Inheritance diagram for javawrapper::MortalityBehaviors:
Public Member Functions | |
MortalityBehaviors (GUIManager oManager) throws ModelException | |
Constructor. | |
void | DoSetup (TreePopulation oPop) throws ModelException |
Adds NCI lambda values. | |
boolean | SetSingleValueByXMLTag (String sXMLTag, String sXMLParentTag, org.xml.sax.Attributes oAttributes, Object oData) throws ModelException |
Overridden to provide backwards compatibility for Weibull snag mortality. | |
void | ValidateData (TreePopulation oPop) throws ModelException |
Validates the data prior to writing it to a parameter file or some such. | |
Behavior | GetBehaviorByXMLTag (String sXMLTag) |
Finds a behavior by its XML tag. | |
void | ChangeOfSpeciesName (String sOldSpecies, String sNewSpecies) |
Updates the lambda neighbor names when a species name is changed. | |
Protected Attributes | |
ModelVector | mp_fMortAtZeroGrowth |
Mortality at zero growth for each species. | |
ModelVector | mp_fLightDependentMortality |
Light-dependent mortality for each species. | |
ModelVector | mp_fRandomMortalityAlpha |
Senescence mortality alpha for each species. | |
ModelVector | mp_fRandomMortalityBeta |
Senescence mortality beta for each species. | |
ModelVector | mp_fAdultRandomMortality |
Random adult mortality for each species. | |
ModelVector | mp_fJuvenileRandomMortality |
Random juvenile mortality for each species. | |
ModelVector | mp_fDbhAtOnsetOfSenescence |
DBH at onset of senescence for each species. | |
ModelVector | mp_fJuvenileSelfThinningSlope |
Juvenile self-thinning slope for each species. | |
ModelVector | mp_fJuvenileSelfThinningIntercept |
Juvenile self-thinning intercept for each species. | |
ModelVector | mp_fAdultSelfThinningSlope |
Adult self-thinning slope for each species. | |
ModelVector | mp_fAdultSelfThinningIntercept |
Adult self-thinning intercept for each species. | |
ModelVector | mp_fAdultSelfThinningMaxDbh |
Adult self-thinning DBH for each species. | |
ModelVector | mp_fSnag1WeibullA |
Weibull snag mortality - snag size class 1 "a" parameter. | |
ModelVector | mp_fSnag2WeibullA |
Weibull snag mortality - snag size class 1 "a" parameter. | |
ModelVector | mp_fSnag3WeibullA |
Weibull snag mortality - snag size class 3 "a" parameter. | |
ModelVector | mp_fSnag1WeibullB |
Weibull snag mortality - snag size class 1 "b" parameter. | |
ModelVector | mp_fSnag2WeibullB |
Weibull snag mortality - snag size class 2 "b" parameter. | |
ModelVector | mp_fSnag3WeibullB |
Weibull snag mortality - snag size class 3 "b" parameter. | |
ModelVector | mp_fSnagSizeClass1Dbh |
Weibull snag mortality - snag size class 1 upper DBH value. | |
ModelVector | mp_fSnagSizeClass2Dbh |
Weibull snag mortality - snag size class 2 upper DBH value. | |
ModelFloat | m_fSnagSizeClass1DbhDep |
Weibull snag mortality - snag size class 1 upper DBH value. | |
ModelFloat | m_fSnagSizeClass2DbhDep |
Weibull snag mortality - snag size class 2 upper DBH value. | |
ModelInt | m_iDbhAtAsymptoticMaximumMortality |
DBH at asymptotic maximum mortality - for senescence. | |
ModelVector | mp_fNCIMaxCrowdingRadius |
NCI Mortality - Maximum crowding radius. | |
ModelVector | mp_fNCINeighDBHEffect |
NCI Mortality - Neighbor DBH effect (alpha) parameter. | |
ModelVector | mp_fNCINeighDistanceEffect |
NCI Mortality - Neighbor distance effect (beta) parameter. | |
ModelVector | mp_fNCIMinNeighborDBH |
NCI minimum DBH for crowding neighbors, for each species; all species required. | |
ModelVector | mp_fNCIShadingEffectCoefficient |
NCI Mortality - Shading coefficient (m). | |
ModelVector | mp_fNCIShadingEffectExponent |
NCI Mortality - Shading exponent (n). | |
ModelVector | mp_fNCISizeSensToNCI |
