lerfob.predictor.hdrelationships.frenchgeneralhdrelationship2014

Class FrenchHDRelationship2014InternalPredictor

java.lang.Object

repicea.simulation.SensitivityAnalysisParameter<ModelParameterEstimates>

repicea.simulation.REpiceaPredictor

repicea.simulation.hdrelationships.HDRelationshipPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>

lerfob.predictor.hdrelationships.frenchgeneralhdrelationship2014.FrenchHDRelationship2014InternalPredictor

All Implemented Interfaces:

java.io.Serializable, FertilityClassEmulator, FrenchHeightPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>, HeightPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>

public class FrenchHDRelationship2014InternalPredictor
extends HDRelationshipPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>
implements FertilityClassEmulator, FrenchHeightPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class repicea.simulation.hdrelationships.HDRelationshipPredictor

HDRelationshipPredictor.GaussianErrorTermForHeight, HDRelationshipPredictor.RegressionElements

Nested classes/interfaces inherited from class repicea.simulation.REpiceaPredictor

REpiceaPredictor.CruiseLine, REpiceaPredictor.ErrorTermGroup, REpiceaPredictor.IntervalNestedInPlotDefinition

Nested classes/interfaces inherited from interface lerfob.predictor.FertilityClassEmulator

FertilityClassEmulator.FertilityClass

Nested classes/interfaces inherited from interface lerfob.predictor.hdrelationships.FrenchHeightPredictor

FrenchHeightPredictor.FrenchHeightPredictorVersion

Field Summary

Fields inherited from class repicea.simulation.hdrelationships.HDRelationshipPredictor

observedHeights

Fields inherited from class repicea.simulation.REpiceaPredictor

DefaultZeroIndex, isRandomEffectsVariabilityEnabled, isResidualVariabilityEnabled, listeners, oXVector

Fields inherited from class repicea.simulation.SensitivityAnalysisParameter

isParametersVariabilityEnabled

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	FrenchHDRelationship2014InternalPredictor(boolean isParameterVariabilityEnabled, boolean isRandomEffectVariabilityEnabled, boolean isResidualVariabilityEnabled, FrenchHDRelationshipTree.FrenchHdSpecies species)

Method Summary

Modifier and Type	Method and Description
void	emulateFertilityClass(FertilityClassEmulator.FertilityClass fertilityClass) This method sets the fertility class.
protected HDRelationshipPredictor.RegressionElements	fixedEffectsPrediction(FrenchHDRelationship2014Stand stand, FrenchHDRelationship2014Tree tree, Matrix beta) This method computes the fixed effect prediction and put the prediction, the Z vector, and the species name into m_oRegressionOutput member.
Estimate<? extends StandardGaussianDistribution>	getBlupsForThisSubject(FrenchHDRelationship2014Stand stand) Returns the estimated blups for the plot.
protected java.util.Map<FertilityClassEmulator.FertilityClass,TruncatedGaussianEstimate>	getFertilityClassMap()
FrenchHDRelationshipTree.FrenchHdSpecies	getSpecies() Returns the species for the internal species-specific height predictor.
protected java.util.Collection<FrenchHDRelationship2014Tree>	getTreesFromStand(FrenchHDRelationship2014Stand stand) This method selects the trees from which the blups must be calculated.
protected void	init() This method reads all the parameters in .csv files and stores the estimates into members defaultBeta, defaultResidualError, and defaultRandomEffects.
protected void	predictHeightRandomEffects(FrenchHDRelationship2014Stand stand) This method computes the best linear unbiased predictors of the random effects
protected void	setDefaultRandomEffects(HierarchicalLevel level, Estimate<? extends StandardGaussianDistribution> estimate)
protected void	setEffectList(Matrix mat)
protected void	setParameterEstimates(ModelParameterEstimates defaultBeta)
protected void	setResidualVariance(Matrix sigma2)

Methods inherited from class repicea.simulation.hdrelationships.HDRelationshipPredictor

blupImplementation, getErrorGroup, predictHeightM, residualImplementation, setSpecificResiduals, wasThisTreeInitiallyMeasured

