javawrapper::EstablishmentBehaviors Class Reference

This is the organizer class for all establishment behaviors. More...

Inheritance diagram for javawrapper::EstablishmentBehaviors:

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

Public Member Functions

 EstablishmentBehaviors (GUIManager oManager)
 Constructor.
void DoSetup (TreePopulation oPop) throws ModelException
 Does setup.
void ValidateData (TreePopulation oPop) throws ModelException
 Validates data.
Behavior GetBehaviorByXMLTag (String sXMLTag)
 Traps for the changed behavior names.
boolean SetSingleValueByXMLTag (String sXMLTag, String sXMLParentTag, org.xml.sax.Attributes oAttributes, Object oData) throws ModelException
 Find light values for PR Establishment and reject those for light behaviors.
boolean SetVectorValueByXMLTag (String sXMLTag, String sXMLParentTag, java.util.Vector p_oData, String[] p_sChildXMLTags, boolean[] p_bAppliesTo, org.xml.sax.Attributes oParentAttributes, org.xml.sax.Attributes[] p_oAttributes) throws ModelException
 Overridden for backwards compatibility and to make sure that only light values that apply to light behaviors are set.
void ChangeOfSpeciesName (String sOldSpecies, String sNewSpecies) throws ModelException
 Changes the names in the grids.

Static Public Attributes

static final int MOUND = 2
static final int GROUND = 3

Protected Attributes

ModelVector[] mp_fFreshLogsFavorability
 Fresh logs favorability for each species.
ModelVector[] mp_fDecayedLogsFavorability
 Decayed logs favorability for each species.
ModelVector[] mp_fScarifiedSoilFavorability
 Scarified soil favorability for each species.
ModelVector[] mp_fForestFloorLitterFavorability
 Forest floor litter favorability for each species.
ModelVector[] mp_fForestFloorMossFavorability
 Forest floor moss favorability for each species.
ModelVector[] mp_fTipUpFavorability
 Tip-Up favorability for each species.
ModelVector mp_fOptimumGLI
 Light-dependent seed survival - Optimum GLI at which establishment is not reduced for each species.
ModelVector mp_fLowSlope
 Light-dependent seed survival - Slope of establishment dropoff below the optimum GLI for each species.
ModelVector mp_fHighSlope
 Light-dependent seed survival - Slope of establishment dropoff above the optimum GLI for each species.
ModelVector mp_fLightExtCoeffNoDmg
 Light-dependent seed survival - Light extinction coefficient of undamaged trees.
ModelVector mp_fLightExtCoeffPartDmg
 Light-dependent seed survival - Light extinction coefficient of medium damaged trees.
ModelVector mp_fLightExtCoeffFullDmg
 Light-dependent seed survival - Light extinction coefficient of complete damaged trees.
ModelVector mp_fSnagClass1LightExtinctionCoefficient
 Light-dependent seed survival - snag age class 1 light extinction coefficient.
ModelVector mp_fSnagClass2LightExtinctionCoefficient
 Light-dependent seed survival - snag age class 2 light extinction coefficient.
ModelVector mp_fSnagClass3LightExtinctionCoefficient
 Light-dependent seed survival - snag age class 3 light extinction coefficient.
ModelVector mp_fDensDepSlope
 Density-dependent seed survival - Density-dependence slope.
ModelVector mp_fDensDepSteepness
 Density-dependent seed survival - Density-dependence steepness.
ModelFloat m_fLightHeight
 Light-dependent seed survival - Height at which to calculate light.
ModelFloat m_fBeamFractionOfGlobalRadiation
 Light-dependent seed survival - Beam fraction of global radiation.
ModelFloat m_fClearSkyTransmissionCoefficient
 Light-dependent seed survival - Clear sky transmission coefficient.
ModelFloat m_fMinSunAngle
 Light-dependent seed survival - Minimum sun angle in radians for GLI.
ModelFloat m_fMoundProportion
 Proportion of the plot which is mound.
ModelFloat m_fMeanMoundHeight
 Mean mound height, in m.
ModelFloat m_fMoundStdDev
 Standard deviation of mound height.
ModelFloat m_fMeanFreshLogHeight
 Mean log height, in m.
ModelFloat m_fFreshLogStdDev
 Standard deviation of fresh log height, in m.
ModelInt m_iMaxRespite
 Number of years of respite from fern shading.
ModelInt m_iNumAziDiv
 Light-dependent seed survival - Number of azimuth divisions for GLI.
ModelInt m_iNumAltDiv
 Light-dependent seed survival - Number of altitude divisions for GLI.
ModelInt m_iJulianDayGrowthStarts
 Light-dependent seed survival - Start of growing season as Julian day.
ModelInt m_iJulianDayGrowthEnds
 Light-dependent seed survival - End of growing season as Julian day.
ModelInt m_iSnagAgeClass1
 Light-dependent seed survival - Upper age limit of snag size class 1.
ModelInt m_iSnagAgeClass2
 Light-dependent seed survival - Upper age limit of snag size class 2.
ModelEnum m_iUseSeedlingEfficiencyRoutine

