bioinactivation: Simulation of Dynamic Microbial Inactivation

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Prediction and adjustment to experimental data of microbial inactivation. Several models available in the literature are implemented.

Author
Alberto Garre [aut, cre], Pablo S. Fernandez [aut], Jose A. Egea [aut]
Date of publication
2016-09-18 13:02:59
Maintainer
Alberto Garre <garre.alberto@gmail.com>
License
GPL-3
Version
1.1.3

View on CRAN

Man pages

Bigelow_iso
Isothermal Bigelow's Model
build_temperature_interpolator
Continuum Interpolation of Discrete Temperatures Values
check_model_params
Correctness Check of Model Parameters
dBigelow_model
First Derivate of the Linear Bigelow Model
dGeeraerd_model
First Derivate of Geeraerd's Model
dMafart_model
First Derivate of the Weibull-Mafart Model
dPeleg_model
First Derivate of the Weibull-Peleg Model
dynamic_inactivation
Example Dynamic Inactivation of a Microorganis
fit_dynamic_inactivation
Fitting of Dynamic Inactivation Models
fit_inactivation_MCMC
Fitting of dynamic inactivation with MCMC
fit_isothermal_inactivation
Fit of Isothermal Experiments
get_isothermal_model_data
Isothermal Model Data
get_model_data
Mapping of Simulation Model Functions
get_prediction_cost
Error of the Prediction of Microbial Inactivation
is.FitInactivation
Test of FitInactivation object
is.FitInactivationMCMC
Test of FitInactivationMCMC object
is.IsoFitInactivation
Test of IsoFitInactivation object
isothermal_inactivation
Example Isothermal Inactivation of a Microorganis
is.PredInactivationMCMC
Test of PredInactivationMCMC object
is.SimulInactivation
Test of SimulInactivation object
laterosporus_dyna
Example Dynamic Inactivation of a Laterosporus
laterosporus_iso
Example Isothermal Inactivation of a Laterosporus
plot.FitInactivation
Plot of FitInactivation Object
plot.FitInactivationMCMC
Plot of FitInactivationMCMC Object
plot.IsoFitInactivation
Plot of IsoFitInactivation Object
plot.PredInactivationMCMC
Plot of PredInactivationMCMC Object
plot.SimulInactivation
Plot of SimulInactivation Object
predict_inactivation
Prediction of Dynamic Inactivation
predict_inactivation_MCMC
Dynamic Prediction Intervals from a Monte Carlo Adjustment
sample_dynaFit
Random sample of the parameters of a FitInactivation object
sample_IsoFit
Random sample of the parameters of a IsoFitInactivation...
sample_MCMCfit
Random sample of the parameters of a FitInactivationMCMC...
summary.FitInactivation
Summary of a FitInactivation object
summary.FitInactivationMCMC
Summary of a FitInactivationMCMC object
summary.IsoFitInactivation
Summary of a IsoFitInactivation object
WeibullMafart_iso
Isothermal Weibull-Mafart Model
WeibullPeleg_iso
Isothermal Weibull-Peleg Model

Files in this package

bioinactivation
bioinactivation/inst
bioinactivation/inst/doc
bioinactivation/inst/doc/inactivation.Rmd
bioinactivation/inst/doc/inactivation.html
bioinactivation/inst/doc/inactivation.R
bioinactivation/tests
bioinactivation/tests/testthat.R
bioinactivation/NAMESPACE
bioinactivation/data
bioinactivation/data/dynamic_inactivation.rda
bioinactivation/data/laterosporus_dyna.rda
bioinactivation/data/laterosporus_iso.rda
bioinactivation/data/isothermal_inactivation.rda
bioinactivation/R
bioinactivation/R/temperature_interpolation.R
bioinactivation/R/methods_s3_others.R
bioinactivation/R/geeraerd_model.R
bioinactivation/R/bigelow_model.R
bioinactivation/R/weibull-mafart_model.R
bioinactivation/R/function_mapping.R
bioinactivation/R/methods_s3_plot.R
bioinactivation/R/isothermal_models.R
bioinactivation/R/predict_MCMC.R
bioinactivation/R/calculate_cost.R
bioinactivation/R/weibull-peleg_model.R
bioinactivation/R/isothermal_fit.R
bioinactivation/R/fit_MCMC.R
bioinactivation/R/dynamic_fit.R
bioinactivation/R/make_predictions.R
bioinactivation/R/doc_examples.R
bioinactivation/vignettes
bioinactivation/vignettes/inactivation.Rmd
bioinactivation/README.md
bioinactivation/MD5
bioinactivation/build
bioinactivation/build/vignette.rds
bioinactivation/DESCRIPTION
bioinactivation/man
bioinactivation/man/predict_inactivation_MCMC.Rd
bioinactivation/man/Bigelow_iso.Rd
bioinactivation/man/is.PredInactivationMCMC.Rd
bioinactivation/man/sample_dynaFit.Rd
bioinactivation/man/check_model_params.Rd
bioinactivation/man/get_isothermal_model_data.Rd
bioinactivation/man/summary.FitInactivationMCMC.Rd
bioinactivation/man/WeibullMafart_iso.Rd
bioinactivation/man/isothermal_inactivation.Rd
bioinactivation/man/dPeleg_model.Rd
bioinactivation/man/predict_inactivation.Rd
bioinactivation/man/fit_isothermal_inactivation.Rd
bioinactivation/man/fit_inactivation_MCMC.Rd
bioinactivation/man/sample_IsoFit.Rd
bioinactivation/man/summary.IsoFitInactivation.Rd
bioinactivation/man/build_temperature_interpolator.Rd
bioinactivation/man/is.SimulInactivation.Rd
bioinactivation/man/plot.SimulInactivation.Rd
bioinactivation/man/plot.PredInactivationMCMC.Rd
bioinactivation/man/laterosporus_iso.Rd
bioinactivation/man/WeibullPeleg_iso.Rd
bioinactivation/man/get_model_data.Rd
bioinactivation/man/dBigelow_model.Rd
bioinactivation/man/fit_dynamic_inactivation.Rd
bioinactivation/man/sample_MCMCfit.Rd
bioinactivation/man/dGeeraerd_model.Rd
bioinactivation/man/plot.FitInactivationMCMC.Rd
bioinactivation/man/is.FitInactivationMCMC.Rd
bioinactivation/man/plot.IsoFitInactivation.Rd
bioinactivation/man/summary.FitInactivation.Rd
bioinactivation/man/laterosporus_dyna.Rd
bioinactivation/man/is.FitInactivation.Rd
bioinactivation/man/plot.FitInactivation.Rd
bioinactivation/man/dMafart_model.Rd
bioinactivation/man/get_prediction_cost.Rd
bioinactivation/man/dynamic_inactivation.Rd
bioinactivation/man/is.IsoFitInactivation.Rd