title": "Cost for the coupled model fitted in two-steps",
      "topics": [
        "cost_coupled_twosteps"
      ]
    },
    {
      "page": "CPM_model",
      "title": "Secondary Cardinal Parameter (CPM) model",
      "topics": [
        "CPM_model"
      ]
    },
    {
      "page": "dBaranyi",
      "title": "Baranyi growth model",
      "topics": [
        "dBaranyi"
      ]
    },
    {
      "page": "distribution_to_logcount",
      "title": "Distribution of times to reach a certain microbial count",
      "topics": [
        "distribution_to_logcount"
      ]
    },
    {
      "page": "DynamicGrowth",
      "title": "DynamicGrowth class",
      "topics": [
        "coef.DynamicGrowth",
        "DynamicGrowth",
        "plot.DynamicGrowth",
        "print.DynamicGrowth"
      ]
    },
    {
      "page": "example_cardinal",
      "title": "Growth rates obtained for several growth experiments",
      "topics": [
        "example_cardinal"
      ]
    },
    {
      "page": "example_coupled_onestep",
      "title": "Example data for two-steps fitting of the Baranyi-Ratkowsky model",
      "topics": [
        "example_coupled_onestep"
      ]
    },
    {
      "page": "example_coupled_twosteps",
      "title": "Example data for two-steps fitting of the Baranyi-Ratkowsky model",
      "topics": [
        "example_coupled_twosteps"
      ]
    },
    {
      "page": "example_dynamic_growth",
      "title": "Microbial growth under dynamic conditions",
      "topics": [
        "example_dynamic_growth"
      ]
    },
    {
      "page": "example_env_conditions",
      "title": "Environmental conditions during a dynamic experiment",
      "topics": [
        "example_env_conditions"
      ]
    },
    {
      "page": "example_od",
      "title": "Example data for TTD calculation and the serial-dilution method",
      "topics": [
        "example_od"
      ]
    },
    {
      "page": "extract_primary_pars",
      "title": "A helper to build the primary models",
      "topics": [
        "extract_primary_pars"
      ]
    },
    {
      "page": "extract_secondary_pars",
      "title": "A helper to build the secondary models",
      "topics": [
        "extract_secondary_pars"
      ]
    },
    {
      "page": "fit_coupled_growth",
      "title": "Growth fitting considering link between mu and lambda for the Baranyi-Ratkowsky model",
      "topics": [
        "fit_coupled_growth"
      ]
    },
    {
      "page": "fit_dynamic_growth",
      "title": "Fit dynamic growth models",
      "topics": [
        "fit_dynamic_growth"
      ]
    },
    {
      "page": "fit_growth",
      "title": "Fitting microbial growth",
      "topics": [
        "fit_growth"
      ]
    },
    {
      "page": "fit_isothermal_growth",
      "title": "Fit primary growth models",
      "topics": [
        "fit_isothermal_growth"
      ]
    },
    {
      "page": "fit_MCMC_growth",
      "title": "Fit growth models using MCMC",
      "topics": [
        "fit_MCMC_growth"
      ]
    },
    {
      "page": "fit_multiple_growth",
      "title": "Fitting growth models to multiple dynamic experiments",
      "topics": [
        "fit_multiple_growth"
      ]
    },
    {
      "page": "fit_multiple_growth_MCMC",
      "title": "Fitting growth models to multiple dynamic experiments using MCMC",
      "topics": [
        "fit_multiple_growth_MCMC"
      ]
    },
    {
      "page": "fit_secondary_growth",
      "title": "Fit secondary growth models",
      "topics": [
        "fit_secondary_growth"
      ]
    },
    {
      "page": "fit_serial_dilution",
      "title": "Serial-fold dilution method",
      "topics": [
        "fit_serial_dilution"
      ]
    },
    {