Methods inherited from class repicea.simulation.REpiceaPredictor

addModelBasedSimulatorListener, doBlupsExistForThisSubject, doesThisSubjectHaveResidualErrorTerm, doRandomDeviatesExistForThisSubject, fireModelBasedSimulatorEvent, fireRandomEffectDeviateGeneratedEvent, getBlupsForThisSubject, getCruiseLineForThisSubject, getDefaultRandomEffects, getDefaultRandomEffects, getDefaultResidualError, getGaussianErrorTerms, getIntervalNestedInPlotDefinition, getParametersForThisRealization, getRandomEffectsForThisSubject, getResidualError, getResidualErrorForThisSubject, getSubjectPlusMonteCarloSpecificId, getSubjectPlusMonteCarloSpecificId, hasSubjectBeenTestedForBlups, recordSubjectTestedForBlups, removeModelBasedSimulatorListener, setBlupsForThisSubject, setDefaultResidualError, setDeviatesForRandomEffectsOfThisSubject, simulateDeviatesForRandomEffectsOfThisSubject

Methods inherited from class repicea.simulation.SensitivityAnalysisParameter

getParameterEstimates

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface repicea.simulation.hdrelationships.HeightPredictor

predictHeightM

Constructor Detail

FrenchHDRelationship2014InternalPredictor

protected FrenchHDRelationship2014InternalPredictor(boolean isParameterVariabilityEnabled,
                                                    boolean isRandomEffectVariabilityEnabled,
                                                    boolean isResidualVariabilityEnabled,
                                                    FrenchHDRelationshipTree.FrenchHdSpecies species)

Method Detail

getFertilityClassMap

protected java.util.Map<FertilityClassEmulator.FertilityClass,TruncatedGaussianEstimate> getFertilityClassMap()

setDefaultRandomEffects

protected void setDefaultRandomEffects(HierarchicalLevel level,
                                       Estimate<? extends StandardGaussianDistribution> estimate)

Overrides:

setDefaultRandomEffects in class REpiceaPredictor

setParameterEstimates

protected void setParameterEstimates(ModelParameterEstimates defaultBeta)

Overrides:

setParameterEstimates in class REpiceaPredictor

emulateFertilityClass

public void emulateFertilityClass(FertilityClassEmulator.FertilityClass fertilityClass)

This method sets the fertility class. However, it must be set before estimating the random effects. Otherwise, it has no effect.

Specified by:

emulateFertilityClass in interface FertilityClassEmulator

Parameters:

fertilityClass - a FertilityClass enum

predictHeightRandomEffects

protected void predictHeightRandomEffects(FrenchHDRelationship2014Stand stand)

Description copied from class: HDRelationshipPredictor

This method computes the best linear unbiased predictors of the random effects

Overrides:

predictHeightRandomEffects in class HDRelationshipPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>

Parameters:

stand - a HeightableStand instance

setResidualVariance

protected void setResidualVariance(Matrix sigma2)

setEffectList

protected void setEffectList(Matrix mat)

fixedEffectsPrediction

protected HDRelationshipPredictor.RegressionElements fixedEffectsPrediction(FrenchHDRelationship2014Stand stand,
                                                                            FrenchHDRelationship2014Tree tree,
                                                                            Matrix beta)

This method computes the fixed effect prediction and put the prediction, the Z vector, and the species name into m_oRegressionOutput member. The method applies in any cases no matter it is deterministic or stochastic.

Specified by:

fixedEffectsPrediction in class HDRelationshipPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>

Parameters:

stand - a HeightableStand instance

tree - a HeightableTree instance

beta - a Matrix that contains the parameters

Returns:

a RegressionElement instance

getBlupsForThisSubject

public Estimate<? extends StandardGaussianDistribution> getBlupsForThisSubject(FrenchHDRelationship2014Stand stand)

Description copied from interface: FrenchHeightPredictor

Returns the estimated blups for the plot.

Specified by:

getBlupsForThisSubject in interface FrenchHeightPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>

Parameters:

stand - a HDRelationshipStand instance that stands for the plot.

Returns:

an Estimate instance

getTreesFromStand

protected java.util.Collection<FrenchHDRelationship2014Tree> getTreesFromStand(FrenchHDRelationship2014Stand stand)

Description copied from class: HDRelationshipPredictor

This method selects the trees from which the blups must be calculated.

Specified by:

getTreesFromStand in class HDRelationshipPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>

Parameters:

stand - a Stand instance

Returns:

return a Collection of Tree instances

init

protected void init()

Description copied from class: REpiceaPredictor

This method reads all the parameters in .csv files and stores the estimates into members defaultBeta, defaultResidualError, and defaultRandomEffects.

Specified by:

init in class REpiceaPredictor

getSpecies

public FrenchHDRelationshipTree.FrenchHdSpecies getSpecies()

Description copied from interface: FrenchHeightPredictor

Returns the species for the internal species-specific height predictor.

Specified by:

getSpecies in interface FrenchHeightPredictor<FrenchHDRelationship2014Stand,FrenchHDRelationship2014Tree>

Returns:

a FrenchHdSpecies instance