Working with Dynamic Crop Models: Methods, Tools and Examples for Agriculture and Environment

Preface

Daniel Wallach, David Makowski, James Jones and François Brun

This second edition covers, for the most part, the same subjects as the first, but other than that it is a very different book. Such methods for working with system models as uncertainty and sensitivity analysis, parameter estimation (model calibration), and model evaluation and data assimilation are all still presented. One major difference is that this edition includes details of how to use R, a very widely used free programming language and platform, to implement all of the methods that are presented. A second major difference is in the examples that are used throughout the book. At the time of the first edition, there were relatively few examples of the application of the proposed techniques to dynamic system models in agronomy. The situation has evolved, and this allows us to show throughout how the methods are applied in real cases. In addition, every chapter has been extensively rewritten, and a substantial amount of new material has been added. Finally, introductory chapters have been added, so that this book can now be used as a self-contained introduction to modeling and modeling methods.

This book is meant as both a textbook for students and a resource for researchers who want to learn the methods for working with dynamic system models. The examples are from agronomy (models for crop growth and water balance), environment (models for soil carbon and soil nitrogen), ecology (population models), and plant pathology (disease dynamics) but the principles and methods apply to dynamic system models in general.

The very wide range of possible applications of agronomic dynamic system models has been discussed and illustrated in numerous journal papers and books. Nonetheless, there is a certain sense of disappointment and impatience that real-world applications have been nowhere near as widespread as imagined. We suggest that one major cause lies in the lack of information, methods, and tools for working with these models.

Most of the modeling efforts in the past have been devoted to better understanding of the processes and interactions involved in the complex systems treated in agro-ecology. This has led to major advances in our knowledge of these systems and our capacity to represent that knowledge in the form of mathematical equations. This aspect of modeling is far from over. As just a few examples we can mention studies of the mechanisms of drought resistance in plants, the effect of increased CO2 concentration on plant processes, the relationship between QTLs and plant behavior in the field, and the dissemination of pollen and thus of genetic modification between fields.

However, additional research aimed at understanding processes is not sufficient to produce models that are useful for solving real-world problems. The difficulty is that for systems as complex as those studied in agronomy and in environmental sciences, models are necessarily only rough approximations to the real world. This has two implications. First, it becomes very important to reduce prediction error as far as possible. Better understanding of processes is of course a major path for improving predictions, but parameter estimation is another very important path since the quality of model predictions depends crucially on both the functional forms of the equations and on the values of the parameters. Injecting additional real-time information (data assimilation) can also lead to a major improvement in prediction. Parameter estimation and data assimilation are covered in detail in this book. Secondly, it is essential to obtain realistic estimates of the error or uncertainty in model predictions. In fact, predictions are not very useful if one knows that the errors are important but one has no estimate of that error. Uncertainty analysis, sensitivity analysis, and model evaluation, all concerned with quantifying the uncertainty in model predictions, are also covered in detail in this book.

Even if one accepts that better methodology could play a major role in leading to more useful models, why a book specifically devoted to methodology for dynamic system models? After all, all of the methods are covered elsewhere. The answer is that it seems important to bring together in one place state-of-the-art methods that are useful for these models, and to illustrate them with examples from agro-ecology. A second motivation is that it is not sufficient to have a basic understanding of these methods; it is necessary to be able to apply them in practice. Previously, this required programming the methods oneself, a difficult undertaking. This is no longer the case, thanks to the R statistical software. This software is free, and there are packages that implement all of the methods presented in this book. This book presents in detail the R implementation of the methods in question.

The organization of this book is as follows: The first section covers preliminary material. Its first chapter explains the principles of dynamic system models. Several examples of dynamic system models are presented in detail, to illustrate concepts for developing such models and the types of models in question. The other chapters concern statistics (Chapter 2), the R language (Chapter 3), and simulation (Chapter 4). Together these chapters provide the background for understanding the rest of this book. This limits the prerequisites for this book to very basic notions of statistics and programming.