Package Attributes

ModelVector mp_fProportionGerminating
 Proportional seed survival - Proportion of each species' seeds that survives.

Detailed Description

This is the organizer class for all establishment behaviors.

Copyright: Copyright (c) Charles D. Canham 2003

Company: Institute of Ecosystem Studies

Author:
Lora E. Murphy
Version:
2.0

Edit history:
------------------
April 28, 2004: Submitted in beta version (LEM)
October 13, 2004: Added Puerto Rico establishment
April 20, 2005: Created new structure for establishment behaviors
June 7, 2005: Updated substrate favorability to match new substrate (LEM)
October 11, 2005: Added Storm Light Seed Survival (LEM)


Constructor & Destructor Documentation

javawrapper::EstablishmentBehaviors::EstablishmentBehaviors GUIManager  oManager  )  [inline]
 

Constructor.

Parameters:
oManager GUIManager object.

Edit history:
------------------
April 28, 2004: Submitted in beta version (LEM)
April 20, 2005: Created new structure for establishment behaviors
June 13, 2005: Added microtopographic establishment


Member Function Documentation

void javawrapper::EstablishmentBehaviors::ChangeOfSpeciesName String  sOldSpecies,
String  sNewSpecies
throws ModelException [inline]
 

Changes the names in the grids.

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)
Exceptions:
ModelException if there is a problem.

Reimplemented from javawrapper::WorkerBase.

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

Does setup.

Sets up the substrate favorability grid.

Parameters:
oPop TreePopulation object.
Exceptions:
ModelException if there's a problem setting behavior use data.

Edit history:
------------------
April 28, 2004: Submitted in beta version (LEM)
June 7, 2005: Added new substrate defaults (LEM)

Implements javawrapper::WorkerBase.

Behavior javawrapper::EstablishmentBehaviors::GetBehaviorByXMLTag String  sXMLTag  )  [inline]
 

Traps for the changed behavior names.

This could be removed probably by about 6.10.

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.

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

Find light values for PR Establishment and reject those for light behaviors.

Parameters:
sXMLTag XML tag of object to assign.
sXMLParentTag The immediate parent tag that sXMLTag is within.
oAttributes Ignored.
oData Data to assign.
Returns:
true if assigned, or false if not.
Exceptions:
ModelException not thrown here.

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

boolean javawrapper::EstablishmentBehaviors::SetVectorValueByXMLTag String  sXMLTag,
String  sXMLParentTag,
java.util.Vector  p_oData,
String[]  p_sChildXMLTags,
boolean[]  p_bAppliesTo,
org.xml.sax.Attributes  oParentAttributes,
org.xml.sax.Attributes[]  p_oAttributes
throws ModelException [inline]
 

Overridden for backwards compatibility and to make sure that only light values that apply to light behaviors are set.

There are other behaviors with light values, and this will make sure that no behavior "steals" these parameters.

