Package: ZeBook 1.1

ZeBook: Working with Dynamic Models for Agriculture and Environment

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.

Authors:Francois Brun, David Makowski, Daniel Wallach, James W. Jones.

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# Install 'ZeBook' in R:
install.packages('ZeBook', repos = c('https://fbrun-acta.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

72 exports 4 stars 0.49 score 3 dependencies 59 scripts 214 downloads

Last updated 6 years agofrom:b892a7e80a. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 14 2024
R-4.5-winOKSep 14 2024
R-4.5-linuxOKSep 14 2024
R-4.4-winOKSep 14 2024
R-4.4-macOKSep 14 2024
R-4.3-winOKSep 14 2024
R-4.3-macOKSep 14 2024

Exports:AICfcarbonsoil.modelcarbonsoil.updatecarcass.define.paramcarcass.EMI.modelcarcass.EMI.model2carcass.EMI.multicarcass.EMI.simulecarcass.modelcarrot.weevil.modelcotton.modelepirice.define.paramepirice.modelepirice.multi.simuleepirice.weatherevaluation.criteriaexponential.modelexponential.model.bisexponential.model.iegoodness.of.fitgraph_epidgraph_epid_slactation.calf.modellactation.calf.model2lactation.calf.simulelactation.define.paramlactation.machine.modellactation.machine.model2magarey.define.parammagarey.modelmagarey.model2magarey.simulemaize_cir_rue_ear.modelmaize_cir_rue.modelmaize_cir.modelmaize.define.parammaize.modelmaize.model2maize.muchow.graphmaize.muchow.modelmaize.multisymaize.multisy240maize.RUEtempmaize.simulemaize.simule_multisy240maize.simule240maize.weathermm.A.fctmm.FAS.fctmm.HI.fctmm.LN.fctparam.rtriangleparam.runifpopulation.age.matrix.modelpopulation.age.modelpopulation.age.model.odepredator.prey.modelq.arg.fast.runifseedweight.modelthreshold.measuresverhulst.modelverhulst.updatewatbal.define.paramwatbal.modelwatbal.model.aridwatbal.updatewatbal.weatherweed.define.paramweed.modelweed.simuleweed.updatezakoks.original.model

