Modelling of Population Growth


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Documentation for package ‘biogrowth’ version 1.0.0-3

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

-- A --

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

-- 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.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
CPM_model Secondary Cardinal Parameter (CPM) model

-- D --

dBaranyi Baranyi growth model
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_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 --

FitDynamicGrowth FitDynamicGrowth class
FitDynamicGrowthMCMC FitDynamicGrowthMCMC class
FitIsoGrowth FitIsoGrowth class
FitMultipleDynamicGrowth FitMultipleDynamicGrowth class
FitMultipleGrowthMCMC FitMultipleGrowthMCMC class
FitSecondaryGrowth FitSecondaryGrowth 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_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
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 --

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_repGompertz Reparameterized Gompertz model

-- L --

lambda_to_Q0 Q0 from lag phase duration
logistic_model Logistic growth model
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

-- 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.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.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
primary_model_data Metainformation of primary growth models
print.DynamicGrowth DynamicGrowth 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 --

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
richards_model Richards growth model

-- 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.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.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