Parameters:
sXMLTag Parent XML tag of data vector whose value is to be set.
sXMLParentTag The immediate parent tag that sXMLTag is within.
p_oData Vector of data values appropriate to the data type
p_sChildXMLTags The XML tags of the child elements
p_bAppliesTo Array of booleans saying which of the vector values should be set. This is important in the case of species-specifics - the vector index is the species number but not all species are set.
oParentAttributes Attributes of parent tag. May be useful when overridding this for unusual tags.
p_oAttributes Attributes passed from parser. This may be needed when overriding this function. Basic species-specific values are already handled by this function.
Returns:
true if the value was set successfully; false if the value could not be found.
Exceptions:
ModelException if the value could not be assigned to the data object.

Edit history:
------------------
January 7, 2005: Created (LEM)
April 20, 2005: Updated for backwards compatibility with substrate (LEM)

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

Validates data.

Parameters:
oPop TreePopulation object.
Exceptions:
ModelException if:
  • Light-dependent seed survival is enabled, and any of the light extinction coefficient values are not between 0 and 1.
  • Light-dependent seed survival is enabled, and the value for m_fLightHeight is not zero or greater.
  • Light-dependent seed survival is enabled, and the values for mp_fOptimumGLI are not between 0 and 100.
  • Light-dependent seed survival is enabled, and m_fBeamFractionOfGlobalRadiation is not a valid proportion.
  • Light-dependent seed survival is enabled, and either m_iJulianDayGrowthStarts or m_iJulianDayGrowthEnds is not between 1 and 365 (inclusive)
  • Light-dependent seed survival is enabled, and either m_iNumAltDiv or m_iNumAziDiv is not greater than 0
  • Light-dependent seed survival is enabled, and m_fClearSkyTransmissionCoefficient is 0.
  • if proportional seed survival is enabled and all values in mp_fProportionGerminating are not proportions.
  • Substrate-dependent seed survival is enabled and a favorability value is not a proportion.
  • Microtopographic seed survival is enabled and the proportion of mound value isn't a proportion
  • If the run has snags in it and the values for the snag light extinction coefficients aren't proportions, or the snag age classes aren't positive numbers.
  • Microtopographic establishment is enabled and: proportion of mound value isn't a proportion, or the Beer's law light filter isn't enabled, or substrate isn't enabled
  • Storm light dependent seed survival is enabled and the storm light behavior isn't.
This will also make sure that establishment is enabled if any of the others are.


Edit history:
------------------
April 28, 2004: Submitted in beta version (LEM)
June 7, 2005: Added new substrate values (LEM)
October 11, 2005: Added storm light dependent seed survival (LEM)

Implements javawrapper::WorkerBase.


Member Data Documentation

ModelFloat javawrapper::EstablishmentBehaviors::m_fBeamFractionOfGlobalRadiation [protected]
 

Initial value:

 new ModelFloat(0,
      "Beam Fraction of Global Radiation", "li_beamFractGlobalRad")
Light-dependent seed survival - Beam fraction of global radiation.

ModelFloat javawrapper::EstablishmentBehaviors::m_fClearSkyTransmissionCoefficient [protected]
 

Initial value:

 new ModelFloat(0,
      "Clear Sky Transmission Coefficient", "li_clearSkyTransCoeff")
Light-dependent seed survival - Clear sky transmission coefficient.

ModelFloat javawrapper::EstablishmentBehaviors::m_fFreshLogStdDev [protected]
 

Initial value:

 new ModelFloat(0,
      "Standard Deviation of Fresh Log Substrate Height, in m",
      "es_freshLogStdDev")
Standard deviation of fresh log height, in m.

ModelFloat javawrapper::EstablishmentBehaviors::m_fLightHeight [protected]
 

Initial value:

 new ModelFloat(0,
      "Height in m At Which to Calculate GLI", "es_lightHeight")
Light-dependent seed survival - Height at which to calculate light.

ModelFloat javawrapper::EstablishmentBehaviors::m_fMeanFreshLogHeight [protected]
 

Initial value:

 new ModelFloat(0,
      "Mean Height of Fresh Log Substrate, in m", "es_meanFreshLogHeight")
Mean log height, in m.

ModelFloat javawrapper::EstablishmentBehaviors::m_fMeanMoundHeight [protected]
 

Initial value:

 new ModelFloat(0,
      "Mean Height of Mounds, in m", "es_meanMoundHeight")
Mean mound height, in m.

