# Working with Dynamic Models for Agriculture and Environment

## Documentation for package ‘ZeBook’ version 1.2

- DESCRIPTION file
- Code demos. Use demo() to run them.

## Help Pages

AICf | Calculate AIC, Akaike's Information Criterion
Bean | Bean gene-based models dataset
carbonsoil.model | The CarbonSoil model - calculate daily values over designated time period
carbonsoil.update | The CarbonSoil model - calculate change in soil carbon for one year
carcass.define.param | Define values of the parameters for the Carcass model
carcass.EMI.model | The Carcass (growth of beef cattle) model with energy as input
carcass.EMI.model2 | The Carcass model function for use with carcass.EMI.simule
carcass.EMI.multi | Wrapper function to run Carcass model on several animals with different conditions
carcass.EMI.simule | Wrapper function to the Carcass model for multiple sets of parameter values
carcass.model | The Carcass (growth of beef cattle) model
carcass_data | Data of growth of beef cattle for Carcass model
carrot.weevil.model | Carrot weevil development model
chicks_data | Data of growth of chicks
cotton.model | The Cotton model (dynamic for numbers of Cotton fruiting points).
epirice.define.param | Define values of the parameters for the Epirice model
epirice.model | The Epirice model (Disease model for rice)
epirice.multi.simule | Wrapper function to run Epirice multiple times (for multiple sets of inputs)
epirice.weather | Read weather data for Epirice (southern Asia weather)
evaluation.criteria | Calcule multiple goodness-of-fit criteria
exponential.model | The Exponential growth model of dynamic of population
exponential.model.bis | The Exponential growth model of dynamic of population - another form
exponential.model.ie | The Exponential growth model of dynamic of population - with improved Euler integration
goodness.of.fit | Calcule multiple goodness-of-fit criteria
graph_epid | Plot output of a Classical SEIR model for plant disease
graph_epid_s | Plot output of a Classical SEIR model for plant disease
lactation.calf.model | The Lactation model
lactation.calf.model2 | The Lactation model for use with lactation.calf.simule
lactation.calf.simule | Wrapper function to run the Lactation model for multiple sets of parameter values
lactation.define.param | Define values of the parameters for the Lactation model
lactation.machine.model | The Lactation model with milking machine
lactation.machine.model2 | The Lactation model for use with lactation.machine.simule
magarey.define.param | Define values of the parameters for the Magarey model
magarey.model | The Magarey model
magarey.model2 | The Magarey model, taking a vector of parameters as argument
magarey.simule | Wrapper function to run the Magarey model multiple times (for multiple sets of inputs)
maize.data_EuropeEU | Maize Biomass and Leaf Area Data
maize.data_MetaModelling | dataset of simulation for maize final biomass
maize.define.param | Define values of the parameters for the Maize model
maize.model | The basic Maize model.
maize.model2 | The basic Maize model for use with maize.simule
maize.muchow.graph | Plot dynamic output of Muchow Maize model.
maize.muchow.model | Maize model, with harvest index and yield from Muchow et al. (1990)
maize.multisy | Wrapping function to run maize model on several site-years
maize.multisy240 | Wrapper function to run Maize model for multiple sets of input variables (site-year) and give Biomass at day240.
maize.RUEtemp | Calculate effect of temperature on RUE for Maize
maize.simule | Wrapper function to run Maize model for multiple sets of parameter values
maize.simule240 | Wrapper function to run Maize model multiple times for multiple sets of parameter values and give Biomass at day240
maize.simule_multisy240 | Wrapper function to run Maize model for multiple sets of parameter values (virtual design) and multiple sets of input variables (site-year) and give Biomass at day240
maize.weather | Read weather data for the Maize model
maize_cir.model | The Maize model with additional state variable CumInt
maize_cir_rue.model | The Maize model with temperature dependent RUE and CumInt
maize_cir_rue_ear.model | The Maize model with temperature dependent RUE, CumInt and ear growth
mm.A.fct | Expanded leaf area function for Muchow et al. (1990) Maize model
mm.FAS.fct | Senescence function for Muchow et al. (1990) Maize model
mm.HI.fct | Harvest index function for Muchow et al. (1990) Maize model
mm.LN.fct | Leaf number function for Muchow et al. (1990) Maize model
param.rtriangle | Generate a random plan as a data frame. Columns are parameters. Values have triangle distribution
param.runif | Generate a random plan as a data frame. Columns are parameters. Values have uniform distribution
population.age.matrix.model | The PopulationAge model (Population Dynamics with Age Classes) - matrix form
population.age.model | The PopulationAge model (Population Dynamics with Age Classes)
population.age.model.ode | The PopulationAge model (Population Dynamics with Age Classes) - ode form
predator.prey.model | The PredatorPrey model (Predator-Prey Lotka-Volterra with logistic equation for prey)
q.arg.fast.runif | Build the q.arg argument for the FAST function (sensitivity analysis)
seedweight.data | Wheat grain weight measurements after anthesis
seedweight.model | The SeedWeight model
Sunflower_Phomopsis | Phomopsis stem canker observations for Sunflower
threshold.measures | Computation of threshold.measures
verhulst.model | The Verhulst (logistic) model - calculate daily values over designated time period
verhulst.update | The Verhulst (logistic) model - calculate change for one day
watbal.define.param | Define values of the parameters for the WaterBalance model
watbal.model | WaterBalance model - calculate soil water over designated time period
watbal.model.arid | WaterBalance model - Variant with another order of calculation and ARID index
watbal.simobsdata | Soil water content measurements and associated simulations with WaterBalance model
watbal.update | WaterBalance model - calculate change in soil water for one day
watbal.weather | Read weather data for the WaterBalance model (West of France Weather)
weather_EuropeEU | Weather Series for Europe (EU) from NASA POWER Agroclimatology
weather_FranceWest | Weather series for western France from NASA POWER agroclimatology
weather_GNS | Weather series for Gainesville (FL, USA) years 1982 and 1983
weather_SouthAsia | Weather series for southern Asia from NASA POWER agroclimatology
weed.define.param | Define parameter values of the Weed model
weed.model | The Weed model - calculate daily values over designated time period
weed.simule | Wrapper function to run the Weed model multiple times (for multiple sets of inputs)
weed.update | The Weed model - calculate change for one year
WheatYieldGreece | National Wheat Yield evolution for Greece from FAO
Wheat_GPC | Grain Protein Contents in Wheat Grains
zakoks.original.model | Classical SEIR model for plant diseases from Zadoks (1971)