      "page": "FitCoupledGrowth",
      "title": "FitCoupledGrowth class",
      "topics": [
        "AIC.FitCoupledGrowth",
        "coef.FitCoupledGrowth",
        "deviance.FitCoupledGrowth",
        "FitCoupledGrowth",
        "fitted.FitCoupledGrowth",
        "logLik.FitCoupledGrowth",
        "plot.FitCoupledGrowth",
        "predict.FitCoupledGrowth",
        "predictMCMC_coupled.FitCoupledGrowth",
        "print.FitCoupledGrowth",
        "residuals.FitCoupledGrowth",
        "summary.FitCoupledGrowth",
        "vcov.FitCoupledGrowth"
      ]
    },
    {
      "page": "FitDynamicGrowth",
      "title": "FitDynamicGrowth class",
      "topics": [
        "AIC.FitDynamicGrowth",
        "coef.FitDynamicGrowth",
        "deviance.FitDynamicGrowth",
        "FitDynamicGrowth",
        "fitted.FitDynamicGrowth",
        "logLik.FitDynamicGrowth",
        "plot.FitDynamicGrowth",
        "predict.FitDynamicGrowth",
        "print.FitDynamicGrowth",
        "residuals.FitDynamicGrowth",
        "summary.FitDynamicGrowth",
        "vcov.FitDynamicGrowth"
      ]
    },
    {
      "page": "FitDynamicGrowthMCMC",
      "title": "FitDynamicGrowthMCMC class",
      "topics": [
        "AIC.FitDynamicGrowthMCMC",
        "coef.FitDynamicGrowthMCMC",
        "deviance.FitDynamicGrowthMCMC",
        "FitDynamicGrowthMCMC",
        "fitted.FitDynamicGrowthMCMC",
        "logLik.FitDynamicGrowthMCMC",
        "plot.FitDynamicGrowthMCMC",
        "predict.FitDynamicGrowthMCMC",
        "predictMCMC.FitDynamicGrowthMCMC",
        "print.FitDynamicGrowthMCMC",
        "residuals.FitDynamicGrowthMCMC",
        "summary.FitDynamicGrowthMCMC",
        "vcov.FitDynamicGrowthMCMC"
      ]
    },
    {
      "page": "FitIsoGrowth",
      "title": "FitIsoGrowth class",
      "topics": [
        "AIC.FitIsoGrowth",
        "coef.FitIsoGrowth",
        "deviance.FitIsoGrowth",
        "FitIsoGrowth",
        "fitted.FitIsoGrowth",
        "logLik.FitIsoGrowth",
        "plot.FitIsoGrowth",
        "predict.FitIsoGrowth",
        "print.FitIsoGrowth",
        "residuals.FitIsoGrowth",
        "summary.FitIsoGrowth",
        "vcov.FitIsoGrowth"
      ]
    },
    {
      "page": "FitMultipleDynamicGrowth",
      "title": "FitMultipleDynamicGrowth class",
      "topics": [
        "AIC.FitMultipleDynamicGrowth",
        "coef.FitMultipleDynamicGrowth",
        "deviance.FitMultipleDynamicGrowth",
        "FitMultipleDynamicGrowth",
        "fitted.FitMultipleDynamicGrowth",
        "logLik.FitMultipleDynamicGrowth",
        "plot.FitMultipleDynamicGrowth",
        "predict.FitMultipleDynamicGrowth",
        "print.FitMultipleDynamicGrowth",
        "residuals.FitMultipleDynamicGrowth",
        "summary.FitMultipleDynamicGrowth",
        "vcov.FitMultipleDynamicGrowth"
      ]
    },
    {
      "page": "FitMultipleGrowthMCMC",
      "title": "FitMultipleGrowthMCMC class",
      "topics": [
        "AIC.FitMultipleGrowthMCMC",
        "coef.FitMultipleGrowthMCMC",
        "deviance.FitMultipleGrowthMCMC",
        "FitMultipleGrowthMCMC",
        "fitted.FitMultipleGrowthMCMC",
        "logLik.FitMultipleGrowthMCMC",
        "plot.FitMultipleGrowthMCMC",
        "predict.FitMultipleGrowthMCMC",
        "predictMCMC.FitMultipleGrowthMCMC",
        "print.FitMultipleGrowthMCMC",
        "residuals.FitMultipleGrowthMCMC",
        "summary.FitMultipleGrowthMCMC",
        "vcov.FitMultipleGrowthMCMC"
      ]
    },
    {
      "page": "FitSecondaryGrowth",
      "title": "FitSecondaryGrowth class",
      "topics": [
        "AIC.FitSecondaryGrowth",
        "coef.FitSecondaryGrowth",
        "deviance.FitSecondaryGrowth",
        "FitSecondaryGrowth",
        "fitted.FitSecondaryGrowth",
