Working with Dynamic Crop Models

This second edition of Working with Dynamic Crop Models is meant for self-learning by researchers or for use in graduate level courses devoted to methods for working with dynamic models in crop, agricultural, and related sciences.

Each chapter focuses on a particular topic and includes an introduction, a detailed explanation of the available methods, applications of the methods to one or two simple models that are followed throughout the book, real-life examples of the methods from literature, and finally a section detailing implementation of the methods using the R programming language.

The consistent use of R makes this book immediately and directly applicable to scientists seeking to develop models quickly and effectively, and the selected examples ensure broad appeal to scientists in various disciplines.

• 50% new content – 100% reviewed and updated
• Clearly explains practical application of the methods presented, including R language examples
• Presents real-life examples of core crop modeling methods, and ones that are translatable to dynamic system models in other fields

Researchers and students in agronomy, agricultural engineering, agricultural economics and agricultural statistics, and advanced biological systems modeling

Preface

Section 1: Basics

Chapter 1. Basics of Agricultural System Models

1 Introduction

2 System Models

3 Developing Dynamic System Models

4 Other Forms of System Models

5 Examples of Dynamic Agricultural System Models

Exercises

References

Chapter 2. Statistical Notions Useful for Modeling

1 Introduction

2 Random Variable

3 The Probability Distribution of a Random Variable

4 Several Random Variables

5 Samples, Estimators, and Estimates

6 Regression Models

7 Bayesian Statistics

Exercises

References

Chapter 3. The R Programming Language and Software

1 Introduction

2 Getting Started

3 Objects in R

4 Vectors (numerical, logical, character)

5 Other Data Structures

6 Read from and Write to File System

7 Control Structures

8 Functions

9 Graphics

10 Statistics and Probability

11 Advanced Data Processing

12 Additional Packages (libraries)

13 Running an External Model from R

14 Reducing Computing Time

Exercises

References

Chapter 4. Simulation with Dynamic System Models

1 Introduction

2 Simulating Continuous Time Models (differential equation form)

3 Simulation of System Models in Difference Equation Form

Exercises

References

Section 2: Methods

Chapter 5. Uncertainty and Sensitivity Analysis

1 Introduction

2 A Simple Example using Uncertainty and Sensitivity Analysis

3 Uncertainty Analysis

4 Sensitivity Analysis

5 Recommendations

6 R code Used in this Chapter

Exercises

References

Chapter 6. Parameter Estimation with Classical Methods (Model Calibration)

1 Introduction

2 An Overview of Model Calibration

3 The Statistics of Parameter Estimation

4 Application of Statistical Principles to System Models

5 Algorithms for OLS

6 R Functions for Parameter Estimation

Exercises

Models for Exercises

References

Chapter 7. Parameter Estimation with Bayesian Methods

1 Introduction

2 Ingredients for Implementing a Bayesian Estimation Method

3 Computation of Posterior Mode

4 Algorithms for Estimating Posterior Probability Distribution

5 Concluding Remarks

Exercises

References

Chapter 8. Data Assimilation for Dynamic Models

1 Introduction

2 Model Specification

3 Filter and Smoother for Gaussian Dynamic Linear Models

4 Filter and Smoother for Non-Linear Models

5 Concluding Remarks

Exercises

References

Chapter 9. Model Evaluation

1 Introduction

2 A Model as a Scientific Hypothesis

3 Comparing Simulated and Observed Values

4 From the Sample to the Population

5 The Predictive Quality of a Model

6 Summary

7 R Functions

Exercises

References

Chapter 10. Putting It All Together in a Case Study

1 Introduction

2 Description of the Case Study

3 How Difficult and Time-Consuming is Each Step?

4 R Code Used in This Chapter

Appendix 1. The Models Included in the ZeBook R Package: Description, R Code, and Examples of Results

1 Introduction

2 SeedWeight Model

3 Magarey Model

4 Soil Carbon Model

5 WaterBalance Model

6 Maize Crop Model

7 Verhulst Model

8 Population Age Model

9 Predator-Prey Model

10 Weed Model

11 EPIRICE Model

References

Appendix 2. An Overview of the R Package ZeBook

1 Introduction

2 Installation

3 Functions and Demos in the Zebook Package

4 How to use the ZeBook Package

5 List of Packages Needed

Index