NCI Mortality - Size sensitivity to NCI parameter (gamma). | |
ModelVector | mp_fNCIMaxProbSurvival |
NCI Mortality - Maximum probability of survival. | |
ModelVector | mp_fNCISizeEffectMode |
NCI Mortality - Size effect mode (X0). | |
ModelVector | mp_fNCISizeEffectVariance |
NCI Mortality - Size effect variance (Xb). | |
ModelVector | mp_fNCISlope |
NCI Mortality - Crowding Effect Slope (C). | |
ModelVector | mp_fNCISteepness |
NCI Mortality - Crowding Effect Steepness (D). | |
ModelVector | mp_fNCIStormEffectMed |
NCI Mortality - Storm effect - medium damage. | |
ModelVector | mp_fNCIStormEffectFull |
NCI Mortality - Storm effect - full damage. | |
ModelVector | mp_fNCINeighStormEffMed |
NCI Mortality - Neighbor storm effect - medium damage. | |
ModelVector | mp_fNCINeighStormEffFull |
NCI Mortality - Neighbor storm effect - full damage. | |
ModelVector | mp_fResMortScalingFactor |
Resource mortality - scaling factor (rho). | |
ModelVector | mp_fResMortFunctionMode |
Resource mortality - function mode (mu). | |
ModelVector | mp_fResMortGrowthIncSurv |
Resource mortality - growth increase in survival (delta). | |
ModelVector | mp_fResMortLoGrowthShape |
Resource mortality - low growth function shape (sigma). | |
ModelVector | mp_fCompMortShape |
Competition mortality - Shape parameter (Z). | |
ModelVector | mp_fCompMortMax |
Competition mortality - maximum parameter (max). | |
ModelVector | mp_fDensSelfThinAsymptote |
Density self-thinning mortality asymptote (A). | |
ModelVector | mp_fDensSelfThinDiamEffect |
Density self-thinning mortality diameter effect (C). | |
ModelVector | mp_fDensSelfThinDensityEffect |
Density self-thinning mortality density effect (S). | |
ModelVector | mp_fDensSelfThinNeighRadius |
Density self-thinning neighborhood radius. | |
ModelVector | mp_fDensSelfThinMinDensity |
Density self-thinning minimum density for mortality. | |
ModelVector | mp_fLogBiLevLoLiteA |
Logistic bi-level mortality - low-light "a". | |
ModelVector | mp_fLogBiLevLoLiteB |
Logistic bi-level mortality - low-light "b". | |
ModelVector | mp_fLogBiLevHiLiteA |
Logistic bi-level mortality - high-light "a". | |
ModelVector | mp_fLogBiLevHiLiteB |
Logistic bi-level mortality - high-light "b". | |
ModelVector | mp_fLogBiLevHiLiteThreshold |
Logistic bi-level mortality - threshold for high-light mortality. | |
ModelVector | mp_fStochBiLevLoLiteMortProb |
Stochastic bi-level mortality - low-light probability of mortality. | |
ModelVector | mp_fStochBiLevHiLiteMortProb |
Stochastic bi-level mortality - high-light probability of mortality. | |
ModelVector | mp_fStochBiLevHiLiteThreshold |
Stochastic bi-level mortality - threshold for high-light mortality. | |
ModelVector | mp_fHeightGLIWeibA |
Height-GLI weibull mortality - a. | |
ModelVector | mp_fHeightGLIWeibB |
Height-GLI weibull mortality - b. | |
ModelVector | mp_fHeightGLIWeibC |
Height-GLI weibull mortality - c. | |
ModelVector | mp_fHeightGLIWeibD |
Height-GLI weibull mortality - d. | |
ModelVector | mp_fHeightGLIWeibMaxMort |
Height-GLI weibull mortality - max mortality. | |
ModelFloat | m_fNCIDbhDivisor |
NCI - NCI DBH divisor. | |
ModelEnum | m_iIncludeSnagsInNCI |
NCI - Whether or not to include snags in NCI calculations - LEM 05/12/05. |
Copyright: Copyright (c) 2003 Charles D. Canham
Company: Institute of Ecosystem Studies
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Constructor.
Edit history: ------------------ April 28, 2004: Submitted in beta version (LEM) |
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Updates the lambda neighbor names when a species name is changed.
Reimplemented from javawrapper::WorkerBase. |
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Adds NCI lambda values.
