Modelling of Population Growth

Documentation for package ‘biogrowth’ version 1.0.6

Help Pages

-- 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