ModelFloat javawrapper::EstablishmentBehaviors::m_fMinSunAngle [protected]
 

Initial value:

 new ModelFloat(0,
      "Minimum Solar Angle for GLI Calculations, in rad", "li_minSunAngle")
Light-dependent seed survival - Minimum sun angle in radians for GLI.

ModelFloat javawrapper::EstablishmentBehaviors::m_fMoundProportion [protected]
 

Initial value:

 new ModelFloat(0,
      "Proportion of Plot Area that is Mound", "es_moundProportion")
Proportion of the plot which is mound.

ModelFloat javawrapper::EstablishmentBehaviors::m_fMoundStdDev [protected]
 

Initial value:

 new ModelFloat(0,
      "Standard Deviation of Mound Height, in m", "es_moundStdDev")
Standard deviation of mound height.

ModelInt javawrapper::EstablishmentBehaviors::m_iJulianDayGrowthEnds [protected]
 

Initial value:

 new ModelInt(0,
      "Last Day of Growing Season for GLI Light Calculations",
      "li_julianDayGrowthEnds")
Light-dependent seed survival - End of growing season as Julian day.

ModelInt javawrapper::EstablishmentBehaviors::m_iJulianDayGrowthStarts [protected]
 

Initial value:

 new ModelInt(0,
      "First Day of Growing Season for GLI Light Calculations",
      "li_julianDayGrowthStarts")
Light-dependent seed survival - Start of growing season as Julian day.

ModelInt javawrapper::EstablishmentBehaviors::m_iMaxRespite [protected]
 

Initial value:

 new ModelInt(0,
                                                  "# Years Respite from Fern Shading for Seeds on Fresh Logs",
                                                  "es_maxRespite")
Number of years of respite from fern shading.

ModelInt javawrapper::EstablishmentBehaviors::m_iNumAltDiv [protected]
 

Initial value:

 new ModelInt(0,
                                                 "Number of Altitude Sky Divisions for GLI Light Calculations",
                                                 "li_numAltGrids")
Light-dependent seed survival - Number of altitude divisions for GLI.

ModelInt javawrapper::EstablishmentBehaviors::m_iNumAziDiv [protected]
 

Initial value:

 new ModelInt(0,
                                                 "Number of Azimuth Sky Divisions for GLI Light Calculations",
                                                 "li_numAziGrids")
Light-dependent seed survival - Number of azimuth divisions for GLI.

ModelInt javawrapper::EstablishmentBehaviors::m_iSnagAgeClass1 [protected]
 

Initial value:

 new ModelInt(0,
      "Upper Age (Yrs) of Snag Light Extinction Class 1", "li_snagAgeClass1")
Light-dependent seed survival - Upper age limit of snag size class 1.

ModelInt javawrapper::EstablishmentBehaviors::m_iSnagAgeClass2 [protected]
 

Initial value:

 new ModelInt(0,
      "Upper Age (Yrs) of Snag Light Extinction Class 2", "li_snagAgeClass2")
Light-dependent seed survival - Upper age limit of snag size class 2.

ModelEnum javawrapper::EstablishmentBehaviors::m_iUseSeedlingEfficiencyRoutine [protected]
 

Initial value:

      new ModelEnum(new int[] {0, 1}
                    ,
                    new String[] {"false", "true"}
                    , "Use Seedling Efficiency Routine",
                    "es_useSeedlingEfficiencyRoutine")
Deprecated:
Remove around 6.10 or so Whether or not to use the seedling efficiency routine

ModelVector javawrapper::EstablishmentBehaviors::mp_fDensDepSlope [protected]
 

Initial value:

 new ModelVector(
      "Slope of Density Dependence", "es_densDepSlope", "es_ddsVal", 0,
      ModelVector.FLOAT)
Density-dependent seed survival - Density-dependence slope.

ModelVector javawrapper::EstablishmentBehaviors::mp_fDensDepSteepness [protected]
 

Initial value:

 new ModelVector(
      "Steepness of Density Dependence", "es_densDepSteepness",
      "es_ddstVal", 0,
      ModelVector.FLOAT)
Density-dependent seed survival - Density-dependence steepness.

