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biogrowth (version 1.0.8)

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

394

Version

1.0.8

License

GPL-3

Maintainer

Alberto Garre

Last Published

December 18th, 2025

Functions in biogrowth (1.0.8)

GrowthComparison

GrowthComparison class

MCMCcoupled class

MCMCgrowth class

GlobalGrowthFit

GlobalGrowthFit class

IsothermalGrowth

IsothermalGrowth class

GrowthUncertainty

GrowthUncertainty class

GrowthFit class

Bilinear model with lag phase

biogrowth-package

biogrowth: Modelling of Population Growth

bilinear_stationary

Bilinear model with stationary phase

TimeDistribution

TimeDistribution class

GrowthPrediction

GrowthPrediction class

Generates functions for linear interpolation of environmental conditions

arabian_tractors

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

cost_coupled_onestep

Residuals of the coupled Baranyi model

Secondary Rosso model for water activity

Lag phase duration from Q0

calculate_gammas

Calculates every gamma factor

conditions_pH_temperature

Conditions during a dynamic growth experiment

check_growth_guess

Visual check of an initial guess of the model parameters

calculate_gammas_secondary

Gamma factors for fitting secondary models

check_primary_pars

Basic check of parameters for primary models

SecondaryComparison

SecondaryComparison class

StochasticGrowth

StochasticGrowth class

compare_growth_fits

Model comparison and selection for growth models

distribution_to_logcount

Distribution of times to reach a certain microbial count

compare_secondary_fits

Model comparison and selection for secondary growth models

example_coupled_onestep

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

extract_primary_pars

A helper to build the primary models

Example data for TTD calculation and the serial-dilution method

example_coupled_twosteps

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

cost_coupled_twosteps

Cost for the coupled model fitted in two-steps

check_secondary_pars

Basic checks of secondary parameters

check_stochastic_pars

Model definition checks for predict_stochastic_growth

example_cardinal

Growth rates obtained for several growth experiments

fit_multiple_growth_MCMC

Fitting growth models to multiple dynamic experiments using MCMC

fit_multiple_growth

Fitting growth models to multiple dynamic experiments

fit_isothermal_growth

Fit primary growth models

Fitting microbial growth

fit_secondary_growth

Fit secondary growth models

Baranyi growth model

fit_serial_dilution

Serial-fold dilution method

get_secondary_residuals

Residuals of secondary models

Number of tractors in Greece according to the World Bank

extract_secondary_pars

A helper to build the secondary models

get_iso_residuals

Residuals of isothermal prediction

get_multi_dyna_residuals

Residuals of multiple dynamic predictions

fit_MCMC_growth

Fit growth models using MCMC

is.GlobalGrowthFit

Test of GlobalGrowthFit object

Test of GrowthFit object

is.FitDynamicGrowth

Test of FitDynamicGrowth object

example_dynamic_growth

Microbial growth under dynamic conditions

is.FitMultipleDynamicGrowth

Test of FitMultipleDynamicGrowth object

Full Ratkowsky model

fit_dynamic_growth

Fit dynamic growth models

is.FitIsoGrowth

Test of FitIsoGrowth object

Estimation of the Time to Detection of OD measurements

fit_coupled_growth

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

is.DynamicGrowth

Test of DynamicGrowth object

growth_salmonella

Growth of Salmonella spp in broth

growth_pH_temperature

Example of dynamic growth

inhibitory_model

Secondary model for inhibitory compounds

example_env_conditions

Environmental conditions during a dynamic experiment

iso_Baranyi_noLag

Isothermal Baranyi model without lag phase

loglinear_model

Loglinear model

Logistic growth model

iso_Baranyi_noStat

Isothermal Baranyi model without stationary phase

is.IsothermalGrowth

Test of IsothermalGrowth object

Test of MCMCgrowth object

is.GrowthPrediction

Test of GrowthPrediction object

make_guess_primary

Initial guesses for fitting primary growth models

is.GrowthUncertainty

Test of GrowthUncertainty object

predict_dynamic_growth

Growth under dynamic conditions

predict_MCMC_growth

Stochastic growth of MCMC fit

multiple_experiments

A set of growth experiments under dynamic conditions

show_guess_primary

Plot of the initial guess for growth under constant environmental conditions

pred_coupled_baranyi

Predictions of the coupled Baranyi model

time_to_logcount

Time to reach a given microbial count

predict_growth_uncertainty

Isothermal growth with parameter uncertainty

multiple_counts

Population growth observed in several dynamic experiments

show_guess_dynamic

Plot of the initial guess for growth under dynamic environmental conditions

show_guess_coupled

Plot of the initial guess for the Baranyi-Ratkowsky model

Prediction of microbial growth

predict_isothermal_growth

Isothermal microbial growth

is.FitDynamicGrowthMCMC

Test of FitDynamicGrowthMCMC object

iso_repGompertz

Reparameterized Gompertz model

make_guess_factor

Initial guesses for the secondary model of one factor

make_guess_coupled

Initial guesses for fitting the Baranyi-Ratkowsky model

Q0 from lag phase duration

predict_stochastic_growth

Deprecated isothermal growth with parameter uncertainty

multiple_conditions

Environmental conditions during several dynamic experiments

get_all_predictions

A helper for making the plots

make_guess_secondary

Initial guesses for the parameters of a secondary model

Richards growth model

primary_model_data

Metainformation of primary growth models

Prediction of the square root of mu for the coupled model

get_dyna_residuals

Residuals of dynamic prediction

secondary_model_data

Metainformation of secondary growth models

Prediction of lambda for the coupled model

trilinear_model

Trilinear growth model

Time for the population to reach a given size

refrigeratorSpain

Temperature recorded in refrigerators

zwietering_gamma

Zwietering gamma model

is.FitSecondaryGrowth

Test of FitSecondaryGrowth object

Isothermal Baranyi model

is.StochasticGrowth

Test of StochasticGrowth object

is.FitMultipleDynamicGrowthMCMC

Test of FitMultipleDynamicGrowthMCMC object

residuals_lambda

Residuals for lambda for the coupled model

predictMCMC_coupled

Generic for calculating predictions with uncertainty from fits

Residuals for the square root of mu for the coupled model

Generic for calculating predictions with uncertainty from fits

FitDynamicGrowth

FitDynamicGrowth class

FitDynamicGrowthMCMC

FitDynamicGrowthMCMC class

FitSerial class

GlobalGrowthComparison

GlobalGrowthComparison class

FitSecondaryGrowth

FitSecondaryGrowth class

FitMultipleGrowthMCMC

FitMultipleGrowthMCMC class

Secondary Cardinal Parameter (CPM) model

Secondary Aryani model

FitMultipleDynamicGrowth

FitMultipleDynamicGrowth class

FitIsoGrowth class

DynamicGrowth class

FitCoupledGrowth

FitCoupledGrowth class