Section 2 concerns methods for working with dynamic system models. The order of the chapters follows approximately the order in which the methods would be used in an overall modeling project. Chapter 5 covers uncertainty analysis and sensitivity analysis. These methods allow one to explore the behavior of the model, get an idea of the uncertainties in prediction, and quantify different contributions to uncertainty. Chapter 6 concerns parameter estimation with classical statistical methods, also sometimes referred to as model calibration. The emphasis is on how statistical principles can be applied to complex system models. Chapter 7 concerns Bayesian parameter estimation. Currently, this method of parameter estimation is quite rare for dynamic system models, but it is reasonable to suppose that in the future it will attain much more importance, as it has in statistics in general. In this approach one uses prior information about the parameters, which is very well adapted to dynamic system models where there is information based on studies of the individual processes. Chapter 8 concerns data assimilation, which applies to the case where one has real-time observations that can be used to improve model predictions for the specific situation that is observed. Chapter 9 concerns the problem of model evaluation. A major emphasis is on the distinction between apparent error and prediction error, and on estimating prediction error. However, the chapter also covers other aspects of model evaluation, such as evaluating how well a model classifies outcomes, or how to evaluate probabilistic predictions. Chapters 5–9 describe and explain the methods in question, using examples of applications to models in agronomy, and present detailed explanations of how the methods can be implemented with R. The last chapter, Chapter 10, applies methods from the previous chapters to a simple dynamic system model, to show how the methods can be combined in an overall analysis.

There is an R package (called ZeBook) that accompanies this book. Like all R packages, this package can be freely obtained from any of the R download sites. It is most easily obtained by using the packages tab within the R software. The package contains many of the R programs used to create the examples in the book. In each case the model is coded as a function called by a main program, so that one could easily adapt these programs to apply the methods in question to one’s own model. The package also contains code and data for use with the exercises, to minimize the work not directly related to the main point of the exercises. The package contents are self-documented and are also described in Appendix 2 in this book. The package contents will evolve over time, to include additional models and data.

The book can be used for a one semester postgraduate course. The chapters can then be presented in the order in which they appear in this book. This corresponds to approximately one week per chapter, which implies a choice in each chapter of the major points. The self-learner has more leeway. The basic material in Section 1 is needed for the rest of the book, but of course one can skip some of those chapters if one is already familiar with the material. In Section 2 one can study the chapters in any order, since each chapter is self-contained.

In writing this book, D. Wallach took major responsibility for the chapters on statistical notions, frequentist parameter estimation, and model evaluation, D. Makowski was in charge of the chapters on uncertainty and sensitivity analysis, Bayesian parameter estimation, and data assimilation, Jim Jones handled the chapters on basics of system models and simulation, and François Brun handled the chapters on the R language and the case study, in addition to helping everywhere with the R programs and with preparing the R package.

Section 1

Basics

Outline

Chapter 1 Basics of Agricultural System Models

Chapter 2 Statistical Notions Useful for Modeling

Chapter 3 The R Programming Language and Software

Chapter 4 Simulation with Dynamic System Models

Chapter 1

Basics of Agricultural System Models

Agricultural systems are complex combinations of various components. These components contain a number of interacting biological, physical, and chemical processes that are manipulated by human managers to produce the most basic of human needs–food, fiber, and energy. In this chapter, we present concepts of system models with examples, along with methods for developing system models. System models can be viewed in two different, yet complementary ways. First, a model can be treated as a system of differential or difference equations that describe the dynamics of the system. Second, the model can be treated as a set of static equations that describe how responses of interest at particular times depend on explanatory variables. We present and discuss these two viewpoints in this chapter. As we shall see, the different methods described in this book may call for one or the other of these viewpoints. In this chapter, we start by presenting general systems concepts and definitions that are needed for modeling systems. Then we go through the process of developing a model of a system using an example with two simple interacting components that will help give students an intuitive understanding of the system modeling process. Example system models are presented for several important agricultural system components, demonstrating some of the key features and relationships used in model development.

