Package index • predmicror

Fitting wrappers

Convenience wrappers for fitting and discovering predictive microbiology models.

fit_growth(): Fit a primary growth model

fit_inactivation(): Fit a microbial inactivation model

fit_cardinal(): Fit a cardinal parameter model

predmicror_models(): List models available through the fitting wrappers

Omnibus modelling

Nonlinear mixed-effects omnibus models using predmicror primary models and secondary covariate formulas.

fit_omnibus() fit_omnibus_growth() fit_omnibus_inactivation(): Fit omnibus predictive microbiology models

omnibus_secondary(): Define an omnibus secondary model

validate_omnibus_leave_one_out(): Validate an omnibus fit by leaving out one group

bias_factor() accuracy_factor(): Bias and accuracy factors

print(<predmicror_omnibus_fit>) summary(<predmicror_omnibus_fit>) coef(<predmicror_omnibus_fit>) fitted(<predmicror_omnibus_fit>) residuals(<predmicror_omnibus_fit>) predict(<predmicror_omnibus_fit>) logLik(<predmicror_omnibus_fit>) AIC(<predmicror_omnibus_fit>) BIC(<predmicror_omnibus_fit>): Methods for omnibus fits

Model diagnostics and comparison

Helpers for extracting fitted values, calculating metrics, and comparing fitted models.

predmicror_augment() as.data.frame(<predmicror_fit>): Extract fitted values and residuals from a predmicror fit

fit_metrics(): Calculate model diagnostics for a fitted predmicror model

compare_models(): Compare fitted predmicror models

print(<predmicror_fit>) summary(<predmicror_fit>) predict(<predmicror_fit>) plot(<predmicror_fit>) coef(<predmicror_fit>) fitted(<predmicror_fit>) residuals(<predmicror_fit>) vcov(<predmicror_fit>) logLik(<predmicror_fit>) AIC(<predmicror_fit>) BIC(<predmicror_fit>): Methods for predmicror_fit objects

Full growth models

Functions for fitting full growth models.

BaranyiFM(): Baranyi and Roberts full growth model

HuangFM(): Huang full growth model

RossoFM(): Rosso full growth model

ZwieteringFM(): Zwietering full growth model

No lag growth models

Functions for fitting no lag growth models.

FangNLM(): Fang no lag growth model

HuangNLM(): Huang no lag growth model

RichardsNLM(): Richards no lag growth model

Reduced growth models

Functions for fitting reduced growth models.

BaranyiRM(): Baranyi and Roberts reduced growth model

BuchananRM(): Buchanan reduced growth model

HuangRM(): Huang reduced growth model

Inactivation models

Functions for fitting inactivation models.

HuangRGS(): Huang reparameterized Gompertz survival model

WeibullM(): Weibull inactivation model Mafart

WeibullMM(): Weibull inactivation modified model Mafart

WeibullPH(): Weibull inactivation model Peleg and Huang

GeeraerdST(): Geeraerd inactivation model

Cardinal models

Functions for fitting cardinal models.

CMTI(): Cardinal model for temperature

CMPH(): Cardinal model for pH

CMAW(): Cardinal model for water activity

CMInh(): Cardinal model for growth inhibitors

Datasets

Datasets of example data.

aw: Data of aw

bixina: Data concerning Staphylococcus aureus microbial inactivation in beef

growthfull: Data of a complete curve of microbial growth

growthnolag: Data of a no lag curve of microbial growth

growthred: Data of a reduced curve of microbial growth

inh: Data of INH antimicrobials

ph: Data pH

salmonella: Potential growth of Salmonella typhimurium on cooked chicken

mafart2005Li11: Data of microbial inactivation Albert and Mafart (2005)

Dynamic models

Dynamic prediction and sensitivity tools for changing environmental profiles.

dynamic_profile(): Create a dynamic environmental profile

predict_dynamic_growth(): Predict microbial growth under dynamic environmental conditions

predict_dynamic_inactivation(): Predict microbial inactivation under dynamic environmental conditions

fit_dynamic_growth(): Fit dynamic microbial growth models

fit_dynamic_inactivation(): Fit dynamic microbial inactivation models

dynamic_sensitivity(): Finite-difference sensitivity for dynamic predictions

Assistant

Local helper for using predmicror.

predmicror_assistant(): Assistant for predmicror

predmicror_assistant_app(): Launch the predmicror assistant Shiny app