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biogrowth (version 1.0.3)

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

537

Version

1.0.3

License

GPL-3

Maintainer

Alberto Garre

Last Published

August 19th, 2023

Functions in biogrowth (1.0.3)

GlobalGrowthComparison

GlobalGrowthComparison class

FitDynamicGrowth

FitDynamicGrowth class

FitSecondaryGrowth

FitSecondaryGrowth class

FitMultipleDynamicGrowth

FitMultipleDynamicGrowth class

Secondary Cardinal Parameter (CPM) model

FitIsoGrowth class

FitDynamicGrowthMCMC

FitDynamicGrowthMCMC class

FitMultipleGrowthMCMC

FitMultipleGrowthMCMC class

DynamicGrowth class

GlobalGrowthFit

GlobalGrowthFit class

Lag phase duration from Q0

GrowthComparison

GrowthComparison class

StochasticGrowth

StochasticGrowth class

IsothermalGrowth

IsothermalGrowth class

TimeDistribution

TimeDistribution class

SecondaryComparison

SecondaryComparison class

GrowthPrediction

GrowthPrediction class

MCMCgrowth class

GrowthFit class

GrowthUncertainty

GrowthUncertainty class

biogrowth-package

biogrowth: Modelling of Population Growth

calculate_gammas

Calculates every gamma factor

check_stochastic_pars

Model definition checks for predict_stochastic_growth

calculate_gammas_secondary

Gamma factors for fitting secondary models

check_primary_pars

Basic check of parameters for primary models

check_growth_guess

Visual check of an initial guess of the model parameters

Generates functions for linear interpolation of environmental conditions

arabian_tractors

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

compare_growth_fits

Model comparison and selection for growth models

example_dynamic_growth

Microbial growth under dynamic conditions

check_secondary_pars

Basic checks of secondary parameters

fit_MCMC_growth

Fit growth models using MCMC

extract_secondary_pars

A helper to build the secondary models

example_cardinal

Growth rates obtained for several growth experiments

compare_secondary_fits

Model comparison and selection for secondary growth models

conditions_pH_temperature

Conditions during a dynamic growth experiment

Baranyi growth model

distribution_to_logcount

Distribution of times to reach a certain microbial count

extract_primary_pars

A helper to build the primary models

fit_multiple_growth_MCMC

Fitting growth models to multiple dynamic experiments using MCMC

fit_dynamic_growth

Fit dynamic growth models

example_env_conditions

Environmental conditions during a dynamic experiment

get_all_predictions

A helper for making the plots

Full Ratkowsky model

Fitting microbial growth

get_dyna_residuals

Residuals of dynamic prediction

fit_multiple_growth

Fitting growth models to multiple dynamic experiments

fit_isothermal_growth

Fit primary growth models

is.FitDynamicGrowth

Test of FitDynamicGrowth object

get_secondary_residuals

Residuals of secondary models

Number of tractors in Greece according to the World Bank

is.FitDynamicGrowthMCMC

Test of FitDynamicGrowthMCMC object

fit_secondary_growth

Fit secondary growth models

get_multi_dyna_residuals

Residuals of multiple dynamic predictions

is.FitMultipleDynamicGrowth

Test of FitMultipleDynamicGrowth object

is.FitIsoGrowth

Test of FitIsoGrowth object

growth_pH_temperature

Example of dynamic growth

iso_repGompertz

Reparameterized Gompertz model

Q0 from lag phase duration

Isothermal Baranyi model

is.StochasticGrowth

Test of StochasticGrowth object

is.FitSecondaryGrowth

Test of FitSecondaryGrowth object

is.FitMultipleDynamicGrowthMCMC

Test of FitMultipleDynamicGrowthMCMC object

make_guess_primary

Initial guesses for fitting primary growth models

Test of MCMCgrowth object

is.IsothermalGrowth

Test of IsothermalGrowth object

multiple_conditions

Environmental conditions during several dynamic experiments

multiple_experiments

A set of growth experiments under dynamic conditions

multiple_counts

Population growth observed in several dynamic experiments

get_iso_residuals

Residuals of isothermal prediction

make_guess_secondary

Initial guesses for the parameters of a secondary model

growth_salmonella

Growth of Salmonella spp in broth

is.GrowthPrediction

Test of GrowthPrediction object

is.DynamicGrowth

Test of DynamicGrowth object

predict_dynamic_growth

Growth under dynamic conditions

is.GrowthUncertainty

Test of GrowthUncertainty object

trilinear_model

Trilinear growth model

predict_MCMC_growth

Stochastic growth of MCMC fit

Generic for calculating predictions with uncertainty from fits

Richards growth model

secondary_model_data

Metainformation of secondary growth models

Test of GrowthFit object

is.GlobalGrowthFit

Test of GlobalGrowthFit object

make_guess_factor

Initial guesses for the secondary model of one factor

Logistic growth model

predict_growth_uncertainty

Isothermal growth with parameter uncertainty

Prediction of microbial growth

refrigeratorSpain

Temperature recorded in refrigerators

primary_model_data

Metainformation of primary growth models

zwietering_gamma

Zwietering gamma model

predict_isothermal_growth

Isothermal microbial growth

predict_stochastic_growth

Deprecated isothermal growth with parameter uncertainty

show_guess_dynamic

Plot of the initial guess for growth under dynamic environmental conditions

time_to_logcount

Time to reach a given microbial count

Time for the population to reach a given size

show_guess_primary

Plot of the initial guess for growth under constant environmental conditions