        "logLik.FitSecondaryGrowth",
        "plot.FitSecondaryGrowth",
        "predict.FitSecondaryGrowth",
        "print.FitSecondaryGrowth",
        "residuals.FitSecondaryGrowth",
        "summary.FitSecondaryGrowth",
        "vcov.FitSecondaryGrowth"
      ]
    },
    {
      "page": "FitSerial",
      "title": "FitSerial class",
      "topics": [
        "AIC.FitSerial",
        "coef.FitSerial",
        "deviance.FitSerial",
        "FitSerial",
        "fitted.FitSerial",
        "logLik.FitSerial",
        "plot.FitSerial",
        "predict.FitSerial",
        "print.FitSerial",
        "residuals.FitSerial",
        "summary.FitSerial",
        "vcov.FitSerial"
      ]
    },
    {
      "page": "full_Ratkowski",
      "title": "Full Ratkowsky model",
      "topics": [
        "full_Ratkowski"
      ]
    },
    {
      "page": "get_all_predictions",
      "title": "A helper for making the plots",
      "topics": [
        "get_all_predictions"
      ]
    },
    {
      "page": "get_dyna_residuals",
      "title": "Residuals of dynamic prediction",
      "topics": [
        "get_dyna_residuals"
      ]
    },
    {
      "page": "get_iso_residuals",
      "title": "Residuals of isothermal prediction",
      "topics": [
        "get_iso_residuals"
      ]
    },
    {
      "page": "get_multi_dyna_residuals",
      "title": "Residuals of multiple dynamic predictions",
      "topics": [
        "get_multi_dyna_residuals"
      ]
    },
    {
      "page": "get_secondary_residuals",
      "title": "Residuals of secondary models",
      "topics": [
        "get_secondary_residuals"
      ]
    },
    {
      "page": "get_TTDs",
      "title": "Estimation of the Time to Detection of OD measurements",
      "topics": [
        "get_TTDs"
      ]
    },
    {
      "page": "GlobalGrowthComparison",
      "title": "GlobalGrowthComparison class",
      "topics": [
        "coef.GlobalGrowthComparison",
        "GlobalGrowthComparison",
        "plot.GlobalGrowthComparison",
        "print.GlobalGrowthComparison",
        "summary.GlobalGrowthComparison"
      ]
    },
    {
      "page": "GlobalGrowthFit",
      "title": "GlobalGrowthFit class",
      "topics": [
        "AIC.GlobalGrowthFit",
        "coef.GlobalGrowthFit",
        "deviance.GlobalGrowthFit",
        "fitted.GlobalGrowthFit",
        "GlobalGrowthFit",
        "logLik.GlobalGrowthFit",
        "plot.GlobalGrowthFit",
        "predict.GlobalGrowthFit",
        "predictMCMC.GlobalGrowthFit",
        "print.GlobalGrowthFit",
        "residuals.GlobalGrowthFit",
        "summary.GlobalGrowthFit",
        "vcov.GlobalGrowthFit"
      ]
    },
    {
      "page": "greek_tractors",
      "title": "Number of tractors in Greece according to the World Bank",
      "topics": [
        "greek_tractors"
      ]
    },
    {
      "page": "growth_pH_temperature",
      "title": "Example of dynamic growth",
      "topics": [
        "growth_pH_temperature"
      ]
    },
    {
      "page": "growth_salmonella",
      "title": "Growth of Salmonella spp in broth",
      "topics": [
        "growth_salmonella"
      ]
    },
    {
      "page": "GrowthComparison",
      "title": "GrowthComparison class",
      "topics": [
        "coef.GrowthComparison",
        "GrowthComparison",
        "plot.GrowthComparison",
        "print.GrowthComparison",
        "summary.GrowthComparison"
      ]
    },
    {
      "page": "GrowthFit",
      "title": "GrowthFit class",
      "topics": [
        "AIC.GrowthFit",
        "coef.GrowthFit",
        "deviance.GrowthFit",
        "fitted.GrowthFit",
        "GrowthFit",
        "logLik.GrowthFit",
        "plot.GrowthFit",
        "predict.GrowthFit",
