Package: bioinactivation 1.3.0.9999

bioinactivation: Mathematical Modelling of (Dynamic) Microbial Inactivation

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.

Authors:Alberto Garre [aut, cre], Pablo S. Fernandez [aut], Jose A. Egea [aut]

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bioinactivation.pdf |bioinactivation.html✨
bioinactivation/json (API)
NEWS

# Install 'bioinactivation' in R:
install.packages('bioinactivation', repos = c('https://albgarre.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/albgarre/bioinactivation/issues

Datasets:

On CRAN:

foodfood-safetyinactivation-modelsisothermal-experimentsprediction

3.95 score 18 scripts 314 downloads 1 mentions 14 exports 40 dependencies

Last updated 2 years agofrom:668e9d2344. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winNOTESep 27 2024
R-4.5-linuxNOTEOct 27 2024
R-4.4-winOKOct 27 2024
R-4.4-macOKOct 27 2024
R-4.3-winOKOct 27 2024
R-4.3-macOKOct 27 2024

Exports:fit_dynamic_inactivationfit_inactivation_MCMCfit_isothermal_inactivationget_isothermal_model_dataget_model_datagoodness_of_fitis.FitInactivationis.FitInactivationMCMCis.IsoFitInactivationis.PredInactivationMCMCis.SimulInactivationpredict_inactivationpredict_inactivation_MCMCtime_to_logreduction

Dependencies:clicodacolorspacedeSolvedplyrfansifarverFMEgenericsggplot2gluegtableisobandlabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvminpack.lmminqamunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcpprlangrootSolvescalestibbletidyselectutf8vctrsviridisLitewithr

bioinactivation: Software for modelling microbial inactivation

Alberto Garre, Pablo S. Fernandez, Jose A. Egea

Rendered frominactivation.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2019-08-02
Started: 2015-10-16

Readme and manuals

Help Manual

Help pageTopics
Isothermal Arrhenius modelArrhenius_iso
Isothermal Bigelow's ModelBigelow_iso
Continuum Interpolation of Discrete Temperatures Valuesbuild_temperature_interpolator
Correctness Check of Model Parameterscheck_model_params
First derivative of the Arrhenius modeldArrhenius_model
First Derivate of the Linear Bigelow ModeldBigelow_model
First Derivate of Geeraerd's ModeldGeeraerd_model
First Derivate of the Weibull-Mafart ModeldMafart_model
First Derivate of the Metselaar ModeldMetselaar_model
First Derivate of the Weibull-Peleg ModeldPeleg_model
Example Dynamic Inactivation of a Microorganisdynamic_inactivation
Fitting of Dynamic Inactivation Modelsfit_dynamic_inactivation
Fitting of dynamic inactivation with MCMCfit_inactivation_MCMC
Fit of Isothermal Experimentsfit_isothermal_inactivation
Isothermal Model Dataget_isothermal_model_data
Mapping of Simulation Model Functionsget_model_data
Error of the Prediction of Microbial Inactivationget_prediction_cost
Goodness of fit for Dynamic fitsgoodness_dyna
Goodness of fit for Isothermal fitsgoodness_iso
Goodness of fit for MCMC fitsgoodness_MCMC
Goodness of fit for microbial inactivation modelsgoodness_of_fit
Test of FitInactivation objectis.FitInactivation
Test of FitInactivationMCMC objectis.FitInactivationMCMC
Test of IsoFitInactivation objectis.IsoFitInactivation
Test of PredInactivationMCMC objectis.PredInactivationMCMC
Test of SimulInactivation objectis.SimulInactivation
Example Isothermal Inactivation of a Microorganisisothermal_inactivation
Example Dynamic Inactivation of a Laterosporuslaterosporus_dyna
Example Isothermal Inactivation of a Laterosporuslaterosporus_iso
Isothermal Metselaar modelMetselaar_iso
Plot of FitInactivation Objectplot.FitInactivation
Plot of FitInactivationMCMC Objectplot.FitInactivationMCMC
Plot of IsoFitInactivation Objectplot.IsoFitInactivation
Plot of PredInactivationMCMC Objectplot.PredInactivationMCMC
Plot of SimulInactivation Objectplot.SimulInactivation
Prediction of Dynamic Inactivationpredict_inactivation
Dynamic Prediction Intervals from a Monte Carlo Adjustmentpredict_inactivation_MCMC
Random sample of the parameters of a FitInactivation objectsample_dynaFit
Random sample of the parameters of a IsoFitInactivation objectsample_IsoFit
Random sample of the parameters of a FitInactivationMCMC objectsample_MCMCfit
Summary of a FitInactivation objectsummary.FitInactivation
Summary of a FitInactivationMCMC objectsummary.FitInactivationMCMC
Summary of a IsoFitInactivation objectsummary.IsoFitInactivation
Time to reach X log reductionstime_to_logreduction
Isothermal Weibull-Mafart ModelWeibullMafart_iso
Isothermal Weibull-Peleg ModelWeibullPeleg_iso