javawrapper.SeedPredationBehaviors Class Reference

This class organizes the seed predation behaviors. More...

Inheritance diagram for javawrapper.SeedPredationBehaviors:

javawrapper.BehaviorTypeBase javawrapper.WorkerBase

List of all members.

Public Member Functions

 SeedPredationBehaviors (GUIManager oManager) throws ModelException
 Constructor.
void DoSetup (TreePopulation oPop) throws ModelException
 Sets up neighbor pn values for neighborhood seed predation.
void ValidateData (TreePopulation oPop) throws javawrapper. ModelException
 Validates the dataset if seed predation is enabled.
void ChangeOfSpeciesName (String sOldSpecies, String sNewSpecies)
 Updates the pn neighbor names when a species name is changed.
void CopySpecies (int iSpeciesCopyFrom, int iSpeciesCopyTo) throws ModelException
 Updates the pn when a species is copied.
boolean SetSingleValueByXMLTag (String sXMLTag, String sXMLParentTag, Attributes oAttributes, Object oData) throws ModelException
 A simple backwards compatibility feature.

Protected Attributes

ModelVector mp_fNeighPredMastingP0
 Neighborhood seed predation - masting "p0".
ModelVector mp_fNeighPredNonMastingP0
 Neighborhood seed predation - non-masting "p0".
ModelVector mp_fNeighPredMinDbh
 Neighborhood seed predation - min neighbor DBH.
ModelVector mp_iNeighPredCounts4Mast
 Neighborhood seed predation - whether species is counted towards masting.
ModelFloat m_fNeighPredMastingDensity
 Neighborhood seed predation - density of seeds for masting, seeds/m2/yr.
ModelFloat m_fNeighPredRadius
 Neighborhood seed predation - neighborhood search radius.
ModelEnum m_iNeighPredMastDecisionMethod
 Neighborhood seed predation - method for deciding mast.
ModelVector mp_fLnkNeighPredP0
 Linked neighborhood seed predation - "p0".
ModelVector mp_fLnkNeighPredMinDbh
 Linked neighborhood seed predation - min neighbor DBH.
ModelFloat m_fLnkNeighPredRadius
 Linked neighborhood seed predation - neighborhood search radius.
ModelFloat m_fFuncRespPredInitDensity
 Functional response predation - predator initial density in number per square meter.
ModelFloat m_fFuncRespMaxInstDeclineRate1
 Functional response predation - max instantaneous rate at which predator abundance declines in the absense of food, in number of predators per week - season 1.
ModelFloat m_fFuncRespMaxInstDeclineRate2
 Functional response predation - max instantaneous rate at which predator abundance declines in the absense of food, in number of predators per week - season 2.
ModelFloat m_fFuncRespDemogEfficiency1
 Functional response predation - predator population's demographic efficiency - season 1.
ModelFloat m_fFuncRespDemogEfficiency2
 Functional response predation - predator population's demographic efficiency - season 2.
ModelFloat m_fFunRespDensDepCoeff1
 Functional response predation - density-dependent coefficient - season 1.
ModelFloat m_fFunRespDensDepCoeff2
 Functional response predation - density-dependent coefficient - season 2.
ModelVector mp_fFuncRespMaxIntake
 Functional response predation - maximum intake rate - number of seeds per predator per day.
ModelVector mp_fFuncRespForagingEff
 Functional response predation - foraging efficiency.