Keywords

Agricultural models; systems; modeling; system models; Forrester diagram; differential equations; difference equations

1 Introduction

Agricultural systems are complex combinations of various components. These components contain a number of interacting biological, physical, and chemical processes that are manipulated by human managers to produce the most basic of human needs–food, fiber, and energy. Whereas the intensity of management varies considerably, agricultural production systems are affected by a number of uncontrolled factors in their environments, being exposed to natural cycles of weather, soil conditions, and pests and diseases. In comparison to physical and chemical systems, agricultural systems are much more difficult to manage and control because of the living system components that respond to their physical, chemical, and biological environmental conditions in highly nonlinear, time-varying ways that are frequently difficult to understand. These interactions and nonlinearities must be considered when attempts are made to understand agricultural systems’ responses to their environments and management. Dynamic system models are increasingly being used to describe agricultural systems to help scientists incorporate their understanding of the interactions among components for use in predicting performance of agricultural systems for better achieving goals of farmers (food production, profits) and of society (environmental quality, sustainability).

In this chapter, we present concepts of system models, with examples of various agricultural system models. We will also present methods for developing system models. Many agricultural system models already exist, and in some cases, there are multiple models of the same agricultural system. Examples include multiple models of cropping systems (Rosenzweig et al., 2013; Rotter et al., 2012); there are over 27 wheat crop production system models (Asseng et al., 2013). Thus, someone interested in analyzing a particular system could select from existing models and not have to worry about how the model was developed. However, it is also very important for model users to understand the models if they adopt an existing one. An understanding of model development methods will allow them to attain a deeper understanding of a particular model’s capabilities and limitations than they would otherwise have. Each model is a simplification of the real system, with assumptions that may or may not be acceptable for a particular application. It will help model users understand the assumptions and relationships used in specific models and enable them to better judge the suitability of a model for their purpose, thereby reducing the potential for using an existing model for purposes for which it was not designed or evaluated. It will also help model users determine if modifications are needed to an existing model, and if so, it will give them a basis for evaluating how this can be done.

System models can be viewed in two different, complementary ways. First, a model can be treated as a system of differential or difference equations that describe the dynamics of the system. Second, the model can be treated as a set of static equations that describe how responses of interest at particular times depend on explanatory variables. We present and discuss these two viewpoints in this chapter. As we shall see, the different methods described in this book may call for one or the other of these viewpoints.

In this chapter, we start off in Section 2 by presenting general systems concepts and definitions that are needed in modeling systems. Then in Section 3, we go through the process of developing a model of a system with two simple interacting components that will help give students an intuitive understanding of the system modeling process. In Section 4, we will present other forms frequently used to present agricultural systems models in various types of applications. Example system models will be presented in Section 5 for several important agricultural system components, demonstrating some of the key features and relationships used in model development.

2 System Models

A system is a set of components and their interrelationships that are grouped together by a person or a group of persons for the purposes of studying some part of the real world. Usually, a group of persons work together to define the system that they intend to analyze, and in many cases individuals are from different disciplines because of the scope of the system they intend to study. The selection of the components to include in a particular system depends on the objectives of analysts and on their understanding and perspectives of the real world. A system may have only a few components that interact or it may have many components that interact with each other and that may be affected by factors that are not included in the system. Conceptually, a system may consist of only one component; however, in this book we focus on the more common situation that exists in agricultural systems where the complexities of interactions among components are required to understand the performance of the system being studied.

2.1 Systems Approach

A systems approach starts with the definition of the system to be studied and includes development of a system model and the use of that model to analyze the system. Thus, it is important that all participants in a study have the same understanding of the objectives of the analyses that will be performed and of the system and its components. The systems approach provides an effective framework for interdisciplinary research, and thus it is important that the analyses include all disciplines at the start of a project and that an explicit definition of the system, its components, the interactions among system components, and the interactions of those components with other factors are agreed upon and communicated.

