public class GARPSummary extends Transformer
This actor examinesof the values in individual pixels in an ascii grid file and summarizes those values.
There are three inputs; 'input'is an ASCI grid (output of GARP);
'pointFileName' is the file of testing locations (long, lat) used to evaluate
the prediction; and 'ruleSetFileName is the ruleSetFile which is needed later
to reproduce the predicted distribution.
The output is a string containing the omission, commission, and the
ruleSetFileName, separated by tabs. These should be saved (in a File?) for
determination of the 'best' result.
Ricardo Periera, provided the following recipe for calculating omission and
commision in an e-mail to Dan Higgins, 10/5/2004
However, those error statistics (omission and commission) could be calculated
outside GARP code. Here is the recipe:
1) Get a set of presence data points (species occurrences - x, y coordinates) to test<br/> 2) Project the GARP model onto geography (map generated by GarpProjection actor)<br/> 3) Overlay the presence points from item #1 onto the map generated on #2. The percentage of those points that fall in a pixed not predicted present is your OMISSION. Say, out of 100 points, only 45 fall on white pixels, the other 55 fall on black ones, your omission is 55% or 0.55.<br/> 4) Commission, when we don't have real absence points (our case) is the proportion of area predicted present with regard to the total area of interest, not counting masked pixels. So if 40% of the area is predicted present, your commission error is 40% or 0.40.<br/> 5) Then, select those GARP runs that show omission below a certain omission threshold, say 5 or 10%.<br/> 6) From those runs selected in #5, sort them by commission error, and then get the 50% of the models that are around the median value for commission. If you got, say, 20 models in item #5, now you have 10 models that make up your best subset of models.<br/> 7) Sum up the maps for the best subset of models in item #6, that is your final prediction map for your species.<br/>
Entity.ContainedObjectsIterator| Modifier and Type | Field and Description |
|---|---|
TypedIOPort |
commissionValue
The commission value
|
TypedIOPort |
omissionValue
The omission value
|
TypedIOPort |
outputRuleSetFileName
output ruleset file name
|
TypedIOPort |
pointFileName
'pointFileName' is the file of testing locations (long, lat) used to
evaluate the prediction
|
TypedIOPort |
ruleSetFileName
'ruleSetFileName is the ruleSetFile which is needed later to reproduce
the predicted distribution.
|
input, output_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 |
|---|
GARPSummary(CompositeEntity container,
java.lang.String name)
constructor
|
| Modifier and Type | Method and Description |
|---|---|
void |
fire()
Do nothing.
|
boolean |
postfire()
Post fire the actor.
|
boolean |
prefire()
Pre fire the actor.
|
_containedTypeConstraints, _customTypeConstraints, _defaultTypeConstraints, _fireAt, _fireAt, attributeTypeChanged, clone, clone, isBackwardTypeInferenceEnabled, newPort, typeConstraintList, typeConstraints_actorFiring, _actorFiring, _declareDelayDependency, addActorFiringListener, addInitializable, connectionsChanged, createReceivers, declareDelayDependency, getCausalityInterface, getDirector, getExecutiveDirector, getManager, initialize, inputPortList, isFireFunctional, isStrict, iterate, newReceiver, outputPortList, 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, stop, stopFire, terminateaddInitializable, initialize, preinitialize, removeInitializable, wrapupdescription, getContainer, getDisplayName, getFullName, getName, getName, setNamegetDerivedLevel, getDerivedList, propagateValuepublic TypedIOPort pointFileName
public TypedIOPort ruleSetFileName
public TypedIOPort omissionValue
public TypedIOPort commissionValue
public TypedIOPort outputRuleSetFileName
public GARPSummary(CompositeEntity container, java.lang.String name) throws NameDuplicationException, IllegalActionException
container - The container.name - The name of this actor.IllegalActionException - If the actor cannot be contained by the proposed
container.NameDuplicationException - If the container already has an actor with this name.public void fire() throws IllegalActionException
AtomicActorfire in interface Executablefire in class AtomicActor<TypedIOPort>IllegalActionException - If there is no director.public boolean postfire() throws IllegalActionException
postfire in interface Executablepostfire in class AtomicActor<TypedIOPort>IllegalActionException - Not thrown in this base class.public boolean prefire() throws IllegalActionException
prefire in interface Executableprefire in class AtomicActor<TypedIOPort>IllegalActionException - Not thrown in this base class.