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ZeBook (version 1.1)

Working with Dynamic Models for Agriculture and Environment

Description

R package accompanying the book Working with dynamic models for agriculture and environment, by Daniel Wallach (INRA), David Makowski (INRA), James W. Jones (U.of Florida), Francois Brun (ACTA). 3rd edition 2018-09-27.

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Version

Install

install.packages('ZeBook')

Monthly Downloads

117

Version

1.1

License

LGPL-3

Maintainer

Francois Brun

Last Published

November 9th, 2018

Functions in ZeBook (1.1)

carcass.EMI.model

The Carcass (growth of beef cattle) model with energy as input

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.define.param

Define values of the parameters for the Carcass model

The Carcass (growth of beef cattle) model

goodness.of.fit

Calcule multiple goodness-of-fit criteria

Plot output of a Classical SEIR model for plant disease

lactation.calf.model

The Lactation model

Grain Protein Contents in Wheat Grains

Working with Dynamic Models for Agriculture and Environment

The Magarey model

Plot output of a Classical SEIR model for plant disease

lactation.calf.model2

The Lactation model for use with lactation.calf.simule

Data of growth of beef cattle for Carcass model

The Magarey model, taking a vector of parameters as argument

maize.define.param

Define values of the parameters for the Maize model

lactation.calf.simule

Wrapper function to run the Lactation model for multiple sets of parameter values

carbonsoil.model

The CarbonSoil model - calculate daily values over designated time period

carrot.weevil.model

Carrot weevil development model

maize.multisy240

Wrapper function to run Maize model for multiple sets of input variables (site-year) and give Biomass at day240.

carbonsoil.update

The CarbonSoil model - calculate change in soil carbon for one year

lactation.define.param

Define values of the parameters for the Lactation model

lactation.machine.model

The Lactation model with milking machine

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

exponential.model.bis

The Exponential growth model of dynamic of population - another form

The basic Maize model.

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

Harvest index function for Muchow et al. (1990) Maize model

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

Leaf number function for Muchow et al. (1990) Maize model

exponential.model.ie

The Exponential growth model of dynamic of population - with improved Euler integration

q.arg.fast.runif

Build the q.arg argument for the FAST function (sensitivity analysis)

maize.muchow.model

Maize model, with harvest index and yield from Muchow et al. (1990)

maize.data_EuropeEU

maize biomass and leaf area data

Wrapping function to run maize model on several site-years

zakoks.original.model

Classical SEIR model for plant diseases from Zadoks (1971)

Read weather data for the Maize model

maize_cir.model

The Maize model with additional state variable CumInt

maize.data_MetaModelling

dataset of simulation for maize final biomass

population.age.model.ode

The PopulationAge model (Population Dynamics with Age Classes) - ode form

Senescence function for Muchow et al. (1990) Maize model

Expanded leaf area function for Muchow et al. (1990) Maize model

population.age.matrix.model

The PopulationAge model (Population Dynamics with Age Classes) - matrix form

predator.prey.model

The PredatorPrey model (Predator-Prey Lotka-Volterra with logistic equation for prey)

The Verhulst (logistic) model - calculate daily values over designated time period

Calculate AIC, Akaike's Information Criterion

Bean gene-based models dataset

verhulst.update

The Verhulst (logistic) model - calculate change for one day

Wrapper function to run the Weed model multiple times (for multiple sets of inputs)

The Weed model - calculate change for one year

epirice.define.param

Define values of the parameters for the Epirice model

The Weed model - calculate daily values over designated time period

weed.define.param

Define parameter values of the Weed model

population.age.model

The PopulationAge model (Population Dynamics with Age Classes)

seedweight.data

Wheat grain weight measurements after anthesis

watbal.define.param

Define values of the parameters for the WaterBalance model

WaterBalance model - calculate soil water over designated time period

Weather series for Gainesville (FL, USA) years 1982 and 1983

weather_SouthAsia

Weather series for southern Asia from NASA POWER agroclimatology

The Epirice model (Disease model for rice)

Sunflower_Phomopsis

Phomopsis stem canker observations for Sunflower

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)

WheatYieldGreece

National Wheat Yield evolution for Greece from FAO

Data of growth of chicks

The Cotton model (dynamic for numbers of Cotton fruiting points).

evaluation.criteria

Calcule multiple goodness-of-fit criteria

Wrapper function to run the Magarey model multiple times (for multiple sets of inputs)

Calculate effect of temperature on RUE for Maize

exponential.model

The Exponential growth model of dynamic of population

lactation.machine.model2

The Lactation model for use with lactation.machine.simule

magarey.define.param

Define values of the parameters for the Magarey model

The basic Maize model for use with maize.simule

maize.muchow.graph

Plot dynamic output of Muchow Maize model.

seedweight.model

The SeedWeight model

maize_cir_rue.model

The Maize model with temperature dependent RUE and CumInt

threshold.measures

Computation of threshold.measures

maize_cir_rue_ear.model

The Maize model with temperature dependent RUE, CumInt and ear growth

weather_EuropeEU

Weather serie for Europe EU from NASA POWER agroclimatology

param.rtriangle

Generate a random plan as a data frame. Columns are parameters. Values have triangle distribution

Generate a random plan as a data frame. Columns are parameters. Values have uniform distribution

weather_FranceWest

Weather series for western France from NASA POWER agroclimatology

WaterBalance model - calculate change in soil water for one day

Read weather data for the WaterBalance model (West of France Weather)

carcass.EMI.model2

The Carcass model function for use with carcass.EMI.simule