Modelling of Population Growth

[Up] [Top]

Documentation for package ‘biogrowth’ version 0.2.2

Help Pages


-- 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
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
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
gompertz Reparameterized Gompertz model
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.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
modGompertz Reparameterized Gompertz model
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