R: Modelling of Population Growth

# Modelling of Population Growth

## Documentation for package ‘biogrowth’ version 1.0.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M P Q R S T V Z

## -- A --

AIC.FitCoupledGrowth | FitCoupledGrowth class
AIC.FitDynamicGrowth | FitDynamicGrowth class
AIC.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
AIC.FitIsoGrowth | FitIsoGrowth class
AIC.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
AIC.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
AIC.FitSecondaryGrowth | FitSecondaryGrowth class
AIC.GlobalGrowthFit | GlobalGrowthFit class
AIC.GrowthFit | GrowthFit class
approx_env | Generates functions for linear interpolation of environmental conditions
arabian_tractors | Number of tractors in the Arab World according to the World Bank
Aryani_model | Secondary Aryani model

## -- B --

bilinear_lag | Bilinear model with lag phase
bilinear_stationary | Bilinear model with stationary phase

## -- C --

calculate_gammas | Calculates every gamma factor
calculate_gammas_secondary | Gamma factors for fitting secondary models
check_growth_guess | Visual check of an initial guess of the model parameters
check_primary_pars | Basic check of parameters for primary models
check_secondary_pars | Basic checks of secondary parameters
check_stochastic_pars | Model definition checks for predict_stochastic_growth
coef.DynamicGrowth | DynamicGrowth class
coef.FitCoupledGrowth | FitCoupledGrowth class
coef.FitDynamicGrowth | FitDynamicGrowth class
coef.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
coef.FitIsoGrowth | FitIsoGrowth class
coef.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
coef.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
coef.FitSecondaryGrowth | FitSecondaryGrowth class
coef.GlobalGrowthComparison | GlobalGrowthComparison class
coef.GlobalGrowthFit | GlobalGrowthFit class
coef.GrowthComparison | GrowthComparison class
coef.GrowthFit | GrowthFit class
coef.GrowthPrediction | GrowthPrediction class
coef.IsothermalGrowth | IsothermalGrowth class
coef.SecondaryComparison | SecondaryComparison class
compare_growth_fits | Model comparison and selection for growth models
compare_secondary_fits | Model comparison and selection for secondary growth models
conditions_pH_temperature | Conditions during a dynamic growth experiment
cost_coupled_onestep | Residuals of the coupled Baranyi model
cost_coupled_twosteps | Cost for the coupled model fitted in two-steps
CPM_model | Secondary Cardinal Parameter (CPM) model

## -- D --

dBaranyi | Baranyi growth model
deviance.FitCoupledGrowth | FitCoupledGrowth class
deviance.FitDynamicGrowth | FitDynamicGrowth class
deviance.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
deviance.FitIsoGrowth | FitIsoGrowth class
deviance.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
deviance.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
deviance.FitSecondaryGrowth | FitSecondaryGrowth class
deviance.GlobalGrowthFit | GlobalGrowthFit class
deviance.GrowthFit | GrowthFit class
distribution_to_logcount | Distribution of times to reach a certain microbial count
DynamicGrowth | DynamicGrowth class

## -- E --

example_cardinal | Growth rates obtained for several growth experiments
example_coupled_onestep | Example data for two-steps fitting of the Baranyi-Ratkowsky model
example_coupled_twosteps | Example data for two-steps fitting of the Baranyi-Ratkowsky model
example_dynamic_growth | Microbial growth under dynamic conditions
example_env_conditions | Environmental conditions during a dynamic experiment
extract_primary_pars | A helper to build the primary models
extract_secondary_pars | A helper to build the secondary models

## -- F --

FitCoupledGrowth | FitCoupledGrowth class
FitDynamicGrowth | FitDynamicGrowth class
FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
FitIsoGrowth | FitIsoGrowth class
FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
FitSecondaryGrowth | FitSecondaryGrowth class
fitted.FitCoupledGrowth | FitCoupledGrowth class
fitted.FitDynamicGrowth | FitDynamicGrowth class
fitted.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
fitted.FitIsoGrowth | FitIsoGrowth class
fitted.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
fitted.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
fitted.FitSecondaryGrowth | FitSecondaryGrowth class
fitted.GlobalGrowthFit | GlobalGrowthFit class
fitted.GrowthFit | GrowthFit class
fit_coupled_growth | Growth fitting considering link between mu and lambda for the Baranyi-Ratkowsky model
fit_dynamic_growth | Fit dynamic growth models
fit_growth | Fitting microbial growth
fit_isothermal_growth | Fit primary growth models
fit_MCMC_growth | Fit growth models using MCMC
fit_multiple_growth | Fitting growth models to multiple dynamic experiments
fit_multiple_growth_MCMC | Fitting growth models to multiple dynamic experiments using MCMC
fit_secondary_growth | Fit secondary growth models
full_Ratkowski | Full Ratkowsky model