Dependencies:assertthatdeSolvetriangle

Readme and manuals

Help Manual

Help pageTopics
Working with Dynamic Models for Agriculture and EnvironmentZeBook-package ZeBook
Calculate AIC, Akaike's Information CriterionAICf
Bean gene-based models datasetBean
The CarbonSoil model - calculate daily values over designated time periodcarbonsoil.model
The CarbonSoil model - calculate change in soil carbon for one yearcarbonsoil.update
Data of growth of beef cattle for Carcass modelcarcass_data
Define values of the parameters for the Carcass modelcarcass.define.param
The Carcass (growth of beef cattle) model with energy as inputcarcass.EMI.model
The Carcass model function for use with carcass.EMI.simulecarcass.EMI.model2
Wrapper function to run Carcass model on several animals with different conditionscarcass.EMI.multi
Wrapper function to the Carcass model for multiple sets of parameter valuescarcass.EMI.simule
The Carcass (growth of beef cattle) modelcarcass.model
Carrot weevil development modelcarrot.weevil.model
Data of growth of chickschicks_data
The Cotton model (dynamic for numbers of Cotton fruiting points).cotton.model
Define values of the parameters for the Epirice modelepirice.define.param
The Epirice model (Disease model for rice)epirice.model
Wrapper function to run Epirice multiple times (for multiple sets of inputs)epirice.multi.simule
Read weather data for Epirice (southern Asia weather)epirice.weather
Calcule multiple goodness-of-fit criteriaevaluation.criteria
The Exponential growth model of dynamic of populationexponential.model
The Exponential growth model of dynamic of population - another formexponential.model.bis
The Exponential growth model of dynamic of population - with improved Euler integrationexponential.model.ie
Calcule multiple goodness-of-fit criteriagoodness.of.fit
Plot output of a Classical SEIR model for plant diseasegraph_epid
Plot output of a Classical SEIR model for plant diseasegraph_epid_s
The Lactation modellactation.calf.model
The Lactation model for use with lactation.calf.simulelactation.calf.model2
Wrapper function to run the Lactation model for multiple sets of parameter valueslactation.calf.simule
Define values of the parameters for the Lactation modellactation.define.param
The Lactation model with milking machinelactation.machine.model
The Lactation model for use with lactation.machine.simulelactation.machine.model2
Define values of the parameters for the Magarey modelmagarey.define.param
The Magarey modelmagarey.model
The Magarey model, taking a vector of parameters as argumentmagarey.model2
Wrapper function to run the Magarey model multiple times (for multiple sets of inputs)magarey.simule
The Maize model with temperature dependent RUE, CumInt and ear growthmaize_cir_rue_ear.model
The Maize model with temperature dependent RUE and CumIntmaize_cir_rue.model
The Maize model with additional state variable CumIntmaize_cir.model
maize biomass and leaf area datamaize.data_EuropeEU
dataset of simulation for maize final biomassmaize.data_MetaModelling
Define values of the parameters for the Maize modelmaize.define.param
The basic Maize model.maize.model
The basic Maize model for use with maize.simulemaize.model2
Plot dynamic output of Muchow Maize model.maize.muchow.graph
Maize model, with harvest index and yield from Muchow et al. (1990)maize.muchow.model
Wrapping function to run maize model on several site-yearsmaize.multisy
Wrapper function to run Maize model for multiple sets of input variables (site-year) and give Biomass at day240.maize.multisy240
Calculate effect of temperature on RUE for Maizemaize.RUEtemp
Wrapper function to run Maize model for multiple sets of parameter valuesmaize.simule
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 day240maize.simule_multisy240
Wrapper function to run Maize model multiple times for multiple sets of parameter values and give Biomass at day240maize.simule240
Read weather data for the Maize modelmaize.weather
Expanded leaf area function for Muchow et al. (1990) Maize modelmm.A.fct
Senescence function for Muchow et al. (1990) Maize modelmm.FAS.fct
Harvest index function for Muchow et al. (1990) Maize modelmm.HI.fct
Leaf number function for Muchow et al. (1990) Maize modelmm.LN.fct
Generate a random plan as a data frame. Columns are parameters. Values have triangle distributionparam.rtriangle
Generate a random plan as a data frame. Columns are parameters. Values have uniform distributionparam.runif
The PopulationAge model (Population Dynamics with Age Classes) - matrix formpopulation.age.matrix.model
The PopulationAge model (Population Dynamics with Age Classes)population.age.model
The PopulationAge model (Population Dynamics with Age Classes) - ode formpopulation.age.model.ode
The PredatorPrey model (Predator-Prey Lotka-Volterra with logistic equation for prey)predator.prey.model
Build the q.arg argument for the FAST function (sensitivity analysis)q.arg.fast.runif
Wheat grain weight measurements after anthesisseedweight.data
The SeedWeight modelseedweight.model
Phomopsis stem canker observations for SunflowerSunflower_Phomopsis
Computation of threshold.measuresthreshold.measures
The Verhulst (logistic) model - calculate daily values over designated time periodverhulst.model
The Verhulst (logistic) model - calculate change for one dayverhulst.update
Define values of the parameters for the WaterBalance modelwatbal.define.param
WaterBalance model - calculate soil water over designated time periodwatbal.model
WaterBalance model - Variant with another order of calculation and ARID indexwatbal.model.arid
Soil water content measurements and associated simulations with WaterBalance modelwatbal.simobsdata
WaterBalance model - calculate change in soil water for one daywatbal.update
Read weather data for the WaterBalance model (West of France Weather)watbal.weather
Weather serie for Europe EU from NASA POWER agroclimatologyweather_EuropeEU
Weather series for western France from NASA POWER agroclimatologyweather_FranceWest
Weather series for Gainesville (FL, USA) years 1982 and 1983weather_GNS
Weather series for southern Asia from NASA POWER agroclimatologyweather_SouthAsia
Define parameter values of the Weed modelweed.define.param
The Weed model - calculate daily values over designated time periodweed.model
Wrapper function to run the Weed model multiple times (for multiple sets of inputs)weed.simule
The Weed model - calculate change for one yearweed.update
Grain Protein Contents in Wheat GrainsWheat_GPC
National Wheat Yield evolution for Greece from FAOWheatYieldGreece
Classical SEIR model for plant diseases from Zadoks (1971)zakoks.original.model