# Modelling of Population Growth

## Documentation for package ‘biogrowth’ version 0.2.0

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

## Help Pages

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

## -- A --

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_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.FitDynamicGrowth | FitDynamicGrowth class
coef.FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class
coef.FitIsoGrowth | FitIsoGrowth class
coef.FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class
coef.FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class
coef.FitSecondaryGrowth | FitSecondaryGrowth class
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
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
fit_dynamic_growth | Fit dynamic growth models
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_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
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.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

## -- M --

MCMCgrowth | MCMCgrowth class
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.IsothermalGrowth | IsothermalGrowth class
plot.MCMCgrowth | MCMCgrowth 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_dynamic_growth | Growth under dynamic conditions
predict_isothermal_growth | Isothermal microbial growth
predict_MCMC_growth | Stochastic growth of MCMC fit
predict_stochastic_growth | Isothermal growth with variability
primary_model_data | Metainformation of primary growth models

## -- 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
richards_model | Richards growth model

## -- S --

secondary_model_data | Metainformation of secondary growth models
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

## -- T --

TimeDistribution | TimeDistribution class
time_to_logcount | Time to reach a given microbial count
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

## -- Z --

zwietering_gamma | Zwietering gamma model