2.2 System Environment and Boundary

A system has an environment as well as components and interactions among them. The boundary of a system separates the system components from its environment. A system environment may include anything in the real world except the components being studied. We usually describe a system environment as factors that affect the behavior of components in the system but are not affected by them. For example, many agricultural systems are affected by weather conditions, but regardless of how the system components behave, they do not affect weather. A cropping system (Figure 1.1) may include soil and a crop which interact with each other and with the environment. The environment may have several variables that define the characteristics of the environment that directly influence some of the system component processes. The soil and crop system is usually defined as a homogenous field or representative area in the field that is exposed to weather throughout the course of a season. The boundary of this system would be an imaginary box immediately surrounding this representative uniform area in the field (e.g., with dimensions of 1 ha by 1 ha or of 1 m by 1 m in area), and a lower boundary in the soil at a 1 m depth. The environment would be everything in the soil and atmosphere outside of this imaginary box that would affect the soil and crop behavior in the system. Note that each system component may have multiple variables that describe the conditions of system components at any particular time. For example, the soil component may include soil water content, mineral nitrogen content, and soil organic matter that change from day to day. The crop component may include above ground biomass, leaf area, and depth of roots in the soil.

Figure 1.1 Schematic diagram of a cropping system model showing interactions between soil and crop components in the system and influences of explanatory variables from the environment. In this system, it is assumed that weather, management, pests in the biotic environment and soil variables in the soil environment (e.g., below 1 m in depth) influence the system but are not affected by system components.

This example also illustrates another important point; assumptions have to be made when choosing a system’s components and its environment. Here it is assumed that the temperature and humidity in the canopy are equal to the values of these variables in the air mass above the canopy. In reality, the soil and crop conditions affect canopy temperature and humidity through the transfer of heat and water vapor into the air above the crop, and thus the system does affect the immediate environment of the crop. This interaction may be important in many situations such that the system would include the canopy temperature and humidity. In the example, the assumption is that those effects are small relative to the influences of external factors, such as that of the external air mass. This assumption is made in most, but not all, existing cropping system models.

This example of a system and its environment can also be used to illustrate the implications of incorporating additional components into a system. If canopy air temperature and humidity are added to the soil and crop components, the system will include another component, the canopy air environment. This will cause the model to become more complex in that explicit mathematical relationships would be needed to model the dynamics of canopy air temperature and humidity in addition to the soil and crop conditions. The environment for this expanded system would still include weather conditions above the crop canopy.

2.3 System Model and Simulation

2.3.1 System Model

A system model is a mathematical representation of the system, including all of the interrelationships among components and effects of the environment on those components. The model description includes all of the equations of processes that cause components to change, all of the environmental variables that influence components in the system, all important properties of the system’s components, and all of the assumptions that were made to develop a particular model. It is common to find two models of the same system that are very different due to choices made by those developing each model. For example, the 27 wheat models used in the Asseng et al. (2013) study differ in the mathematical formulations used to model the same overall components and in the assumptions that were made to develop each model. This is true even though most of these wheat crop models have the same components and respond to the same environmental factors. The differences in the models are due to differences in assumptions among models about what controls the development and growth processes in the crop and how soil water and nitrogen change over time. These differences lead to differences in mathematical functions used to represent system dynamics and even to the variables used to describe the status of the crop and soil conditions at any point in time.

2.3.2 Simulation

Simulation refers to the numerical solution of the system model to produce values of the variables that represent the system components over time. Although in some literature, a model is referred to as a simulation model, this terminology hides an important and distinctive difference between a system model and its solution. Computer code should be developed based on the mathematical description and explicit assumptions. Otherwise, the assumptions and relationships may be hidden in the computer code and not easily understood or communicated to each modeling team member and to the outside world. Simulation is discussed in more detail in Chapter 4.

2.3.3 General Form of a Dynamic System Model

The general form of a dynamic system model in continuous time is:

(1)

Where t is time, U(t)=[U1(t),…,US(t)]T is the vector of state variables (defined below) at time t, X(t) is the vector of environmental variables at time t (sometimes referred to as exogenous, forcing, or driving variables), θ is the vector of system component properties that are included in the model to compute rates of change, and g1, g2, …, gS are mathematical relationships that describe the relationships among state variables, parameters, and environmental variables. The state variables U(t) could include, for example, leaf area index (leaf area per unit soil area), crop biomass, root depth, soil water content in each of several soil layers, etc. The explanatory variables X(t) typically include climate variables (such as daily maximum and minimum temperatures) and management variables (such as irrigation dates and amounts). As discussed in section 2.5 below, in the rest of this book we will use X(t) and θ to refer to explanatory variables and parameters, respectively, which is not quite the same definition as above.

