bioinactivation: Simulation of Dynamic Microbial Inactivation

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

Install the latest version of this package by entering the following in R:
install.packages("bioinactivation")
AuthorAlberto Garre [aut, cre], Pablo S. Fernandez [aut], Jose A. Egea [aut]
Date of publication2017-01-29 14:54:36
MaintainerAlberto Garre <garre.alberto@gmail.com>
LicenseGPL-3
Version1.1.5

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

Functions

Bigelow_iso Man page
build_temperature_interpolator Man page
check_model_params Man page
dBigelow_model Man page
dGeeraerd_model Man page
dMafart_model Man page
dPeleg_model Man page
dynamic_inactivation Man page
fit_dynamic_inactivation Man page
fit_inactivation_MCMC Man page
fit_isothermal_inactivation Man page
get_isothermal_model_data Man page
get_model_data Man page
get_prediction_cost Man page
is.FitInactivation Man page
is.FitInactivationMCMC Man page
is.IsoFitInactivation Man page
isothermal_inactivation Man page
is.PredInactivationMCMC Man page
is.SimulInactivation Man page
laterosporus_dyna Man page
laterosporus_iso Man page
plot.FitInactivation Man page
plot.FitInactivationMCMC Man page
plot.IsoFitInactivation Man page
plot.PredInactivationMCMC Man page
plot.SimulInactivation Man page
predict_inactivation Man page
predict_inactivation_MCMC Man page
sample_dynaFit Man page
sample_IsoFit Man page
sample_MCMCfit Man page
summary.FitInactivation Man page
summary.FitInactivationMCMC Man page
summary.IsoFitInactivation Man page
WeibullMafart_iso Man page
WeibullPeleg_iso Man page

Files

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

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