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bioinactivation: a package for modelling microbial inactivation in R.

The bioinactivation package implements several function for the modelization of microbial inactivation in R. It includes:

  • functions for the prediction of isothermal or non-isothermal microbial inactivation.
  • functions for the adjustment of inactivation models to isothermal experiments.
  • functions for the fitting of inactivation models to dynamic experiments.
  • functions for the calculation of prediction intervals for isothermal or non-isothermal microbial inactivation processes.

The inactivation models most commonly used in industry and academia are implemented in this package:

  • Bigelow’s model.
  • Peleg’s model.
  • Mafart’s model.
  • Geeraerd’s model.

Furthermore, this package includes some training data sets mimicking isothermal and non-isothermal inactivation experiments.

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Version

Install

install.packages('bioinactivation')

Monthly Downloads

387

Version

1.3.1

License

GPL-3

Maintainer

Alberto Garre

Last Published

November 3rd, 2025

Functions in bioinactivation (1.3.1)

is.FitInactivation

Test of FitInactivation object
goodness_of_fit

Goodness of fit for microbial inactivation models
get_prediction_cost

Error of the Prediction of Microbial Inactivation
dGeeraerd_model

First Derivate of Geeraerd's Model
dPeleg_model

First Derivate of the Weibull-Peleg Model
dMafart_model

First Derivate of the Weibull-Mafart Model
goodness_MCMC

Goodness of fit for MCMC fits
dMetselaar_model

First Derivate of the Metselaar Model
get_isothermal_model_data

Isothermal Model Data
get_model_data

Mapping of Simulation Model Functions
laterosporus_iso

Example Isothermal Inactivation of a Laterosporus
is.SimulInactivation

Test of SimulInactivation object
is.PredInactivationMCMC

Test of PredInactivationMCMC object
plot.IsoFitInactivation

Plot of IsoFitInactivation Object
plot.FitInactivationMCMC

Plot of FitInactivationMCMC Object
time_to_logreduction

Time to reach X log reductions
fit_isothermal_inactivation

Fit of Isothermal Experiments
is.IsoFitInactivation

Test of IsoFitInactivation object
fit_inactivation_MCMC

Fitting of dynamic inactivation with MCMC
predict_inactivation

Prediction of Dynamic Inactivation
is.FitInactivationMCMC

Test of FitInactivationMCMC object
plot.SimulInactivation

Plot of SimulInactivation Object
sample_dynaFit

Random sample of the parameters of a FitInactivation object
plot.PredInactivationMCMC

Plot of PredInactivationMCMC Object
fit_dynamic_inactivation

Fitting of Dynamic Inactivation Models
goodness_iso

Goodness of fit for Isothermal fits
summary.FitInactivation

Summary of a FitInactivation object
dynamic_inactivation

Example Dynamic Inactivation of a Microorganis
goodness_dyna

Goodness of fit for Dynamic fits
isothermal_inactivation

Example Isothermal Inactivation of a Microorganis
predict_inactivation_MCMC

Dynamic Prediction Intervals from a Monte Carlo Adjustment
summary.FitInactivationMCMC

Summary of a FitInactivationMCMC object
summary.IsoFitInactivation

Summary of a IsoFitInactivation object
laterosporus_dyna

Example Dynamic Inactivation of a Laterosporus
plot.FitInactivation

Plot of FitInactivation Object
sample_IsoFit

Random sample of the parameters of a IsoFitInactivation object
sample_MCMCfit

Random sample of the parameters of a FitInactivationMCMC object
dArrhenius_model

First derivative of the Arrhenius model
dBigelow_model

First Derivate of the Linear Bigelow Model
Arrhenius_iso

Isothermal Arrhenius model
WeibullMafart_iso

Isothermal Weibull-Mafart Model
Bigelow_iso

Isothermal Bigelow's Model
check_model_params

Correctness Check of Model Parameters
build_temperature_interpolator

Continuum Interpolation of Discrete Temperatures Values
WeibullPeleg_iso

Isothermal Weibull-Peleg Model
Metselaar_iso

Isothermal Metselaar model
Geeraerd_iso

Isothermal Geeraerd Model