The model of Equation (1) is a system of first order differential equations that describe rates of changes in each of the state variables of the system. It is dynamic in the sense that the solution (simulation) of the system of equations describes how the state variables evolve over time. It describes a system in the sense that there are several state variables that interact.

Continuous time dynamic systems are sometimes modeled using discrete time steps; in this case, the models are mathematically represented as a set of difference equations. We will later show how this is useful in simulation of the dynamic system model and the interpretation of dynamic models as response functions. By writing the left-hand side of Equation (1) as a discrete approximation of the derivative, it is straightforward to develop the general form of a dynamic system model in discrete time:

(2)

There is a very important concept underlying the use of Equations (1) and (2) to represent dynamic systems. Note that numerical methods are almost always needed to solve for behavior of system model variables over time, and Equation (2) is a highly useful and simple approach for solving dynamic system models. However, if the intent is to closely approximate the exact mathematical solution of a dynamic system model (i.e., if it could be solved analytically), one needs to select the time step Δt such that the numerical errors associated with approximating continuous time by discrete time steps are acceptable. Operationally when solving the model, one can evaluate the effects of choosing different values of Δt on important model results. On the other hand, model developers may select the Δt when developing the model because of the level of understanding of processes in the system and on the availability of environmental variables. In this case, all of the model equations and explanatory variables have to be developed specifically for the chosen time step, and this may require different approximations to the processes than those used when solving a model using continuous time. The mathematical form of such discrete time models may be represented as in Equation (2), and such models were referred to as ‘functional models’ by Addiscot and Wagenet (1985). An example is modeling soil water flow vs. soil depth and over time using the Richards equation (continuous time model) vs. using a so-called tipping bucket approach (with a daily time step). This will be discussed more in Chapter 4.

In some agricultural system models, such as many dynamic crop models, Δt is one day. One reason for this choice of time steps in many crop models is that highly important weather data may be available only at a daily time step (e.g., daily rainfall). In this case, the Δt on the left side becomes 1 and it disappears on the right-hand side of the equation. Note that Equation (2) is an approximation to the continuous model form. The choice of difference equations to model dynamic systems may mean that the model developer must use functional relationships that approximate the underlying physical, chemical, or biological processes involved. Thus, the development of functions (gi) that compute changes in the state variables need to take into account the time step used in discrete time models.

2.4 State Variables U(t)

State variables are quantities that describe the conditions of system components at any particular time. These state variables change with time in dynamic system models as components interact with each other and with the environment. A system may have only a few or many state variables. State variables play a central role in dynamic system models. The collection of state variables determines what is included in the system under study. A fundamental choice is involved here. For example, if it is decided to include soil mineral nitrogen within the system being studied, then soil mineral nitrogen will be a state variable and the model will include an equation to describe the evolution over time of this variable. If soil mineral nitrogen is not included as a state variable, it could still be included as an explanatory variable, i.e., its effect on plant growth and development could still be considered. However, in this case the values of soil mineral nitrogen over time would have to be supplied to the model; they would not be calculated within the model. The limits of the system being modeled are different in the two cases.

The choice of state variables is also fundamental for a second reason. It is assumed that the state variables at time t give a description of the system that is sufficient for calculating the future trajectory of the system. For example, if only root depth is included among the state variables and not variables describing root geometry, the implicit assumption is that the evolution of the system can be calculated on the basis of just root depth.

Furthermore, past values of root depth are not needed. Whatever effect they had is assumed to be taken into account once one knows all the state variables at time t. Given a dynamic model in the form of Equation (1) or (2), it is quite easy to identify the state variables. A state variable is a variable that appears both on the left side of an equation, so that the value is calculated by the model, and on the right side, since the values of the state variables determine the future trajectory of the system.