Edit history: ------------------ April 28, 2004: Submitted in beta version (LEM) October 4, 2004: Added NCI stuff (LEM) March 16, 2005: Added NCI array setup to aid backwards compatibility (LEM) Implements javawrapper::WorkerBase. |
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Finds a behavior by its XML tag. For backwards compatibility, we'll watch out for the old name of the NCI Mortality behavior for a while.
Reimplemented from javawrapper::BehaviorTypeBase. |
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Overridden to provide backwards compatibility for Weibull snag mortality.
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Validates the data prior to writing it to a parameter file or some such.
Edit history: ------------------ April 28, 2004: Submitted in beta version (LEM) April 30, 2004: Fixed some validation bugs (LEM) March 17, 2005: Added density self-thinning validation (LEM) May 6, 2005: Added logistic bi-level validation (LEM) October 31, 2005: Added stochastic bi-level validation (LEM) January 26, 2006: Added Height-GlI weibull validation (LEM) Implements javawrapper::WorkerBase. |
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Initial value: new ModelFloat(1, "NCI DBH Divisor (q)", "mo_nciDbhDivisor")
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Initial value: new ModelFloat(0, "Upper DBH of Snag Size Class 1", "mo_snagSizeClass1")
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Initial value: new ModelFloat(0, "Upper DBH of Snag Size Class 2", "mo_snagSizeClass2")
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Initial value: new ModelInt(0, "DBH of Maximum Senescence Mortality Rate, as an integer in cm", "mo_dbhAtAsympMaxMort")
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Initial value: new ModelEnum(new int[] {0, 1} , new String[] {"false", "true"} , "Include Snags in NCI Calculations", "mo_nciIncludeSnagsInNCI")
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Initial value: new ModelVector( "Adult Background Mortality Rate", "mo_nonSizeDepMort", "mo_nsdmVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Adult Self-Thinning Intercept", "mo_adultSelfThinIntercept", "mo_astiVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Maximum DBH for Adult Self-Thinning", "mo_adultSelfThinMaxDbh", "mo_astmdVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Adult Self-Thinning Slope", "mo_adultSelfThinSlope", "mo_astsVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Competition Mortality Maximum Parameter (max)", "mo_CompMortMax", "mo_cmmVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Competition Mortality Shape Parameter (Z)", "mo_CompMort", "mo_cmVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "DBH at Onset of Senescence, in cm", "mo_dbhAtOnsetOfSenescence", "mo_daoosVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Density Self-Thinning Asymptote (A)", "mo_selfThinAsymptote", "mo_staVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Density Self-Thinning Density Effect (S)", "mo_selfThinDensityEffect", "mo_stdeeVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Density Self-Thinning Diameter Effect (C)", "mo_selfThinDiamEffect", "mo_stdieVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Density Self-Thinning Minimum Density for Mortality (#/ha)", "mo_minDensityForMort", "mo_mdfmVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Density Self-Thinning Neighborhood Radius, in m", "mo_selfThinRadius", "mo_strVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Height-GLI Weibull - a", "mo_heightGLIWeibA", "mo_hgwaVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Height-GLI Weibull - b", "mo_heightGLIWeibB", "mo_hgwbVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Height-GLI Weibull - c", "mo_heightGLIWeibC", "mo_hgwcVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Height-GLI Weibull - d", "mo_heightGLIWeibD", "mo_hgwdVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Height-GLI Weibull - Max Mortality (0 - 1)", "mo_heightGLIWeibMaxMort", "mo_hgwmmVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Juvenile Background Mortality Rate", "mo_randomJuvenileMortality", "mo_rjmVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Juvenile Self-Thinning Intercept", "mo_juvSelfThinIntercept", "mo_jstiVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Juvenile Self-Thinning Slope", "mo_juvSelfThinSlope", "mo_jstsVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Light-Dependent Mortality", "mo_lightDependentMortality", "mo_ldmVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Logistic Bi-Level - High-Light \"a\"", "mo_logBilevHiLiteA", "mo_lbhlaVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Logistic Bi-Level - High-Light \"b\"", "mo_logBilevHiLiteB", "mo_lbhlbVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Logistic Bi-Level - High-Light Mortality Threshold (0-100)", "mo_logBilevHiLiteThreshold", "mo_lbhltVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Logistic Bi-Level - Low-Light \"a\"", "mo_logBilevLoLiteA", "mo_lbllaVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Logistic Bi-Level - Low-Light \"b\"", "mo_logBilevLoLiteB", "mo_lbllbVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Mortality at Zero Growth", "mo_mortAtZeroGrowth", "mo_mazgVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Max Radius of Crowding Neighbors, in m", "mo_prnciMaxCrowdingRadius", "mo_pmcrVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Max Survival Probability (0-1)", "mo_prnciMaxPotentialSurvival", "mo_pmpsVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Minimum Neighbor DBH, in cm", "mo_nciMinNeighborDBH", "mo_nmndVal", 0, ModelVector.FLOAT, true)
