javawrapper::MortalityBehaviors Class Reference

Manages mortality behaviors and data. More...

Inheritance diagram for javawrapper::MortalityBehaviors:

javawrapper::BehaviorTypeBase javawrapper::WorkerBase List of all members.

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.
void CopySpecies (int iSpeciesCopyFrom, int iSpeciesCopyTo) throws ModelException
 Updates the lambda when a species is copied.

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.
ModelVector mp_fHeightGLIWeibBrowsedA
 Height-GLI weibull mortality - browsed a.
ModelVector mp_fHeightGLIWeibBrowsedB
 Height-GLI weibull mortality - browsed b.
ModelVector mp_fHeightGLIWeibBrowsedC
 Height-GLI weibull mortality - browsed c.
ModelVector mp_fHeightGLIWeibBrowsedD
 Height-GLI weibull mortality - browsed d.
ModelVector mp_fHeightGLIWeibBrowsedMaxMort
 Height-GLI weibull mortality - browsed max mortality.
ModelVector mp_fExpResourceMortA
 Exponential growth-resource mortality - "a".
ModelVector mp_fExpResourceMortB
 Exponential growth-resource mortality - "b".
ModelVector mp_fExpResourceMortC
 Exponential growth-resource mortality - "c".
ModelVector mp_fExpResourceMortD
 Exponential growth-resource mortality - "d".
ModelVector mp_fBrowsedJuvenileRandomMortality
 Browsed random juvenile mortality for each species.
ModelFloat m_fNCIDbhDivisor
 NCI - NCI DBH divisor.
ModelFloat m_fAggMortEpisodeReturnInterval
 Aggregated mortality - mortality episode return interval in years.
ModelFloat m_fAggMortPropToKill
 Aggregated mortality - mortality rate per year of a mortality episode, 0-1.
ModelFloat m_fAggMortNumTreesToAggregate
 Aggregated mortality - number of trees to aggregate.
ModelFloat m_fAggMortClumpingParameter
 Aggregated mortality - clumping parameter for negative binomial distribution, if required.
ModelEnum m_iAggMortClumpDeterministic
 Aggregated mortality - whether clump size is deterministic (true) or from the negative binomial probability distribution (false).
ModelEnum m_iIncludeSnagsInNCI
 NCI - Whether or not to include snags in NCI calculations - LEM 05/12/05.

Detailed Description

Manages mortality behaviors and data.

Copyright: Copyright (c) 2003 Charles D. Canham

Company: Institute of Ecosystem Studies

Author:
Lora E. Murphy
Version:
1.0

Edit history:
------------------
April 28, 2004: Submitted in beta version (LEM)
October 4, 2004: Added Puerto Rico NCI mortality (LEM)
February 9, 2005: Added the growth-and-resource mortality (LEM)
February 23, 2005: Added competition mortality (LEM)
March 8, 2005: Made weibull snag size classes species-specific (LEM)
March 16, 2005: Upgraded NCI mort to v. 2.0 (LEM)
March 17, 2005: Added the density self thinning behavior (LEM)
May 6, 2005: Added logistic bi-level mortality behavior (LEM)
October 31, 2005: Added stochastic bi-level mortality behavior (LEM)
January 26, 2006: Added height-GLI weibull mortality behavior (LEM)
July 6, 2006: Added exponential resource growth and mortality (LEM)
July 28, 2006: Added aggregated mortality (LEM)
November 28, 2006: Changed NCI neighbor etas to not be required for all species (LEM)
April 2, 2007: Added the browsed stochastic mortality behavior (LEM)


Constructor & Destructor Documentation

javawrapper::MortalityBehaviors::MortalityBehaviors ( GUIManager  oManager  )  throws ModelException [inline]

Constructor.

Parameters:
oManager GUIManager object.
Exceptions:
ModelException passed through from called functions. Should never be thrown.

Edit history:
------------------
April 28, 2004: Submitted in beta version (LEM)


Member Function Documentation

void javawrapper::MortalityBehaviors::DoSetup ( TreePopulation  oPop  )  throws ModelException [inline, virtual]

Adds NCI lambda values.

Parameters:
oPop Tree population
Exceptions:
ModelException Not thrown.

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.

boolean javawrapper::MortalityBehaviors::SetSingleValueByXMLTag ( String  sXMLTag,
String  sXMLParentTag,
org.xml.sax.Attributes  oAttributes,
Object  oData 
) throws ModelException [inline]

Overridden to provide backwards compatibility for Weibull snag mortality.