        "predictMCMC.GrowthFit",
        "print.GrowthFit",
        "residuals.GrowthFit",
        "summary.GrowthFit",
        "vcov.GrowthFit"
      ]
    },
    {
      "page": "GrowthPrediction",
      "title": "GrowthPrediction class",
      "topics": [
        "coef.GrowthPrediction",
        "GrowthPrediction",
        "plot.GrowthPrediction",
        "print.GrowthPrediction",
        "summary.GrowthPrediction"
      ]
    },
    {
      "page": "GrowthUncertainty",
      "title": "GrowthUncertainty class",
      "topics": [
        "GrowthUncertainty",
        "plot.GrowthUncertainty",
        "print.GrowthUncertainty"
      ]
    },
    {
      "page": "inhibitory_model",
      "title": "Secondary model for inhibitory compounds",
      "topics": [
        "inhibitory_model"
      ]
    },
    {
      "page": "is.DynamicGrowth",
      "title": "Test of DynamicGrowth object",
      "topics": [
        "is.DynamicGrowth"
      ]
    },
    {
      "page": "is.FitDynamicGrowth",
      "title": "Test of FitDynamicGrowth object",
      "topics": [
        "is.FitDynamicGrowth"
      ]
    },
    {
      "page": "is.FitDynamicGrowthMCMC",
      "title": "Test of FitDynamicGrowthMCMC object",
      "topics": [
        "is.FitDynamicGrowthMCMC"
      ]
    },
    {
      "page": "is.FitIsoGrowth",
      "title": "Test of FitIsoGrowth object",
      "topics": [
        "is.FitIsoGrowth"
      ]
    },
    {
      "page": "is.FitMultipleDynamicGrowth",
      "title": "Test of FitMultipleDynamicGrowth object",
      "topics": [
        "is.FitMultipleDynamicGrowth"
      ]
    },
    {
      "page": "is.FitMultipleDynamicGrowthMCMC",
      "title": "Test of FitMultipleDynamicGrowthMCMC object",
      "topics": [
        "is.FitMultipleDynamicGrowthMCMC"
      ]
    },
    {
      "page": "is.FitSecondaryGrowth",
      "title": "Test of FitSecondaryGrowth object",
      "topics": [
        "is.FitSecondaryGrowth"
      ]
    },
    {
      "page": "is.GlobalGrowthFit",
      "title": "Test of GlobalGrowthFit object",
      "topics": [
        "is.GlobalGrowthFit"
      ]
    },
    {
      "page": "is.GrowthFit",
      "title": "Test of GrowthFit object",
      "topics": [
        "is.GrowthFit"
      ]
    },
    {
      "page": "is.GrowthPrediction",
      "title": "Test of GrowthPrediction object",
      "topics": [
        "is.GrowthPrediction"
      ]
    },
    {
      "page": "is.GrowthUncertainty",
      "title": "Test of GrowthUncertainty object",
      "topics": [
        "is.GrowthUncertainty"
      ]
    },
    {
      "page": "is.IsothermalGrowth",
      "title": "Test of IsothermalGrowth object",
      "topics": [
        "is.IsothermalGrowth"
      ]
    },
    {
      "page": "is.MCMCgrowth",
      "title": "Test of MCMCgrowth object",
      "topics": [
        "is.MCMCgrowth"
      ]
    },
    {
      "page": "is.StochasticGrowth",
      "title": "Test of StochasticGrowth object",
      "topics": [
        "is.StochasticGrowth"
      ]
    },
    {
      "page": "iso_Baranyi",
      "title": "Isothermal Baranyi model",
      "topics": [
        "iso_Baranyi"
      ]
    },
    {
      "page": "iso_Baranyi_noLag",
      "title": "Isothermal Baranyi model without lag phase",
      "topics": [
        "iso_Baranyi_noLag"
      ]
    },
    {
      "page": "iso_Baranyi_noStat",
      "title": "Isothermal Baranyi model without stationary phase",
      "topics": [
        "iso_Baranyi_noStat"
      ]
    },
    {
      "page": "iso_repGompertz",
      "title": "Reparameterized Gompertz model",
      "topics": [
        "gompertz",
        "iso_repGompertz",
        "modGompertz"
      ]
    },
    {
      "page": "IsothermalGrowth",