ModelFloat m_fFuncRespPropGerm
 Functional response predation - proportion of seeds, between 0 and 1, germinating each week in the germination period.
ModelInt m_iFuncRespNumWeeksSeedFall
 Functional response predation - number of weeks for which seedfall occurs.
ModelInt m_iFuncRespNumWeeksToModel
 Functional response predation - number of weeks to run model - must be less than or equal to 52.
ModelInt m_iFuncRespWeekGermStarts
 Functional response predation - week number in which germination begins.
ModelInt m_iFuncRespWeekSeason2Starts
 Functional response predation - week number in which season 2 begins.
ModelString m_sFuncRespOutputFilename
 Functional response predation - output filename.
ModelEnum m_iPreservePredatorDensities
 Functional response predation - whether or not to preserve predator densities between model timesteps (true) or re-initialize with predator initial density (false).
ModelFloat m_fLnkFuncRespPredInitDensity
 Linked functional response predation - predator initial density in number per square meter.
ModelFloat m_fLnkFuncRespMaxInstDeclineRate1
 Linked functional response predation - max instantaneous rate at which predator abundance declines in the absense of food, in number of predators per week - season 1.
ModelFloat m_fLnkFuncRespMaxInstDeclineRate2
 Linked functional response predation - max instantaneous rate at which predator abundance declines in the absense of food, in number of predators per week - season 2.
ModelFloat m_fLnkFuncRespDemogEfficiency1
 Linked functional response predation - predator population's demographic efficiency - season 1.
ModelFloat m_fLnkFuncRespDemogEfficiency2
 Linked functional response predation - predator population's demographic efficiency - season 2.
ModelFloat m_fLnkFunRespDensDepCoeff1
 Linked functional response predation - density-dependent coefficient - season 1.
ModelFloat m_fLnkFunRespDensDepCoeff2
 Linked functional response predation - density-dependent coefficient - season 2.
ModelVector mp_fLnkFuncRespMaxIntake
 Linked functional response predation - maximum intake rate - number of seeds per predator per day.
ModelVector mp_fLnkFuncRespForagingEff
 Linked functional response predation - foraging efficiency.
ModelFloat m_fLnkFuncRespPropGerm
 Linked functional response predation - proportion of seeds, between 0 and 1, germinating each week in the germination period.
ModelInt m_iLnkFuncRespNumWeeksSeedFall
 Linked functional response predation - number of weeks for which seedfall occurs.
ModelInt m_iLnkFuncRespNumWeeksToModel
 Linked functional response predation - number of weeks to run model - must be less than or equal to 52.
ModelInt m_iLnkFuncRespWeekGermStarts
 Linked functional response predation - week number in which germination begins.
ModelInt m_iLnkFuncRespWeekSeason2Starts
 Linked functional response predation - week number in which season 2 begins.
ModelString m_sLnkFuncRespOutputFilename
 Linked functional response predation - output filename.
ModelEnum m_iLnkPreservePredatorDensities
 Linked functional response predation - whether or not to preserve predator densities between model timesteps (true) or re-initialize with predator initial density (false).