ModelVector javawrapper::EstablishmentBehaviors::mp_fHighSlope [protected]
 

Initial value:

 new ModelVector(
      "Slope of Dropoff Above the Optimum GLI", "es_highSlope", "es_hsVal", 0,
      ModelVector.FLOAT)
Light-dependent seed survival - Slope of establishment dropoff above the optimum GLI for each species.

ModelVector javawrapper::EstablishmentBehaviors::mp_fLightExtCoeffFullDmg [protected]
 

Initial value:

 new ModelVector(
      "Light Extinction Coeff of Complete Damage Trees (0-1)",
      "es_lightExtCoeffFullDmg", "es_lecfdVal", 0,
      ModelVector.FLOAT, true)
Light-dependent seed survival - Light extinction coefficient of complete damaged trees.

ModelVector javawrapper::EstablishmentBehaviors::mp_fLightExtCoeffNoDmg [protected]
 

Initial value:

 new ModelVector(
      "Light Extinction Coeff of Undamaged Trees (0-1)",
      "li_lightExtinctionCoefficient", "li_lecVal", 0,
      ModelVector.FLOAT, true)
Light-dependent seed survival - Light extinction coefficient of undamaged trees.

ModelVector javawrapper::EstablishmentBehaviors::mp_fLightExtCoeffPartDmg [protected]
 

Initial value:

 new ModelVector(
      "Light Extinction Coeff of Medium Damage Trees (0-1)",
      "es_lightExtCoeffPartDmg", "es_lecpdVal", 0,
      ModelVector.FLOAT, true)
Light-dependent seed survival - Light extinction coefficient of medium damaged trees.

ModelVector javawrapper::EstablishmentBehaviors::mp_fLowSlope [protected]
 

Initial value:

 new ModelVector(
      "Slope of Dropoff Below Optimum GLI", "es_lowSlope", "es_lsVal", 0,
      ModelVector.FLOAT)
Light-dependent seed survival - Slope of establishment dropoff below the optimum GLI for each species.

ModelVector javawrapper::EstablishmentBehaviors::mp_fOptimumGLI [protected]
 

Initial value:

 new ModelVector(
      "GLI of Optimum Establishment, 0-100", "es_optimumGLI", "es_ogVal", 0,
      ModelVector.FLOAT)
Light-dependent seed survival - Optimum GLI at which establishment is not reduced for each species.

ModelVector javawrapper::EstablishmentBehaviors::mp_fProportionGerminating [package]
 

Initial value:

 new ModelVector(
      "Proportion Germinating Between 0 and 1",
      "ge_proportionGerminating", "ge_pgVal", 0, ModelVector.FLOAT)
Proportional seed survival - Proportion of each species' seeds that survives.

ModelVector javawrapper::EstablishmentBehaviors::mp_fSnagClass1LightExtinctionCoefficient [protected]
 

Initial value:

 new
      ModelVector("Snag Age Class 1 Light Extinction Coefficient (0-1)",
                  "li_snag1LightExtinctionCoefficient", "li_s1lecVal", 0,
                  ModelVector.FLOAT, true)
Light-dependent seed survival - snag age class 1 light extinction coefficient.

ModelVector javawrapper::EstablishmentBehaviors::mp_fSnagClass2LightExtinctionCoefficient [protected]
 

Initial value:

 new
      ModelVector("Snag Age Class 2 Light Extinction Coefficient (0-1)",
                  "li_snag2LightExtinctionCoefficient", "li_s2lecVal", 0,
                  ModelVector.FLOAT, true)
Light-dependent seed survival - snag age class 2 light extinction coefficient.

ModelVector javawrapper::EstablishmentBehaviors::mp_fSnagClass3LightExtinctionCoefficient [protected]
 

Initial value:

 new
      ModelVector("Snag Age Class 3 Light Extinction Coefficient (0-1)",
                  "li_snag3LightExtinctionCoefficient", "li_s3lecVal", 0,
                  ModelVector.FLOAT, true)
Light-dependent seed survival - snag age class 3 light extinction coefficient.


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