## Reference

Tue, 27/11/2007 - 14:28 — jonathanmThis section provides reference material for Simile.

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## Chapter 3. The submodel concept

Tue, 27/11/2007 - 14:26 — jonathanmThis chapter describes the submodel concept as used in Simile. This construct is a key feature of Simile.

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## Population dynamics models

Tue, 27/11/2007 - 14:21 — jonathanmYou will probably by now appreciate that you have a variety of options when it comes to modelling population dynamics. You can adopt a lumped approach in System Dynamics, using a compartment to represent population size, and flows to represent demographic processes of reproduction, migration and mortality. Or, you can adopt a disaggregated System Dynamics approach, using a compartment-flow structure to represent the dynamics of one age/size/sex class, embedded in a multiple-instance submodel to represent all the classes.

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## Modular models

Tue, 27/11/2007 - 14:20 — jonathanmThe term "modular modelling" usually refers to the use of interchangeable components (or modules) in a model. The component may be a single equation, but typically it is a large component: for example, a plant submodel or a soil water submodel. There have been calls for the development of modular modelling approaches for some two decades, and some working systems, motivated by the advantages that this would confer on the modelling process in terms of model construction, testing and reuseability of components.

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## Spatial models

Tue, 27/11/2007 - 14:20 — jonathanmThe term "spatial modelling" refers to a particular form of disaggregation, in which an area is divided into a number (often a large number) of similar units: typically grid squares or polygons. The model may be linked to a GIS for data input and display. The transition from non-spatial to spatial modelling is often considered to be pretty significant, and there are a number of modelling packages that advertise their spatial modelling capabilities: indeed, many are labelled as landscape or landuse modelling tools.

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## Object-oriented models

Tue, 27/11/2007 - 14:19 — jonathanmThe term "object-oriented" has a formal meaning in software engineering: it is not just "modelling with objects" in the sense of individual-based modelling. Rather, it reflects a commitment to a number of principles which together characterise the object-oriented approach, including message-passing, encapsulation (hiding internal detail), inheritance (from class to subclass), and polymorphism (the same procedure can operate on different data types). There is a strong movement towards the adoption of object-oriented software engineering approaches in ecological modelling.

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## Individual/object-based models

Tue, 27/11/2007 - 14:17 — jonathanmModelling the individuals that constitute a population is an extreme form of disaggregation. It is being increasingly recognised as a highly effective approach, for two main reasons. First, it enables the modeller to capture interactions critical to system behaviour that are lost in any more aggregated approach. Second, it frequently is much easier to construct individual-based models, since the behaviour of and interactions between individuals are frequently quite simple, but can lead to complex patterns of behaviour of the whole population (e.g. ant colonies).

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## Matrix models

Tue, 27/11/2007 - 14:16 — jonathanmModels based on matrix algebra are frequently used in ecology for modelling population dynamics, with the population disaggregated into age- or size-classes. Simile does have the ability to do matrix calculations with arrays but, as mentioned above, a more appropriate way of handling such problems is to view a class as being an object, and then specify that there are as many instances as there are classes. Class attributes, such as age-specific fecundity and mortality rates, can then be expressed as attributes of each instance.

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## Disaggregated models

Tue, 27/11/2007 - 14:15 — jonathanm"Disaggregation" refers to modelling in which some component is divided into a number of parts. For example, a lumped (non-disaggregated) model of soil water dynamics might use a single compartment to represent the amount of water in the soil. A disaggregated version of the same model might divide the soil into a number of layers, and represent the amount of water in each layer. Or: a population may be divided into age-classes; an area may be divided into subareas; a single "vegetation" component may be divided into the separate species.

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## Differential/difference equation models

Tue, 27/11/2007 - 14:14 — jonathanmSystem Dynamics is nothing more than a palatable front-end to a set of Differential-Algebraic Equations (DAEs): i.e. a set of differential equations, with a set of subsidiary algebraic equations for defining intermediate and rate quantities. Each compartment is a state variable, and each flow contributes to the rate-of-change expression for the associated state variable(s).

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