Detailed Description

This class organizes the seed predation behaviors.

Copyright: Copyright (c) Charles D. Canham 2003

Company: Institute of Ecosystem Studies

Author:
Lora E. Murphy
Version:
1.0

Edit history:
------------------
April 28, 2004: Submitted in beta version (LEM)
May 22, 2007: Added neighborhood seed predation (LEM)
May 13, 2008: Added linked seed predation (LEM)

Constructor & Destructor Documentation

javawrapper.SeedPredationBehaviors.SeedPredationBehaviors ( GUIManager  oManager  )  throws ModelException

Constructor.

Sets up the child behavior list and adds data appropriately.

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


Member Function Documentation

void javawrapper.SeedPredationBehaviors.DoSetup ( TreePopulation  oPop  )  throws ModelException [virtual]

Sets up neighbor pn values for neighborhood seed predation.

Parameters:
oPop Tree population
Exceptions:
ModelException 

Implements javawrapper.WorkerBase.

void javawrapper.SeedPredationBehaviors.ValidateData ( TreePopulation  oPop  )  throws javawrapper. ModelException [virtual]

Validates the dataset if seed predation is enabled.

Parameters:
oPop TreePopulation object.
Exceptions:
javawrapper.ModelException if:
  • Number of weeks of seedfall is less than or equal to zero
  • Initial predator density is less than or equal to zero
  • Number of weeks to run the model is less than 0 or greater than 52
  • Week to start germination is less than 0 or greater than 52
  • Proportion germinating is not a proportion
  • Neighborhood predation minimum neighbor DBH is less than zero
  • Neighborhood predation neighbor radius is less than zero
  • Neighborhood predation masting seed density threshold is less than zero
  • Either seed predation behavior is present without a disperse behavior also enabled

Implements javawrapper.WorkerBase.

void javawrapper.SeedPredationBehaviors.ChangeOfSpeciesName ( String  sOldSpecies,
String  sNewSpecies 
)

Updates the pn 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.SeedPredationBehaviors.CopySpecies ( int  iSpeciesCopyFrom,
int  iSpeciesCopyTo 
) throws ModelException

Updates the pn when a species is copied.

The pn's for that neighbor are made identical to those being copied as well as entries for species within the pn.

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

Reimplemented from javawrapper.BehaviorTypeBase.

boolean javawrapper.SeedPredationBehaviors.SetSingleValueByXMLTag ( String  sXMLTag,
String  sXMLParentTag,
Attributes  oAttributes,
Object  oData 
) throws ModelException

A simple backwards compatibility feature.

A parameter was transformed from a single value to a species specific one. This traps the single value so parameter files containing it can be read. This can be eliminated in release 6.11.

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.

Reimplemented from javawrapper.WorkerBase.


Member Data Documentation

Initial value:

 new ModelVector(
                        "Neighborhood Predation - Masting \"p0\"",      "pr_neighPredMastingP0", 
                        "pr_npmp0Val", 0, ModelVector.FLOAT)
Neighborhood seed predation - masting "p0".

Initial value:

 new ModelVector(
                        "Neighborhood Predation - Non-Masting \"p0\"",  
                        "pr_neighPredNonMastingP0", "pr_npnmp0Val", 0, ModelVector.FLOAT)
Neighborhood seed predation - non-masting "p0".

Initial value:

 new ModelVector(
      "Neighborhood Predation - Minimum Neighbor DBH (cm)", 
      "pr_neighPredMinNeighDBH", "pr_npmndVal", 0, ModelVector.FLOAT, true)
Neighborhood seed predation - min neighbor DBH.

Initial value:

 new ModelVector(
      "Neighborhood Predation - Counts For Masting?",
      "pr_neighPredCounts4Mast", "pr_npc4mVal", 0, ModelVector.MODEL_ENUM)
Neighborhood seed predation - whether species is counted towards masting.

Initial value:

 new ModelFloat(0,
      "Neighborhood Predation - Masting Seed Density, #/m2/yr", 
      "pr_neighPredMastingDensity")
Neighborhood seed predation - density of seeds for masting, seeds/m2/yr.

Initial value:

 new ModelFloat(0,
      "Neighborhood Predation - Neighbor Search Radius (m)", 
      "pr_neighPredRadius")
Neighborhood seed predation - neighborhood search radius.

Initial value:

      new ModelEnum(new int[] {0, 1},
                    new String[] {"Seed threshold", "Ask disperse"},
                    "Neighborhood Predation - Mast Event Decision Method",
                    "pr_neighPredMastDecisionMethod")
Neighborhood seed predation - method for deciding mast.

Initial value:

 new ModelVector(
      "(Lnk) Neighborhood Predation - \"p0\"",  "pr_neighPredLnkP0", 
      "pr_npmlp0Val", 0, ModelVector.FLOAT)
Linked neighborhood seed predation - "p0".

Initial value:

 new ModelVector(
      "(Lnk) Neighborhood Predation - Minimum Neighbor DBH (cm)", 
      "pr_neighPredLnkMinNeighDBH", "pr_nplmndVal", 0, ModelVector.FLOAT, true)
Linked neighborhood seed predation - min neighbor DBH.

Initial value:

 new ModelFloat(0,
      "(Lnk) Neighborhood Predation - Neighbor Search Radius (m)", 
      "pr_neighPredRadiusLnk")
Linked neighborhood seed predation - neighborhood search radius.