2.5 Explanatory Variables and Parameters

We adopt definitions for parameters and explanatory variables that are consistent with the various applications used throughout the rest of this book. Parameters are quantities that are unknown and are not measured directly. They must be estimated using observations of system behavior. Examples are the photoperiod sensitivity of a crop cultivar or the relative rate of decomposition of soil organic matter. These quantities are properties of the components of a system model. There may be other characteristics that can be measured, such as the soil depth or the carbon content in soil organic matter. Those are referred to as explanatory variables. In order to simulate dynamic system models, the values of all state variables must be known at time t=0 when the simulation begins. Some or all of these state variable initial values could possibly be measured and thus not be considered as parameters. However, initial conditions of state variables can also be considered as parameters if they are not measured but are rather estimated from past data.

Explanatory variables include the variables that are measured directly or known in some other way for each situation where the model is applied. They are variable in the sense that they may vary between situations. They include all environmental and management variables as well as system component properties that are known or measured.

Parameters and constants are used in the mathematical relationships of the system model, quantifying how component state variables change. Constants are quantities that remain the same regardless of the conditions and assumptions made about model components. Examples of constants include the molecular weight of glucose, the gravitational constant, and the number of minutes in a day.

Environmental variables help explain the influence of the environment on the system and are assumed not to be influenced at all by the system. Explanatory variables (including environmental variables) and parameters can be recognized by the fact that they appear only on the right-hand side of Equations (1) and (2). They enter into the calculation of the system dynamics but are not themselves calculated by the model. Another difference between explanatory variables and parameters is that explanatory variables are measured or observed for each situation where the model is applied. Thus for example daily maximum and minimum temperatures are measured values that influence crop growth and soil water processes in a system but are assumed not to be influenced by the status of the crop and soil water. Parameters, on the other hand, are estimated from a set of past data. Generally, an explanatory variable can differ depending on the situation, while a parameter is by definition constant across all situations of interest.

The explanatory variables likewise imply a basic decision about what is important in determining the dynamics of the system. In the chapter on model evaluation, we will discuss in detail how the choice of explanatory variables affects model predictive quality. Briefly, adding additional explanatory variables have two opposite effects. On the one hand, added explanatory variables permit one to explain more of the variability in the system, and thus offer the possibility of improved predictions. On the other hand, the additional explanatory variables normally require additional equations and may lead to a need for more parameters that need to be estimated, which can lead to additional errors and thus less accurate predictions (see Chapter 9).

3 Developing Dynamic System Models

3.1 Methods

We present one method that is widely used in developing models of dynamic systems that was first used in modeling industrial management systems (Forrester, 1961, 1971). This approach has been used to schematically represent various agricultural, biological, and ecological systems and to develop the mathematical relationships to represent interactions among system components (e.g., Dent and Blackie, 1979; Odum, 1973; Penning de Vries and van Laar, 1982; Jones and Luyten, 1998). A number of software packages have been developed to help users develop these diagrams of dynamic systems and to develop a set of first order differential equations for the system (e.g., Stella, http://www.iseesystems.com/softwares/Education/StellaSoftware.aspx; and MATLAB, http://www.mathworks.com/products/matlab/). The basic idea of this approach is to define the components of a system, define the state variables that are to be used to represent each of the components in the system, and then identify the processes that cause the state variables to change. This approach is particularly effective in conceptualizing what components to include and how they interact during model development and it provides an easily understood picture for documenting the model structure in publications. One key feature of these diagrams is that first order differential equations like those in Equation (1) can be developed from the diagram itself. This feature will be shown below.

A system component may have more than one state variable to represent its status at any particular time, such as variables of leaf, stem, and grain biomass of a crop component. In Forrester diagrams, each state variable is represented by a box or a compartment in the Forrester terminology (Figure 1.2). Generally, these compartments can represent any state variable that changes over time in response to flows into and/or out of the compartments, including mass, volume, energy, numbers of entities, dollars, etc. Compartments may be used to represent a state variable that is assumed to be homogenous over some spatial dimension, such as the average soil water content in a soil 1 m in depth and 1 km² in area. If model developers want to represent spatial variability in their model, then their overall spatial domain can be divided into multiple compartments within which state variables are assumed to be homogenous within the smaller spatial units, and processes to represent the transport among spatial units of the variable that is ‘stored’ in the compartment. We will show an example of such a system model later in this chapter.

