public class GarpAlgorithm extends TypedAtomicActor
GARP is a computer program for predicting species locations based on various spatial data sets of environment variables and known species locations. GARP is an acronym for Genetic Algorithm for Rule Set Production. GARP was originally ceated by David Stockwell. The version in Kepler is based on 'Desktop GARP', http://www.lifemapper.org/desktopgarp/. The GarpAlgorithm actor takes information from the GarpPresampleLayers actor (A randomly generated set of spatial locations and associated environment data.) and calculates a 'RuleSet' using a genetic algorithm. The RuleSet can then be used to determine whether the environmental data for some location is similar enough to the environment at known location positions to predict presence/absence.
This is a JNI-based actor. It requires the following: linux: libgarp.so windows: garp.dll, libexpat.dll MacOSX - currently not available for the Mac (3/16/2006)
Entity.ContainedObjectsIterator| Modifier and Type | Field and Description |
|---|---|
TypedIOPort |
cellSetFileName
This is the name of the file containing the cellSet information.
|
FileParameter |
cellSetFileNameParameter
This is the name of the file containing the cellSet information.
|
TypedIOPort |
ruleSetFilename
This is the name to be given to the file containing the RuleSet
information.
|
TypedIOPort |
ruleSetFilenameOutput
This is the name of the file containing the RuleSet information.
|
FileParameter |
ruleSetFilenameParameter
This is the name to be given to the file containing the RuleSet
information.
|
_typesValid_actorFiringListeners, _initializables, _notifyingActorFiring, _stopRequested_changeListeners, _changeLock, _changeRequests, _debugging, _debugListeners, _deferChangeRequests, _elementName, _isPersistent, _verbose, _workspace, ATTRIBUTES, CLASSNAME, COMPLETE, CONTENTS, DEEP, FULLNAME, LINKSCOMPLETED, NOT_READY, STOP_ITERATING| Constructor and Description |
|---|
GarpAlgorithm(CompositeEntity container,
java.lang.String name)
GarpAlgorithm Actor
|
| Modifier and Type | Method and Description |
|---|---|
void |
fire()
Do nothing.
|
void |
initialize()
Initialize this actor.
|
boolean |
prefire()
Return true.
|
_containedTypeConstraints, _customTypeConstraints, _defaultTypeConstraints, _fireAt, _fireAt, attributeTypeChanged, clone, clone, isBackwardTypeInferenceEnabled, newPort, typeConstraintList, typeConstraints_actorFiring, _actorFiring, _declareDelayDependency, addActorFiringListener, addInitializable, connectionsChanged, createReceivers, declareDelayDependency, getCausalityInterface, getDirector, getExecutiveDirector, getManager, inputPortList, isFireFunctional, isStrict, iterate, newReceiver, outputPortList, postfire, preinitialize, pruneDependencies, recordFiring, removeActorFiringListener, removeDependency, removeInitializable, setContainer, stop, stopFire, terminate, wrapup_adjustDeferrals, _checkContainer, _getContainedObject, _propagateExistence, getContainer, instantiate, isAtomic, isOpaque, moveDown, moveToFirst, moveToIndex, moveToLast, moveUp, propagateExistence, setName_addPort, _description, _exportMoMLContents, _removePort, _validateSettables, connectedPortList, connectedPorts, containedObjectsIterator, getAttribute, getPort, getPorts, linkedRelationList, linkedRelations, portList, removeAllPorts, setClassDefinition, uniqueName_setParent, exportMoML, getChildren, getElementName, getParent, getPrototypeList, isClassDefinition, isWithinClassDefinition_addAttribute, _adjustOverride, _attachText, _cloneFixAttributeFields, _containedDecorators, _copyChangeRequestList, _debug, _debug, _debug, _debug, _debug, _executeChangeRequests, _getIndentPrefix, _isMoMLSuppressed, _markContentsDerived, _notifyHierarchyListenersAfterChange, _notifyHierarchyListenersBeforeChange, _propagateValue, _removeAttribute, _splitName, _stripNumericSuffix, addChangeListener, addDebugListener, addHierarchyListener, attributeChanged, attributeDeleted, attributeList, attributeList, decorators, deepContains, depthInHierarchy, description, description, event, executeChangeRequests, exportMoML, exportMoML, exportMoML, exportMoML, exportMoMLPlain, getAttribute, getAttributes, getChangeListeners, getClassName, getDecoratorAttribute, getDecoratorAttributes, getDerivedLevel, getDerivedList, getDisplayName, getFullName, getModelErrorHandler, getName, getName, getSource, handleModelError, isDeferringChangeRequests, isOverridden, isPersistent, lazyContainedObjectsIterator, message, notifyOfNameChange, propagateValue, propagateValues, removeAttribute, removeChangeListener, removeDebugListener, removeHierarchyListener, requestChange, setClassName, setDeferringChangeRequests, setDerivedLevel, setDisplayName, setModelErrorHandler, setPersistent, setSource, sortContainedObjects, toplevel, toString, validateSettables, workspaceequals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitcreateReceivers, getCausalityInterface, getDirector, getExecutiveDirector, getManager, inputPortList, newReceiver, outputPortListisFireFunctional, isStrict, iterate, postfire, stop, stopFire, terminateaddInitializable, preinitialize, removeInitializable, wrapupdescription, getContainer, getDisplayName, getFullName, getName, getName, setNamegetDerivedLevel, getDerivedList, propagateValuepublic FileParameter cellSetFileNameParameter
public FileParameter ruleSetFilenameParameter
public TypedIOPort cellSetFileName
public TypedIOPort ruleSetFilename
public TypedIOPort ruleSetFilenameOutput
public GarpAlgorithm(CompositeEntity container, java.lang.String name) throws NameDuplicationException, IllegalActionException
public void initialize() throws IllegalActionException
AtomicActorinitialize in interface Initializableinitialize in class AtomicActor<TypedIOPort>IllegalActionException - If a derived class throws it.public boolean prefire() throws IllegalActionException
AtomicActorprefire in interface Executableprefire in class AtomicActor<TypedIOPort>IllegalActionException - Not thrown in this base class.public void fire() throws IllegalActionException
AtomicActorfire in interface Executablefire in class AtomicActor<TypedIOPort>IllegalActionException - Not thrown in this base class.