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biogrowth (version 1.0.6)

Modelling of Population Growth

Description

Modelling of population growth under static and dynamic environmental conditions. Includes functions for model fitting and making prediction under isothermal and dynamic conditions. The methods (algorithms & models) are based on predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).

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Version

Install

install.packages('biogrowth')

Monthly Downloads

852

Version

1.0.6

License

GPL-3

Maintainer

Alberto Garre

Last Published

March 17th, 2025

Functions in biogrowth (1.0.6)

FitDynamicGrowthMCMC

FitDynamicGrowthMCMC class
FitMultipleGrowthMCMC

FitMultipleGrowthMCMC class
FitMultipleDynamicGrowth

FitMultipleDynamicGrowth class
FitIsoGrowth

FitIsoGrowth class
FitDynamicGrowth

FitDynamicGrowth class
FitSecondaryGrowth

FitSecondaryGrowth class
FitCoupledGrowth

FitCoupledGrowth class
DynamicGrowth

DynamicGrowth class
CPM_model

Secondary Cardinal Parameter (CPM) model
Aryani_model

Secondary Aryani model
GrowthFit

GrowthFit class
GrowthUncertainty

GrowthUncertainty class
GrowthPrediction

GrowthPrediction class
GlobalGrowthFit

GlobalGrowthFit class
GrowthComparison

GrowthComparison class
IsothermalGrowth

IsothermalGrowth class
Rossoaw_model

Secondary Rosso model for water activity
Q0_to_lambda

Lag phase duration from Q0
GlobalGrowthComparison

GlobalGrowthComparison class
approx_env

Generates functions for linear interpolation of environmental conditions
MCMCgrowth

MCMCgrowth class
TimeDistribution

TimeDistribution class
check_secondary_pars

Basic checks of secondary parameters
SecondaryComparison

SecondaryComparison class
StochasticGrowth

StochasticGrowth class
arabian_tractors

Number of tractors in the Arab World according to the World Bank
bilinear_lag

Bilinear model with lag phase
check_stochastic_pars

Model definition checks for predict_stochastic_growth
cost_coupled_twosteps

Cost for the coupled model fitted in two-steps
dBaranyi

Baranyi growth model
conditions_pH_temperature

Conditions during a dynamic growth experiment
calculate_gammas_secondary

Gamma factors for fitting secondary models
check_growth_guess

Visual check of an initial guess of the model parameters
calculate_gammas

Calculates every gamma factor
distribution_to_logcount

Distribution of times to reach a certain microbial count
example_cardinal

Growth rates obtained for several growth experiments
cost_coupled_onestep

Residuals of the coupled Baranyi model
check_primary_pars

Basic check of parameters for primary models
full_Ratkowski

Full Ratkowsky model
bilinear_stationary

Bilinear model with stationary phase
example_coupled_twosteps

Example data for two-steps fitting of the Baranyi-Ratkowsky model
biogrowth-package

biogrowth: Modelling of Population Growth
example_coupled_onestep

Example data for two-steps fitting of the Baranyi-Ratkowsky model
example_env_conditions

Environmental conditions during a dynamic experiment
compare_growth_fits

Model comparison and selection for growth models
compare_secondary_fits

Model comparison and selection for secondary growth models
fit_dynamic_growth

Fit dynamic growth models
extract_primary_pars

A helper to build the primary models
fit_multiple_growth_MCMC

Fitting growth models to multiple dynamic experiments using MCMC
fit_secondary_growth

Fit secondary growth models
fit_MCMC_growth

Fit growth models using MCMC
example_dynamic_growth

Microbial growth under dynamic conditions
get_dyna_residuals

Residuals of dynamic prediction
extract_secondary_pars

A helper to build the secondary models
is.DynamicGrowth

Test of DynamicGrowth object
is.FitDynamicGrowth

Test of FitDynamicGrowth object
get_all_predictions

A helper for making the plots
fit_growth

Fitting microbial growth
is.FitMultipleDynamicGrowth

Test of FitMultipleDynamicGrowth object
is.FitIsoGrowth

Test of FitIsoGrowth object
is.FitDynamicGrowthMCMC

Test of FitDynamicGrowthMCMC object
is.GrowthPrediction

Test of GrowthPrediction object
is.GrowthFit

Test of GrowthFit object
fit_multiple_growth

Fitting growth models to multiple dynamic experiments
fit_isothermal_growth

Fit primary growth models
get_iso_residuals

Residuals of isothermal prediction
is.GlobalGrowthFit

Test of GlobalGrowthFit object
is.FitSecondaryGrowth

Test of FitSecondaryGrowth object
get_multi_dyna_residuals

Residuals of multiple dynamic predictions
is.MCMCgrowth

Test of MCMCgrowth object
fit_coupled_growth

Growth fitting considering link between mu and lambda for the Baranyi-Ratkowsky model
greek_tractors

Number of tractors in Greece according to the World Bank
make_guess_primary

Initial guesses for fitting primary growth models
inhibitory_model

Secondary model for inhibitory compounds
make_guess_secondary

Initial guesses for the parameters of a secondary model
growth_pH_temperature

Example of dynamic growth
growth_salmonella

Growth of Salmonella spp in broth
pred_lambda

Prediction of lambda for the coupled model
pred_sqmu

Prediction of the square root of mu for the coupled model
iso_Baranyi_noStat

Isothermal Baranyi model without stationary phase
get_secondary_residuals

Residuals of secondary models
is.GrowthUncertainty

Test of GrowthUncertainty object
is.IsothermalGrowth

Test of IsothermalGrowth object
predict_growth_uncertainty

Isothermal growth with parameter uncertainty
is.StochasticGrowth

Test of StochasticGrowth object
iso_Baranyi

Isothermal Baranyi model
multiple_conditions

Environmental conditions during several dynamic experiments
is.FitMultipleDynamicGrowthMCMC

Test of FitMultipleDynamicGrowthMCMC object
loglinear_model

Loglinear model
predict_isothermal_growth

Isothermal microbial growth
make_guess_factor

Initial guesses for the secondary model of one factor
multiple_counts

Population growth observed in several dynamic experiments
iso_Baranyi_noLag

Isothermal Baranyi model without lag phase
time_to_logcount

Time to reach a given microbial count
predictMCMC

Generic for calculating predictions with uncertainty from fits
show_guess_primary

Plot of the initial guess for growth under constant environmental conditions
predict_MCMC_growth

Stochastic growth of MCMC fit
iso_repGompertz

Reparameterized Gompertz model
secondary_model_data

Metainformation of secondary growth models
predict_growth

Prediction of microbial growth
predict_dynamic_growth

Growth under dynamic conditions
refrigeratorSpain

Temperature recorded in refrigerators
primary_model_data

Metainformation of primary growth models
predict_stochastic_growth

Deprecated isothermal growth with parameter uncertainty
show_guess_dynamic

Plot of the initial guess for growth under dynamic environmental conditions
residuals_lambda

Residuals for lambda for the coupled model
time_to_size

Time for the population to reach a given size
trilinear_model

Trilinear growth model
logistic_model

Logistic growth model
lambda_to_Q0

Q0 from lag phase duration
multiple_experiments

A set of growth experiments under dynamic conditions
richards_model

Richards growth model
pred_coupled_baranyi

Predictions of the coupled Baranyi model
residuals_sqmu

Residuals for the square root of mu for the coupled model
zwietering_gamma

Zwietering gamma model