Initial value:

 new ModelFloat(0,
      "Func Resp - Predator Initial Density - num/sq m", "pr_funcRespPredatorInitialDensity")
Functional response predation - predator initial density in number per square meter.

Initial value:

 new ModelFloat(0,
      "Func Resp - Max Decline Rate, Season 1, predators/week",
      "pr_funcRespMaxInstDeclineRate1")
Functional response predation - max instantaneous rate at which predator abundance declines in the absense of food, in number of predators per week - season 1.

Initial value:

 new ModelFloat(0,
      "Func Resp - Max Decline Rate, Season 2, predators/week",
      "pr_funcRespMaxInstDeclineRate2")
Functional response predation - max instantaneous rate at which predator abundance declines in the absense of food, in number of predators per week - season 2.

Initial value:

 new ModelFloat(0,
      "Func Resp - Demographic Efficiency, Season 1", 
      "pr_funcRespDemographicEfficiency1")
Functional response predation - predator population's demographic efficiency - season 1.

Initial value:

 new ModelFloat(0,
      "Func Resp - Demographic Efficiency, Season 2", 
      "pr_funcRespDemographicEfficiency2")
Functional response predation - predator population's demographic efficiency - season 2.

Initial value:

 new ModelFloat(0,
      "Func Resp - Density Dependent Coeff, Season 1", 
      "pr_funcRespDensityDependentCoefficient1")
Functional response predation - density-dependent coefficient - season 1.

Initial value:

 new ModelFloat(0,
      "Func Resp - Density Dependent Coeff, Season 2", 
      "pr_funcRespDensityDependentCoefficient2")
Functional response predation - density-dependent coefficient - season 2.

Initial value:

 new ModelVector(
      "Func Resp - Max Intake Rate - seeds per predator per day", 
      "pr_funcRespMaxIntakeRate", "pr_frmirVal", 0, ModelVector.FLOAT)
Functional response predation - maximum intake rate - number of seeds per predator per day.

Initial value:

 new ModelVector(
      "Func Resp - Foraging Efficiency", "pr_funcRespForagingEfficiency", "pr_frfeVal", 
      0, ModelVector.FLOAT)
Functional response predation - foraging efficiency.

Initial value:

 new ModelFloat(0,
      "Func Resp - Proportion of Seeds Germinating Each Week",
      "pr_funcRespProportionGerminating")
Functional response predation - proportion of seeds, between 0 and 1, germinating each week in the germination period.

Initial value:

 new ModelInt(0,
      "Func Resp - Number of Weeks in Which Seedfall Occurs", 
      "pr_funcRespNumWeeksSeedFall")
Functional response predation - number of weeks for which seedfall occurs.

Initial value:

 new ModelInt(0,
      "Func Resp - Weeks to Run Seed Predation Model (1 - 52)",
      "pr_funcRespNumWeeksToModel")
Functional response predation - number of weeks to run model - must be less than or equal to 52.

Initial value:

 new ModelInt(0,
      "Func Resp - Week Germination Begins",
      "pr_funcRespWeekGerminationStarts")
Functional response predation - week number in which germination begins.

Initial value:

 new ModelInt(0,
      "Func Resp - Week Season 2 Begins",
      "pr_funcRespWeekSeason2Starts")
Functional response predation - week number in which season 2 begins.

Initial value:

 new ModelString("",
      "Func Resp - Seed Predation Output Filename, If Desired", 
      "pr_funcRespOutputFilename")
Functional response predation - output filename.

Initial value:

 new ModelEnum(
                  new int[] {0, 1}, new String[] {"false", "true"},
      "Func Resp - Keep Predator Densities Between Timesteps",
      "pr_funcRespPreservePredatorDensities")
Functional response predation - whether or not to preserve predator densities between model timesteps (true) or re-initialize with predator initial density (false).

Initial value:

 new ModelFloat(0,
      "(Lnk) Func Resp - Predator Initial Density - num/sq m", "pr_funcRespPredatorInitialDensityLnk")
Linked functional response predation - predator initial density in number per square meter.

