Working with Dynamic Crop Models

Methods, Tools and Examples for Agriculture and Environment

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

• Publisher: Academic Press
• Year: 2018
• eBook ISBN: 9780128117576
• Edition: 3
• Topic: Technology & Engineering
• Subtopic: Botany
• Index: Technology & Engineering

Working with Dynamic Crop Models: Methods, Tools and Examples for Agriculture and Environment, 3e, is a complete guide to working with dynamic system models, with emphasis on models in agronomy and environmental science. The introductory section presents the foundational information for the book including the basics of system models, simulation, the R programming language, and the statistical notions necessary for working with system models. The most important methods of working with dynamic system models, namely uncertainty and sensitivity analysis, model calibration (frequentist and Bayesian), model evaluation, and data assimilation are all treated in detail, in individual chapters. New chapters cover the use of multi-model ensembles, the creation of metamodels that emulate the more complex dynamic system models, the combination of genetic and environmental information in gene-based crop models, and the use of dynamic system models to aid in sampling. The book emphasizes both understanding and practical implementation of the methods that are covered. Each chapter simply and clearly explains the underlying principles and assumptions of each method that is presented, with numerous examples and illustrations. R code for applying the methods is given throughout. This code is designed so that it can be adapted relatively easily to new problems. - An expanded introductory section presents the basics of dynamic system modeling, with numerous examples from multiple fields, plus chapters on numerical simulation, statistics for modelers, and the R language - Covers in detail the basic methods: uncertainty and sensitivity analysis, model calibration (both frequentist and Bayesian), model evaluation, and data assimilation - Every method chapter has numerous examples of applications based on real problems, as well as detailed instructions for applying the methods to new problems using R - Each chapter has multiple exercises for self-testing or for classroom use - An R package with much of the code from the book can be freely downloaded from the CRAN package repository

Appendix 1

The Models Included in the ZeBook R Package: Description, R Code, and Examples of Results

1 Introduction

This appendix describes the models used in this book for which the R code is available in the ZeBook R package (Table A1.1). The models come from the domains of agronomy, plant protection, ecology, and the environment (linked to agronomy). All are dynamic with the exception of the SeedWeight and Magarey models. The more complex models referred to in this book are not included in the R package. For more details about those models, see the references given in the chapters.

Table A1.1

Models Included in the ZeBook R Package Used in This Book

Short Name	Description	Field	R Function in the ZeBook Package
SeedWeight	Grain filling for wheat (from Darroch and Baker, 1990)	Agronomy	seedweight.model
Magarey	Generic model of infection for foliar diseases caused by fungi (from Magarey et al., 2005)	Plant protection	magarey.model
CarbonSoil	Model of soil carbon content, annual time step (adapted from Hénin-Dupuis model, Jones et al., 2004)	Agronomy environment	carbonsoil.model
WaterBalance	Budget-based soil water balance model for grass (from Woli, 2010)	Agronomy	watbal.model
Maize	Model of crop growth for maize cultivated in potential conditions (based on widely used concepts for crop modeling)	Agronomy	maize.model
Verhulst	Homogenous population with limited food supply	Ecology	verhulst.model
PopulationAge	Population dynamics model with age classes	Ecology	population.age.model population.age.matrix.model population.age.model.ode
PredatorPrey	Predator-prey population dynamics model	Ecology	predator.prey.model
Weed	Model of wheat yield under conditions of a weed infestation of blackgrass (from Munier-Jolain et al., 2002)	Agronomy Plant protection	weed.model
Epirice	Disease model for rice (from Savary et al., 2012)	Plant protection	epirice.model
Cotton	Model of dynamic for numbers of cotton fruiting points (Wallach...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• Preface
• Acknowledgments
• Section A: Background
• Section B: Basic Methods
• Section C: Advanced Methods
• Appendix 1: The Models Included in the ZeBook R Package: Description, R Code, and Examples of Results
• Appendix 2: An Overview of the R Package ZeBook
• Index