## -- G --

get_all_predictions | A helper for making the plots
get_dyna_residuals | Residuals of dynamic prediction
get_iso_residuals | Residuals of isothermal prediction
get_multi_dyna_residuals | Residuals of multiple dynamic predictions
get_secondary_residuals | Residuals of secondary models
GlobalGrowthComparison | GlobalGrowthComparison class
GlobalGrowthFit | GlobalGrowthFit class
gompertz | Reparameterized Gompertz model
greek_tractors | Number of tractors in Greece according to the World Bank
GrowthComparison | GrowthComparison class
GrowthFit | GrowthFit class
GrowthPrediction | GrowthPrediction class
GrowthUncertainty | GrowthUncertainty class
growth_pH_temperature | Example of dynamic growth
growth_salmonella | Growth of Salmonella spp in broth

## -- I --

inhibitory_model | Secondary model for inhibitory compounds
is.DynamicGrowth | Test of DynamicGrowth object
is.FitDynamicGrowth | Test of FitDynamicGrowth object
is.FitDynamicGrowthMCMC | Test of FitDynamicGrowthMCMC object
is.FitIsoGrowth | Test of FitIsoGrowth object
is.FitMultipleDynamicGrowth | Test of FitMultipleDynamicGrowth object
is.FitMultipleDynamicGrowthMCMC | Test of FitMultipleDynamicGrowthMCMC object
is.FitSecondaryGrowth | Test of FitSecondaryGrowth object
is.GlobalGrowthFit | Test of GlobalGrowthFit object
is.GrowthFit | Test of GrowthFit object
is.GrowthPrediction | Test of GrowthPrediction object
is.GrowthUncertainty | Test of GrowthUncertainty object
is.IsothermalGrowth | Test of IsothermalGrowth object
is.MCMCgrowth | Test of MCMCgrowth object
is.StochasticGrowth | Test of StochasticGrowth object
IsothermalGrowth | IsothermalGrowth class
iso_Baranyi | Isothermal Baranyi model
iso_Baranyi_noLag | Isothermal Baranyi model without lag phase
iso_Baranyi_noStat | Isothermal Baranyi model without stationary phase
iso_repGompertz | Reparameterized Gompertz model

## -- L --

lambda_to_Q0 | Q0 from lag phase duration
logistic_model | Logistic growth model
logLik.FitCoupledGrowth | FitCoupledGrowth class
logLik.FitDynamicGrowth | FitDynamicGrowth class
logLik.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
logLik.FitIsoGrowth | FitIsoGrowth class
logLik.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
logLik.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
logLik.FitSecondaryGrowth | FitSecondaryGrowth class
logLik.GlobalGrowthFit | GlobalGrowthFit class
logLik.GrowthFit | GrowthFit class
loglinear_model | Loglinear model

## -- M --

make_guess_factor | Initial guesses for the secondary model of one factor
make_guess_primary | Initial guesses for fitting primary growth models
make_guess_secondary | Initial guesses for the parameters of a secondary model
MCMCgrowth | MCMCgrowth class
modGompertz | Reparameterized Gompertz model
multiple_conditions | Environmental conditions during several dynamic experiments
multiple_counts | Population growth observed in several dynamic experiments
multiple_experiments | A set of growth experiments under dynamic conditions

