lerfob.predictor.mathilde.mortality

Class MathildeMortalityPredictor

java.lang.Object

repicea.simulation.SensitivityAnalysisParameter<ModelParameterEstimates>

repicea.simulation.REpiceaPredictor

repicea.simulation.REpiceaBinaryEventPredictor<MathildeMortalityStand,MathildeTree>

lerfob.predictor.mathilde.mortality.MathildeMortalityPredictor

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

MathildeImprovedMortalityPredictor

public class MathildeMortalityPredictor
extends REpiceaBinaryEventPredictor<MathildeMortalityStand,MathildeTree>

This class implements the mortality submodel in Mathilde model. All the details of this module are available in Manso et al. 2015. Forest Ecology and Management 354: 243-253.

See Also:

Manso, R., Morneau, F., Ningre, F., and Fortin, M. 2015. Incorporating stochasticity from extreme climatic events and multi-species competition relationships into single-tree mortality models. Forest Ecology and Management 354: 243-253, Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	MathildeMortalityPredictor.InternalMathematicalFunction

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

REpiceaPredictor.CruiseLine, REpiceaPredictor.ErrorTermGroup, REpiceaPredictor.IntervalNestedInPlotDefinition

Field Summary

Fields

Modifier and Type	Field and Description
protected GaussHermiteQuadrature	ghq
protected static boolean	isGaussianQuadratureEnabled
protected LinkFunction	linkFunction
protected int	numberOfParameters
protected java.util.Map<java.lang.Integer,lerfob.predictor.mathilde.mortality.MathildeMortalitySubModule>	subModules

Fields inherited from class repicea.simulation.REpiceaPredictor

DefaultZeroIndex, isRandomEffectsVariabilityEnabled, isResidualVariabilityEnabled, listeners, oXVector

Fields inherited from class repicea.simulation.SensitivityAnalysisParameter

isParametersVariabilityEnabled

Constructor Summary

Constructors

Constructor and Description
MathildeMortalityPredictor(boolean isVariabilityEnabled) Constructor.

Method Summary

Modifier and Type	Method and Description
protected double	getFixedEffectOnlyPrediction(Matrix beta, MathildeMortalityStand stand, MathildeTree tree)
protected void	init() This method reads all the parameters in .csv files and stores the estimates into members defaultBeta, defaultResidualError, and defaultRandomEffects.
java.lang.Object	predictEvent(MathildeMortalityStand stand, MathildeTree tree, java.lang.Object... parms) This method returns either a boolean if isResidualVariabilityEnabled was set to true or the probability otherwise.
double	predictEventProbability(MathildeMortalityStand stand, MathildeTree tree, java.lang.Object... parms) This method returns the probability of event for a particular tree represented by the parameter "tree".

Methods inherited from class repicea.simulation.REpiceaBinaryEventPredictor

findFirstParameterOfThisClass

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, setDefaultRandomEffects, setDefaultResidualError, setDeviatesForRandomEffectsOfThisSubject, setParameterEstimates, 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

Field Detail

isGaussianQuadratureEnabled

protected static boolean isGaussianQuadratureEnabled

subModules

protected final java.util.Map<java.lang.Integer,lerfob.predictor.mathilde.mortality.MathildeMortalitySubModule> subModules

linkFunction

protected final LinkFunction linkFunction

numberOfParameters

protected int numberOfParameters

ghq

protected GaussHermiteQuadrature ghq

Constructor Detail

MathildeMortalityPredictor

public MathildeMortalityPredictor(boolean isVariabilityEnabled)

Constructor.

Parameters:

isVariabilityEnabled -

Method Detail

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

getFixedEffectOnlyPrediction

protected double getFixedEffectOnlyPrediction(Matrix beta,
                                              MathildeMortalityStand stand,
                                              MathildeTree tree)

predictEventProbability

public double predictEventProbability(MathildeMortalityStand stand,
                                      MathildeTree tree,
                                      java.lang.Object... parms)

Description copied from class: REpiceaBinaryEventPredictor

This method returns the probability of event for a particular tree represented by the parameter "tree".

Specified by:

predictEventProbability in class REpiceaBinaryEventPredictor<MathildeMortalityStand,MathildeTree>

Parameters:

stand - a S-derived instance

tree - a T-derived instance

parms - some additional parameters

Returns:

the event probability

predictEvent

public java.lang.Object predictEvent(MathildeMortalityStand stand,
                                     MathildeTree tree,
                                     java.lang.Object... parms)

This method returns either a boolean if isResidualVariabilityEnabled was set to true or the probability otherwise.

Overrides:

predictEvent in class REpiceaBinaryEventPredictor<MathildeMortalityStand,MathildeTree>

Parameters:

stand - a S-derived instance

tree - a T-derived instance

parms - some additional parameters

Returns:

a Boolean or a double