Behaviors

In this document:
Defining the scope of a behavior's actions
Behavior order and dependencies
Behavior data
Links to individual behavior documentation

Behaviors perform all the action when a simulation is running. Each behavior represents a step in the overall simulation. It retrieves data, manipulates it, and stores the result. Usually, a behavior roughly corresponds to a biological process, such as tree growth. When you define a simulation, the most important step is to choose which behaviors will run, to what data they will apply, and in what order they will run.

Defining the scope of a behavior's actions

Behaviors act on data to achieve a result. The data in the model is trees and grids. For those behaviors that act on trees, you must tell them what trees to act on. For instance, if you had a behavior which applied a Michaelis-Menton growth function to trees, you may tell it to act on saplings of species 1, 2, and 3; adults of those species may have a different growth behavior applied to them. The individual behavior documentation tells you how each behavior can be applied.

Behaviors often have some rules about how they can be applied, but these tend to be limited in the interests of maximum flexibility. The model doesn't try to second-guess what you are doing or warn you against things that don't make sense. Therefore, it is important to carefully check the behavior setup yourself before starting a run. Common mistakes include applying two different behaviors of the same type to the same set of trees, and failing to provide a complete set of behaviors to a particular type of tree. These types of situations make "computer" sense, and a simulation can be run when they occur. However, they do not make scientific sense and unexpected results may occur.

To choose which behaviors to include in the run and how to apply them, use the Model flow window.

Behavior order and dependencies

The parameter file specifies which behaviors to include in the simulation, and in which order they should be run. Theoretically it is possible to put behaviors in any order, but of course, most simulations constructed that way would not make sense. When you structure a run, the behaviors are placed in functional groups. To prevent nonsensical simulations, you cannot move a behavior outside of its functional group in the overall run order; however, you can re-order behaviors within the functional groups. Sometimes this will have an effect on the overall simulation outcome, and sometimes it won't. Refer to the documentation for individual behaviors to learn how run order might affect a behavior.

Behaviors work on data in sequence. Some behaviors require that a specific step has been taken before they can do their job. This means that, in order to use some behaviors, you must also use certain other behaviors. The individual behavior documentation will tell you about its requirements.

To change the order in which behaviors act, use the Model flow window.

Behavior data

Behaviors help define trees and grids based on the work they need to do. They will create a grid if they need one, or they may attach a new piece of data to the trees to which they are applied. Other behaviors rely on the presence of the grids and tree data members in order to read the results of previous behaviors and make their own calculations. For specifics on these data and what behaviors create them, see the list of grids that can be created and list of tree data members that can be added. To view this data, save a detailed output file.

Usually, a behavior also needs settings and inputs from you to do its job. This data is included in the parameter file. To edit settings for behaviors, use the Parameters window. If a behavior does not have all of the data it requires, you will receive an error message.

Links to individual behavior documentation


Harvest and disturbance behaviors
Light behaviors
Growth behaviors
Mortality behaviors
Substrate behaviors
Tree removal behaviors
Disperse behaviors
Germination behaviors
Seed predation behaviors
Establishment behaviors
Planting behaviors

25-Jan-2005 12:22 PM