Man pages for biogrowth
Modelling of Population Growth
| approx_env | Generates functions for linear interpolation of environmental... |
| arabian_tractors | Number of tractors in the Arab World according to the World... |
| Aryani_model | Secondary Aryani model |
| bilinear_lag | Bilinear model with lag phase |
| bilinear_stationary | Bilinear model with stationary phase |
| biogrowth-package | biogrowth: Modelling of Population Growth |
| 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 |
| 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 |
| dBaranyi | Baranyi growth model |
| distribution_to_logcount | Distribution of times to reach a certain microbial count |
| DynamicGrowth | DynamicGrowth class |
| example_cardinal | Growth rates obtained for several growth experiments |
| example_coupled_onestep | Example data for two-steps fitting of the Baranyi-Ratkowsky... |
| example_coupled_twosteps | Example data for two-steps fitting of the Baranyi-Ratkowsky... |
| 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 |
| fit_coupled_growth | Growth fitting considering link between mu and lambda for the... |
| FitCoupledGrowth | FitCoupledGrowth class |
| fit_dynamic_growth | Fit dynamic growth models |
| FitDynamicGrowth | FitDynamicGrowth class |
| FitDynamicGrowthMCMC | FitDynamicGrowthMCMC class |
| fit_growth | Fitting microbial growth |
| FitIsoGrowth | FitIsoGrowth class |
| fit_isothermal_growth | Fit primary growth models |
| fit_MCMC_growth | Fit growth models using MCMC |
| FitMultipleDynamicGrowth | FitMultipleDynamicGrowth class |
| fit_multiple_growth | Fitting growth models to multiple dynamic experiments |
| fit_multiple_growth_MCMC | Fitting growth models to multiple dynamic experiments using... |
| FitMultipleGrowthMCMC | FitMultipleGrowthMCMC class |
| fit_secondary_growth | Fit secondary growth models |
| FitSecondaryGrowth | FitSecondaryGrowth class |
| full_Ratkowski | Full Ratkowsky model |
| 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 |
| greek_tractors | Number of tractors in Greece according to the World Bank |
| GrowthComparison | GrowthComparison class |
| GrowthFit | GrowthFit class |
| growth_pH_temperature | Example of dynamic growth |
| GrowthPrediction | GrowthPrediction class |
| growth_salmonella | Growth of Salmonella spp in broth |
| GrowthUncertainty | GrowthUncertainty class |
| 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 |
| 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 |
| IsothermalGrowth | IsothermalGrowth class |
| is.StochasticGrowth | Test of StochasticGrowth object |
| lambda_to_Q0 | Q0 from lag phase duration |
| logistic_model | Logistic growth model |
| loglinear_model | Loglinear model |
| 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 |
| 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 |
| pred_coupled_baranyi | Predictions of the coupled Baranyi model |
| 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 |
| predictMCMC | Generic for calculating predictions with uncertainty from... |
| predict_MCMC_growth | Stochastic growth of MCMC fit |
| predict_stochastic_growth | Deprecated isothermal growth with parameter uncertainty |
| 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 |
| Q0_to_lambda | Lag phase duration from Q0 |
| refrigeratorSpain | Temperature recorded in refrigerators |
| 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 |
| SecondaryComparison | SecondaryComparison class |
| secondary_model_data | Metainformation of secondary growth models |
| show_guess_dynamic | Plot of the initial guess for growth under dynamic... |
| show_guess_primary | Plot of the initial guess for growth under constant... |
| StochasticGrowth | StochasticGrowth class |
| 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 |
| zwietering_gamma | Zwietering gamma model |
