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bioinactivation  

Mathematical Modelling of (Dynamic) Microbial Inactivation
View on CRAN: Click here


Download and install bioinactivation package within the R console
Install from CRAN:
install.packages("bioinactivation")

Install from Github:
library("remotes")
install_github("cran/bioinactivation")

Install by package version:
library("remotes")
install_version("bioinactivation", "1.3.1")



Attach the package and use:
library("bioinactivation")
Maintained by
Alberto Garre
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-12-11
Latest Update: 2025-04-06
Description:
Functions for modelling microbial inactivation under isothermal or dynamic conditions. The calculations are based on several mathematical models broadly used by the scientific community and industry. Functions enable to make predictions for cases where the kinetic parameters are known. It also implements functions for parameter estimation for isothermal and dynamic conditions. The model fitting capabilities include an Adaptive Monte Carlo method for a Bayesian approach to parameter estimation.
How to cite:
Alberto Garre (2015). bioinactivation: Mathematical Modelling of (Dynamic) Microbial Inactivation. R package version 1.3.1, https://cran.r-project.org/web/packages/bioinactivation. Accessed 05 Jun. 2026.
Previous versions and publish date:
1.0.1 (2015-12-11 13:54), 1.1.1 (2016-02-04 14:57), 1.1.2 (2016-03-21 23:00), 1.1.3 (2016-09-18 13:03), 1.1.5 (2017-01-29 14:54), 1.2.0 (2017-11-23 22:03), 1.2.1 (2017-12-15 13:09), 1.2.2 (2019-06-05 10:40), 1.2.3 (2019-08-01 18:40), 1.3.0 (2025-04-06 12:40)
Other packages that cited bioinactivation R package
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Other R packages that bioinactivation depends, imports, suggests or enhances
Complete documentation for bioinactivation
Functions, R codes and Examples using the bioinactivation R package
Some associated functions: Arrhenius_iso . Bigelow_iso . Metselaar_iso . WeibullMafart_iso . WeibullPeleg_iso . build_temperature_interpolator . check_model_params . dArrhenius_model . dBigelow_model . dGeeraerd_model . dMafart_model . dMetselaar_model . dPeleg_model . dynamic_inactivation . fit_dynamic_inactivation . fit_inactivation_MCMC . fit_isothermal_inactivation . get_isothermal_model_data . get_model_data . get_prediction_cost . goodness_MCMC . goodness_dyna . goodness_iso . goodness_of_fit . is.FitInactivation . is.FitInactivationMCMC . is.IsoFitInactivation . is.PredInactivationMCMC . is.SimulInactivation . isothermal_inactivation . laterosporus_dyna . laterosporus_iso . plot.FitInactivation . plot.FitInactivationMCMC . plot.IsoFitInactivation . plot.PredInactivationMCMC . plot.SimulInactivation . predict_inactivation . predict_inactivation_MCMC . sample_IsoFit . sample_MCMCfit . sample_dynaFit . summary.FitInactivation . summary.FitInactivationMCMC . summary.IsoFitInactivation . time_to_logreduction . 
Some associated R codes: AIC_functions.R . arrhenius_model.R . bigelow_model.R . calculate_cost.R . doc_examples.R . dynamic_fit.R . fit_MCMC.R . function_mapping.R . geeraerd_model.R . isothermal_fit.R . isothermal_models.R . make_predictions.R . methods_s3_others.R . methods_s3_plot.R . metselaar_model.R . predict_MCMC.R . temperature_interpolation.R . time_to_reduction.R . weibull-mafart_model.R . weibull-peleg_model.R .  Full bioinactivation package functions and examples
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