Parameters:
sXMLTag XML tag of data object whose value is to be set.
sXMLParentTag The immediate parent tag that sXMLTag is within.
oAttributes Attributes of the object. Ignored, but may be needed by overriding objects.
oData Data value, either String or type appropriate to the data type
Returns:
true if the value was set successfully; false if the value could not be found. (This would not be an error, because I need a way to cycle through the objects until one of the objects comes up with a match.)
Exceptions:
ModelException if the value could not be assigned to the data object.

void javawrapper::MortalityBehaviors::ValidateData ( TreePopulation  oPop  )  throws ModelException [inline, virtual]

Validates the data prior to writing it to a parameter file or some such.

Parameters:
oPop TreePopulation
Exceptions:
ModelException if:
  • Any of the following are not expressed as a proportion:
    • mp_fAdultRandomMortality
    • mp_fJuvenileRandomMortality
    • mp_fMortAtZeroGrowth
  • If adult self-thinning is used and any mp_fAdultSelfThinningMaxDbh value is less than zero.
  • Any value in mp_fDbhAtOnsetOfSenescence is less than zero.
  • Any vector is not sized correctly to equal total number of species.
  • GMF mortality is enabled and the timestep length is not five years.
  • Any value in light dependent mortality is zero.
  • Competition mortality is enabled and the timestep length is not one year.
  • Competition mortality is enabled and NCI growth is not.
  • NCI Mortality is enabled and any of the following is true:
    • NCI Max. radius of neighbor effects is <= 0 for any species
    • NCI Max growth is <= 0 for any species
    • NCI size effect mode for any species is <= 0
    • NCI Size effect variance = 0 for any species
    • NCI Eta for any species for any damage category is not between 0 and 1
    • NCI Storm Effect parameters for any species for any damage category are not between 0 and 1
    • NCI DBH divisor is <= 0
    • Minimun neighbor DBH value is < 0
  • Density self-thinning is enabled, and any of the following are true:
    • The timestep length is greater than 1.
    • The neighborhood radius is not greater than 0.
    • The minimum density for mortality is less than 0.
    • The self-thinning asymptote is not greater than 0.
    • The density effect is not greater than 0.
  • Logistic bi-level is enabled, and the threshold for high-light mortality is not between 0 and 100.
  • Stochastic bi-level is enabled, and the threshold for high-light mortality is not between 0 and 100.
  • Stochastic bi-level is enabled, and values for high- and low-light mortality probability are not between 0 and 1.
  • Stochastic bi-level is enabled, and Storm Light is not.
  • Weibull snag mortality is enabled, and either a is 0 or a is negative and b is not a whole number for any size class.
  • Height-GLI Weibull mortality is enabled, and max mortality is not a proportion.

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)
July 28, 2006: Added aggregated mortality validation (LEM)

Implements javawrapper::WorkerBase.

Behavior javawrapper::MortalityBehaviors::GetBehaviorByXMLTag ( String  sXMLTag  )  [inline]

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.

Parameters:
sXMLTag String The XML tag for which to find a behavior.
Returns:
Behavior Behavior for the XML tag, or NULL if none of the behaviors has that tag.

Reimplemented from javawrapper::BehaviorTypeBase.

void javawrapper::MortalityBehaviors::ChangeOfSpeciesName ( String  sOldSpecies,
String  sNewSpecies 
) [inline]

Updates the lambda neighbor names when a species name is changed.

Parameters:
sOldSpecies String Old name of the species, with underscores instead of spaces (like the species names would come from the tree population)
sNewSpecies String New name of the species, with underscores instead of spaces (like the species names would come from the tree population)

Reimplemented from javawrapper::WorkerBase.

void javawrapper::MortalityBehaviors::CopySpecies ( int  iSpeciesCopyFrom,
int  iSpeciesCopyTo 
) throws ModelException [inline]

Updates the lambda when a species is copied.

The lambdas for that neighbor are made identical to those being copied as well as entries for species within the lambda.

Parameters:
iSpeciesCopyFrom int Species to copy.
iSpeciesCopyTo int Species that is the copy.
Exceptions:
ModelException if there is a problem.

Reimplemented from javawrapper::BehaviorTypeBase.


Member Data Documentation

ModelFloat javawrapper::MortalityBehaviors::m_fSnagSizeClass1DbhDep [protected]

Initial value:

 new ModelFloat(0,
      "Upper DBH of Snag Size Class 1", "mo_snagSizeClass1")
Weibull snag mortality - snag size class 1 upper DBH value.

Deprecated:
This value now has a species-specific version and this one will eventually be eliminated.

ModelFloat javawrapper::MortalityBehaviors::m_fSnagSizeClass2DbhDep [protected]

Initial value:

 new ModelFloat(0,
      "Upper DBH of Snag Size Class 2", "mo_snagSizeClass2")
Weibull snag mortality - snag size class 2 upper DBH value.

Deprecated:
This value now has a species-specific version and this one will eventually be eliminated.


The documentation for this class was generated from the following file:
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