Package: bioinactivation 1.3.0

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]

bioinactivation_1.3.0.tar.gz
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bioinactivation_1.3.0.tgz(r-4.6-any)bioinactivation_1.3.0.tgz(r-4.5-any)
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bioinactivation_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bioinactivation/json (API)

# Install 'bioinactivation' in R:

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

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

Datasets:

dynamic_inactivation - Example Dynamic Inactivation of a Microorganis
isothermal_inactivation - Example Isothermal Inactivation of a Microorganis
laterosporus_dyna - Example Dynamic Inactivation of a Laterosporus
laterosporus_iso - Example Isothermal Inactivation of a Laterosporus

On CRAN:

food food-safety inactivation-models isothermal-experiments prediction

4.02 score 21 scripts 374 downloads 1 mentions 14 exports 36 dependencies

Last updated from:3ca6bffa46. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	151
source / vignettes	OK	201
linux-release-x86_64	NOTE	145
macos-release-arm64	NOTE	96
macos-oldrel-arm64	NOTE	133
windows-devel	NOTE	105
windows-release	NOTE	113
windows-oldrel	NOTE	96
wasm-release	OK	117

Exports:fit_dynamic_inactivation fit_inactivation_MCMC fit_isothermal_inactivation get_isothermal_model_data get_model_data goodness_of_fit is.FitInactivation is.FitInactivationMCMC is.IsoFitInactivation is.PredInactivationMCMC is.SimulInactivation predict_inactivation predict_inactivation_MCMC time_to_logreduction

Dependencies:cli coda cpp11 deSolve dplyr farver FME generics ggplot2 glue gtable isoband labeling lattice lazyeval lifecycle magrittr MASS minpack.lm minqa pillar pkgconfig purrr R6 RColorBrewer Rcpp rlang rootSolve S7 scales tibble tidyselect utf8 vctrs viridisLite withr

bioinactivation: Software for modelling microbial inactivation

Rendered frominactivation.Rmdusingknitr::rmarkdown

Last update: 2025-04-07
Started: 2015-10-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Isothermal Arrhenius model	Arrhenius_iso
Isothermal Bigelow's Model	Bigelow_iso
Continuum Interpolation of Discrete Temperatures Values	build_temperature_interpolator
Correctness Check of Model Parameters	check_model_params
First derivative of the Arrhenius model	dArrhenius_model
First Derivate of the Linear Bigelow Model	dBigelow_model
First Derivate of Geeraerd's Model	dGeeraerd_model
First Derivate of the Weibull-Mafart Model	dMafart_model
First Derivate of the Metselaar Model	dMetselaar_model
First Derivate of the Weibull-Peleg Model	dPeleg_model
Example Dynamic Inactivation of a Microorganis	dynamic_inactivation
Fitting of Dynamic Inactivation Models	fit_dynamic_inactivation
Fitting of dynamic inactivation with MCMC	fit_inactivation_MCMC
Fit of Isothermal Experiments	fit_isothermal_inactivation
Isothermal Geeraerd Model	Geeraerd_iso
Isothermal Model Data	get_isothermal_model_data
Mapping of Simulation Model Functions	get_model_data
Error of the Prediction of Microbial Inactivation	get_prediction_cost
Goodness of fit for Dynamic fits	goodness_dyna
Goodness of fit for Isothermal fits	goodness_iso
Goodness of fit for MCMC fits	goodness_MCMC
Goodness of fit for microbial inactivation models	goodness_of_fit
Test of FitInactivation object	is.FitInactivation
Test of FitInactivationMCMC object	is.FitInactivationMCMC
Test of IsoFitInactivation object	is.IsoFitInactivation
Test of PredInactivationMCMC object	is.PredInactivationMCMC
Test of SimulInactivation object	is.SimulInactivation
Example Isothermal Inactivation of a Microorganis	isothermal_inactivation
Example Dynamic Inactivation of a Laterosporus	laterosporus_dyna
Example Isothermal Inactivation of a Laterosporus	laterosporus_iso
Isothermal Metselaar model	Metselaar_iso
Plot of FitInactivation Object	plot.FitInactivation
Plot of FitInactivationMCMC Object	plot.FitInactivationMCMC
Plot of IsoFitInactivation Object	plot.IsoFitInactivation
Plot of PredInactivationMCMC Object	plot.PredInactivationMCMC
Plot of SimulInactivation Object	plot.SimulInactivation
Prediction of Dynamic Inactivation	predict_inactivation
Dynamic Prediction Intervals from a Monte Carlo Adjustment	predict_inactivation_MCMC
Random sample of the parameters of a FitInactivation object	sample_dynaFit
Random sample of the parameters of a IsoFitInactivation object	sample_IsoFit
Random sample of the parameters of a FitInactivationMCMC object	sample_MCMCfit
Summary of a FitInactivation object	summary.FitInactivation
Summary of a FitInactivationMCMC object	summary.FitInactivationMCMC
Summary of a IsoFitInactivation object	summary.IsoFitInactivation
Time to reach X log reductions	time_to_logreduction
Isothermal Weibull-Mafart Model	WeibullMafart_iso
Isothermal Weibull-Peleg Model	WeibullPeleg_iso