## -- P --

plot.DynamicGrowth | DynamicGrowth class
plot.FitCoupledGrowth | FitCoupledGrowth class
plot.FitDynamicGrowth | FitDynamicGrowth class
plot.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
plot.FitIsoGrowth | FitIsoGrowth class
plot.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
plot.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
plot.FitSecondaryGrowth | FitSecondaryGrowth class
plot.GlobalGrowthComparison | GlobalGrowthComparison class
plot.GlobalGrowthFit | GlobalGrowthFit class
plot.GrowthComparison | GrowthComparison class
plot.GrowthFit | GrowthFit class
plot.GrowthPrediction | GrowthPrediction class
plot.GrowthUncertainty | GrowthUncertainty class
plot.IsothermalGrowth | IsothermalGrowth class
plot.MCMCgrowth | MCMCgrowth class
plot.SecondaryComparison | SecondaryComparison class
plot.StochasticGrowth | StochasticGrowth class
plot.TimeDistribution | TimeDistribution class
predict.FitCoupledGrowth | FitCoupledGrowth class
predict.FitDynamicGrowth | FitDynamicGrowth class
predict.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
predict.FitIsoGrowth | FitIsoGrowth class
predict.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
predict.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
predict.FitSecondaryGrowth | FitSecondaryGrowth class
predict.GlobalGrowthFit | GlobalGrowthFit class
predict.GrowthFit | GrowthFit class
predictMCMC | Generic for calculating predictions with uncertainty from fits
predictMCMC.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
predictMCMC.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
predictMCMC.GlobalGrowthFit | GlobalGrowthFit class
predictMCMC.GrowthFit | GrowthFit class
predict_dynamic_growth | Growth under dynamic conditions
predict_growth | Prediction of microbial growth
predict_growth_uncertainty | Isothermal growth with parameter uncertainty
predict_isothermal_growth | Isothermal microbial growth
predict_MCMC_growth | Stochastic growth of MCMC fit
predict_stochastic_growth | Deprecated isothermal growth with parameter uncertainty
pred_coupled_baranyi | Predictions of the coupled Baranyi model
pred_lambda | Prediction of lambda for the coupled model
pred_sqmu | Prediction of the square root of mu for the coupled model
primary_model_data | Metainformation of primary growth models
print.DynamicGrowth | DynamicGrowth class
print.FitCoupledGrowth | FitCoupledGrowth class
print.FitDynamicGrowth | FitDynamicGrowth class
print.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
print.FitIsoGrowth | FitIsoGrowth class
print.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
print.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
print.FitSecondaryGrowth | FitSecondaryGrowth class
print.GlobalGrowthComparison | GlobalGrowthComparison class
print.GlobalGrowthFit | GlobalGrowthFit class
print.GrowthComparison | GrowthComparison class
print.GrowthFit | GrowthFit class
print.GrowthPrediction | GrowthPrediction class
print.GrowthUncertainty | GrowthUncertainty class
print.IsothermalGrowth | IsothermalGrowth class
print.MCMCgrowth | MCMCgrowth class
print.SecondaryComparison | SecondaryComparison class
print.StochasticGrowth | StochasticGrowth class
print.TimeDistribution | TimeDistribution class

## -- Q --

Q0_to_lambda | Lag phase duration from Q0

## -- R --

refrigeratorSpain | Temperature recorded in refrigerators
residuals.FitCoupledGrowth | FitCoupledGrowth class
residuals.FitDynamicGrowth | FitDynamicGrowth class
residuals.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
residuals.FitIsoGrowth | FitIsoGrowth class
residuals.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
residuals.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
residuals.FitSecondaryGrowth | FitSecondaryGrowth class
residuals.GlobalGrowthFit | GlobalGrowthFit class
residuals.GrowthFit | GrowthFit class
residuals_lambda | Residuals for lambda for the coupled model
residuals_sqmu | Residuals for the square root of mu for the coupled model
richards_model | Richards growth model
Rossoaw_model | Secondary Rosso model for water activity

## -- S --

SecondaryComparison | SecondaryComparison class
secondary_model_data | Metainformation of secondary growth models
show_guess_dynamic | Plot of the initial guess for growth under dynamic environmental conditions
show_guess_primary | Plot of the initial guess for growth under constant environmental conditions
StochasticGrowth | StochasticGrowth class
summary.FitCoupledGrowth | FitCoupledGrowth class
summary.FitDynamicGrowth | FitDynamicGrowth class
summary.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
summary.FitIsoGrowth | FitIsoGrowth class
summary.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
summary.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
summary.FitSecondaryGrowth | FitSecondaryGrowth class
summary.GlobalGrowthComparison | GlobalGrowthComparison class
summary.GlobalGrowthFit | GlobalGrowthFit class
summary.GrowthComparison | GrowthComparison class
summary.GrowthFit | GrowthFit class
summary.GrowthPrediction | GrowthPrediction class
summary.SecondaryComparison | SecondaryComparison class
summary.TimeDistribution | TimeDistribution class

## -- T --

TimeDistribution | TimeDistribution class
time_to_logcount | Time to reach a given microbial count
time_to_size | Time for the population to reach a given size
trilinear_model | Trilinear growth model

## -- V --

vcov.FitCoupledGrowth | FitCoupledGrowth class
vcov.FitDynamicGrowth | FitDynamicGrowth class
vcov.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
vcov.FitIsoGrowth | FitIsoGrowth class
vcov.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
vcov.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
vcov.FitSecondaryGrowth | FitSecondaryGrowth class
vcov.GlobalGrowthFit | GlobalGrowthFit class
vcov.GrowthFit | GrowthFit class

## -- Z --

zwietering_gamma | Zwietering gamma model