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Initial value: new ModelVector( "NCI Neighbor DBH Effect (alpha)", "mo_prnciNeighDBHEff", "mo_pndeVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Neighbor Distance Effect (beta)", "mo_prnciNeighDistEff", "mo_pndseVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Neighbor Storm Damage (eta) - Complete (0-1)", "mo_prnciNeighStormEffFullDmg", "mo_pnsefdVal", 0, ModelVector.FLOAT, true)
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Initial value: new ModelVector( "NCI Neighbor Storm Damage (eta) - Medium (0-1)", "mo_prnciNeighStormEffMedDmg", "mo_pnsemdVal", 0, ModelVector.FLOAT, true)
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Initial value: new ModelVector( "NCI Shading Effect Coefficient (m)", "mo_nciShadingCoefficient", "mo_nscVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Shading Effect Exponent (n)", "mo_nciShadingExponent", "mo_nseVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Size Effect Mode, in cm", "mo_prnciSizeEffectMode", "mo_psemVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Size Effect Variance, in cm", "mo_prnciSizeEffectVar", "mo_psevVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Size Sensitivity to NCI (gamma)", "mo_prnciSizeSensNCI", "mo_pssnVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Crowding Effect Slope (C)", "mo_prnciNCISlope", "mo_pnslVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Crowding Effect Steepness (D)", "mo_prnciNCISteepness", "mo_pnstVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Storm Effect - Complete Damage (0-1)", "mo_prnciStormEffFullDmg", "mo_psefdVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "NCI Storm Effect - Medium Damage (0-1)", "mo_prnciStormEffMedDmg", "mo_psemdVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Senescence Mortality Alpha", "mo_randomMortAlpha", "mo_rmaVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Senescence Mortality Beta", "mo_randomMortBeta", "mo_rmbVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Growth/Resource - Function Mode (mu)", "mo_resMortMode", "mo_rmmVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Growth/Resource - Survival Increase with Growth (delta)", "mo_resMortGrowthIncSurv", "mo_rmgisVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Growth/Resource - Low-Growth Survival Parameter (sigma)", "mo_resMortLoGrowthShape", "mo_rmlgsVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Growth/Resource - Scaling Factor (rho)", "mo_resMortScalingFactor", "mo_rmsfVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Weibull Annual \"a\" Parameter for Snag Size Class 1 Mortality", "mo_snag1WeibullA", "mo_s1waVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Weibull Annual \"b\" Parameter for Snag Size Class 1 Mortality", "mo_snag1WeibullB", "mo_s1wbVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Weibull Annual \"a\" Parameter for Snag Size Class 2 Mortality", "mo_snag2WeibullA", "mo_s2waVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Weibull Annual \"b\" Parameter for Snag Size Class 2 Mortality", "mo_snag2WeibullB", "mo_s2wbVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Weibull Annual \"a\" Parameter for Snag Size Class 3 Mortality", "mo_snag3WeibullA", "mo_s3waVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Weibull Annual \"b\" Parameter for Snag Size Class 3 Mortality", "mo_snag3WeibullB", "mo_s3wbVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Weibull Upper DBH of Snag Size Class 1", "mo_snagSizeClass1DBH", "mo_sc1dVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Weibull Upper DBH of Snag Size Class 2", "mo_snagSizeClass2DBH", "mo_sc2dVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Stochastic Bi-Level - High-Light Mortality Probability (0-1)", "mo_stochBilevHiLiteMortProb", "mo_sbhlmpVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Stochastic Bi-Level - High-Light Mortality Threshold (0-100)", "mo_stochBilevHiLiteThreshold", "mo_sbhltVal", 0, ModelVector.FLOAT)
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Initial value: new ModelVector( "Stochastic Bi-Level - Low-Light Mortality Probability (0-1)", "mo_stochBilevLoLiteMortProb", "mo_sbllmpVal", 0, ModelVector.FLOAT)
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