      "title": "IsothermalGrowth class",
      "topics": [
        "coef.IsothermalGrowth",
        "IsothermalGrowth",
        "plot.IsothermalGrowth",
        "print.IsothermalGrowth"
      ]
    },
    {
      "page": "lambda_to_Q0",
      "title": "Q0 from lag phase duration",
      "topics": [
        "lambda_to_Q0"
      ]
    },
    {
      "page": "logistic_model",
      "title": "Logistic growth model",
      "topics": [
        "logistic_model"
      ]
    },
    {
      "page": "loglinear_model",
      "title": "Loglinear model",
      "topics": [
        "loglinear_model"
      ]
    },
    {
      "page": "make_guess_coupled",
      "title": "Initial guesses for fitting the Baranyi-Ratkowsky model",
      "topics": [
        "make_guess_coupled"
      ]
    },
    {
      "page": "make_guess_factor",
      "title": "Initial guesses for the secondary model of one factor",
      "topics": [
        "make_guess_factor"
      ]
    },
    {
      "page": "make_guess_primary",
      "title": "Initial guesses for fitting primary growth models",
      "topics": [
        "make_guess_primary"
      ]
    },
    {
      "page": "make_guess_secondary",
      "title": "Initial guesses for the parameters of a secondary model",
      "topics": [
        "make_guess_secondary"
      ]
    },
    {
      "page": "MCMCcoupled",
      "title": "MCMCcoupled class",
      "topics": [
        "MCMCcoupled",
        "plot.MCMCcoupled"
      ]
    },
    {
      "page": "MCMCgrowth",
      "title": "MCMCgrowth class",
      "topics": [
        "MCMCgrowth",
        "plot.MCMCgrowth",
        "print.MCMCgrowth"
      ]
    },
    {
      "page": "multiple_conditions",
      "title": "Environmental conditions during several dynamic experiments",
      "topics": [
        "multiple_conditions"
      ]
    },
    {
      "page": "multiple_counts",
      "title": "Population growth observed in several dynamic experiments",
      "topics": [
        "multiple_counts"
      ]
    },
    {
      "page": "multiple_experiments",
      "title": "A set of growth experiments under dynamic conditions",
      "topics": [
        "multiple_experiments"
      ]
    },
    {
      "page": "pred_coupled_baranyi",
      "title": "Predictions of the coupled Baranyi model",
      "topics": [
        "pred_coupled_baranyi"
      ]
    },
    {
      "page": "pred_lambda",
      "title": "Prediction of lambda for the coupled model",
      "topics": [
        "pred_lambda"
      ]
    },
    {
      "page": "pred_sqmu",
      "title": "Prediction of the square root of mu for the coupled model",
      "topics": [
        "pred_sqmu"
      ]
    },
    {
      "page": "predict_dynamic_growth",
      "title": "Growth under dynamic conditions",
      "topics": [
        "predict_dynamic_growth"
      ]
    },
    {
      "page": "predict_growth",
      "title": "Prediction of microbial growth",
      "topics": [
        "predict_growth"
      ]
    },
    {
      "page": "predict_growth_uncertainty",
      "title": "Isothermal growth with parameter uncertainty",
      "topics": [
        "predict_growth_uncertainty"
      ]
    },
    {
      "page": "predict_isothermal_growth",
      "title": "Isothermal microbial growth",
      "topics": [
        "predict_isothermal_growth"
      ]
    },
    {
      "page": "predict_MCMC_growth",
      "title": "Stochastic growth of MCMC fit",
      "topics": [
        "predict_MCMC_growth"
      ]
    },
    {
      "page": "predict_stochastic_growth",
      "title": "Deprecated isothermal growth with parameter uncertainty",
      "topics": [
        "predict_stochastic_growth"
      ]
    },
    {
      "page": "predictMCMC",