Figure 1.2 Basic symbols adapted from Forrester (1961) that are used to build conceptual system models: (a) the ‘level’ of the material that is stored in the compartment, which is a state variable of a system component; (b) a rate of transport or transformation of the stored material; (c) a source of material that enters the system from the environment or a sink that represents flow of material from the system into the environment (with the arrow pointing to the cloud symbol); (d) an auxiliary variable affecting some compartment or flow; (e) pathway for material flow; and (f) pathway for information flow, showing influences among components.

A conceptual model represented by Forrester diagrams shows a network of system compartments representing all relevant components in the system. The compartments are connected by lines that represent the flow of quantities among compartments and between the system environment and the components. Dashed lines in the diagrams represent information flow or influence of some auxiliary variable (such as a parameter). Figure 1.2 shows an abbreviated set of symbols from Forrester (1961); these are the most commonly used symbols and the ones needed to represent the overall structure of a system model. Another way to understand this approach is that it usually represents a mass, energy, or other material balance, with flows of some quantity among compartments.

The ‘level’ represents the state variable at a point in time and is shown by a rectangle. Conceptually, these levels should be selected based on what is stored and flows among compartments, such as mass or volume of water or biomass. This is important when developing the overall system of equations for the model. For example, the water volume in a soil component of a particular dimension is what is stored and what flows into and from the component. However, one may be interested in the concentration of water in the soil volume, which can be computed by dividing the soil water volume by the total volume of the soil component. Note that water volume (e.g., mm³ of water per unit area) is the variable that is transported into and out of the homogenous unit area compartment and is stored, not the concentration (the volumetric soil water content, mm³[water]/mm³[soil volume]). First, developing the Forrester diagrams using variables that are stored in the compartments as state variables helps one develop the right system equations and also check the equations for dimensional consistency.

The ‘rate’ symbol always has a solid arrow representing the pathway for material flow, or rate of accumulation of some variable, with the arrow showing direction of flow. Flow can occur in both directions, so the solid lines can have arrowheads on each end. These rate symbols represent processes that cause the level or state variable in a compartment to change. Thus, there is always one or more equations that are required to represent each flow. Auxiliary variables are shown by circles with dashed lines pointing to the rate or level symbols showing influence of explanatory variables, parameters, and constants. For example, temperature of the environment may affect the biomass accumulation rate in a crop model. Dashed lines without the circle are used to show causal influences on rates or levels.

In practice, system modelers usually develop an initial diagram showing all of the compartments that represent state variables and show rates of transformation or transport among compartments without showing auxiliary variables because they may not be known yet. After a compartment model is constructed, even though it may not show auxiliary variables, one can write the overall mathematical model representing the system (Equation (1)) using the structure of the Forrester diagram and component descriptions. From the diagram itself, one can write differential equations for each compartment (i.e., for each state variable):

(3)

where

Uj(t)=value or level of the jth state variable

=net rate of change in the level of the jth state variable

Ii,j(t)=rate of flow into level j from the ith state variable at time t

Oj,k(t)=rate of flow from the jth state variable into level k at time t

inj(t)=rate of flow into compartment j from outside the system

outj(t)=rate of flow out of compartment j, with the flow leaving the system

By applying this equation to each compartment in the system, a set of first order differential equations is obtained. The number of these first order differential equations, referred to as the dimensionality of the system model, is thus equal to the number of state variables. However, this is only the first step in developing the complete mathematical model. Each of the flows must be described using mathematical functions in terms of the system state variables, explanatory variables, and parameters. This is not a trivial task; it requires knowledge of what drives the process rates. Sometimes, this knowledge comes from basic principles, such as the flow of heat from an object of higher temperature into an object with lower temperature. However, in many cases, the flow equations are not easily derived from basic laws of physics and thermodynamics. This is true in most agricultural system models, partly due to the scale at which these systems are modeled (time and space) and the complexities of the processes involved. In these cases, model developers rely on simple functions to represent flows, based on empirical data and reasonable assumptions. This fact is one of the main reasons that multiple models for the same system are different; different model developers may use different empirical data, functional relationships, and assumptions about these process