      "title": "Generic for calculating predictions with uncertainty from fits",
      "topics": [
        "predictMCMC"
      ]
    },
    {
      "page": "predictMCMC_coupled",
      "title": "Generic for calculating predictions with uncertainty from fits",
      "topics": [
        "predictMCMC_coupled"
      ]
    },
    {
      "page": "primary_model_data",
      "title": "Metainformation of primary growth models",
      "topics": [
        "primary_model_data"
      ]
    },
    {
      "page": "Q0_to_lambda",
      "title": "Lag phase duration from Q0",
      "topics": [
        "Q0_to_lambda"
      ]
    },
    {
      "page": "refrigeratorSpain",
      "title": "Temperature recorded in refrigerators",
      "topics": [
        "refrigeratorSpain"
      ]
    },
    {
      "page": "residuals_lambda",
      "title": "Residuals for lambda for the coupled model",
      "topics": [
        "residuals_lambda"
      ]
    },
    {
      "page": "residuals_sqmu",
      "title": "Residuals for the square root of mu for the coupled model",
      "topics": [
        "residuals_sqmu"
      ]
    },
    {
      "page": "richards_model",
      "title": "Richards growth model",
      "topics": [
        "richards_model"
      ]
    },
    {
      "page": "Rossoaw_model",
      "title": "Secondary Rosso model for water activity",
      "topics": [
        "Rossoaw_model"
      ]
    },
    {
      "page": "secondary_model_data",
      "title": "Metainformation of secondary growth models",
      "topics": [
        "secondary_model_data"
      ]
    },
    {
      "page": "SecondaryComparison",
      "title": "SecondaryComparison class",
      "topics": [
        "coef.SecondaryComparison",
        "plot.SecondaryComparison",
        "print.SecondaryComparison",
        "SecondaryComparison",
        "summary.SecondaryComparison"
      ]
    },
    {
      "page": "show_guess_coupled",
      "title": "Plot of the initial guess for the Baranyi-Ratkowsky model",
      "topics": [
        "show_guess_coupled"
      ]
    },
    {
      "page": "show_guess_dynamic",
      "title": "Plot of the initial guess for growth under dynamic environmental conditions",
      "topics": [
        "show_guess_dynamic"
      ]
    },
    {
      "page": "show_guess_primary",
      "title": "Plot of the initial guess for growth under constant environmental conditions",
      "topics": [
        "show_guess_primary"
      ]
    },
    {
      "page": "StochasticGrowth",
      "title": "StochasticGrowth class",
      "topics": [
        "plot.StochasticGrowth",
        "print.StochasticGrowth",
        "StochasticGrowth"
      ]
    },
    {
      "page": "time_to_logcount",
      "title": "Time to reach a given microbial count",
      "topics": [
        "time_to_logcount"
      ]
    },
    {
      "page": "time_to_size",
      "title": "Time for the population to reach a given size",
      "topics": [
        "time_to_size"
      ]
    },
    {
      "page": "TimeDistribution",
      "title": "TimeDistribution class",
      "topics": [
        "plot.TimeDistribution",
        "print.TimeDistribution",
        "summary.TimeDistribution",
        "TimeDistribution"
      ]
    },
    {
      "page": "trilinear_model",
      "title": "Trilinear growth model",
      "topics": [
        "trilinear_model"
      ]
    },
    {
      "page": "zwietering_gamma",
      "title": "Zwietering gamma model",
      "topics": [
        "zwietering_gamma"
      ]
    }
  ],
  "_pkglogo": "https://github.com/albgarre/biogrowth/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/albgarre/biogrowth/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "coda",
    "cowplot",
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