Initial value:

 new ModelFloat(0,
      "(Lnk) Func Resp - Max Decline Rate, Season 1, predators/week",
      "pr_funcRespMaxInstDeclineRate1Lnk")
Linked functional response predation - max instantaneous rate at which predator abundance declines in the absense of food, in number of predators per week - season 1.

Initial value:

 new ModelFloat(0,
      "(Lnk) Func Resp - Max Decline Rate, Season 2, predators/week",
      "pr_funcRespMaxInstDeclineRate2Lnk")
Linked functional response predation - max instantaneous rate at which predator abundance declines in the absense of food, in number of predators per week - season 2.

Initial value:

 new ModelFloat(0,
      "(Lnk) Func Resp - Demographic Efficiency, Season 1", 
      "pr_funcRespDemographicEfficiency1Lnk")
Linked functional response predation - predator population's demographic efficiency - season 1.

Initial value:

 new ModelFloat(0,
      "(Lnk) Func Resp - Demographic Efficiency, Season 2", 
      "pr_funcRespDemographicEfficiency2Lnk")
Linked functional response predation - predator population's demographic efficiency - season 2.

Initial value:

 new ModelFloat(0,
      "(Lnk) Func Resp - Density Dependent Coeff, Season 1", 
      "pr_funcRespDensityDependentCoefficient1Lnk")
Linked functional response predation - density-dependent coefficient - season 1.

Initial value:

 new ModelFloat(0,
      "(Lnk) Func Resp - Density Dependent Coeff, Season 2", 
      "pr_funcRespDensityDependentCoefficient2Lnk")
Linked functional response predation - density-dependent coefficient - season 2.

Initial value:

 new ModelVector(
      "(Lnk) Func Resp - Max Intake Rate - seeds per predator per day", 
      "pr_funcRespMaxIntakeRateLnk", "pr_frmirlVal", 0, ModelVector.FLOAT)
Linked functional response predation - maximum intake rate - number of seeds per predator per day.

Initial value:

 new ModelVector(
      "(Lnk) Func Resp - Foraging Efficiency", "pr_funcRespForagingEfficiencyLnk", "pr_frfelVal", 
      0, ModelVector.FLOAT)
Linked functional response predation - foraging efficiency.

Initial value:

 new ModelFloat(0,
      "(Lnk) Func Resp - Proportion of Seeds Germinating Each Week",
      "pr_funcRespProportionGerminatingLnk")
Linked functional response predation - proportion of seeds, between 0 and 1, germinating each week in the germination period.

Initial value:

 new ModelInt(0,
      "(Lnk) Func Resp - Number of Weeks in Which Seedfall Occurs", 
      "pr_funcRespNumWeeksSeedFallLnk")
Linked functional response predation - number of weeks for which seedfall occurs.

Initial value:

 new ModelInt(0,
      "(Lnk) Func Resp - Weeks to Run Seed Predation Model (1 - 52)",
      "pr_funcRespNumWeeksToModelLnk")
Linked functional response predation - number of weeks to run model - must be less than or equal to 52.

Initial value:

 new ModelInt(0,
      "(Lnk) Func Resp - Week Germination Begins",
      "pr_funcRespWeekGerminationStartsLnk")
Linked functional response predation - week number in which germination begins.

Initial value:

 new ModelInt(0,
      "(Lnk) Func Resp - Week Season 2 Begins",
      "pr_funcRespWeekSeason2StartsLnk")
Linked functional response predation - week number in which season 2 begins.

Initial value:

 new ModelString("",
      "(Lnk) Func Resp - Seed Predation Output Filename, If Desired", 
      "pr_funcRespOutputFilenameLnk")
Linked functional response predation - output filename.

Initial value:

 new ModelEnum(
      new int[] {0, 1}, new String[] {"false", "true"},
      "(Lnk) Func Resp - Keep Predator Densities Between Timesteps",
      "pr_funcRespPreservePredatorDensitiesLnk")
Linked functional response predation - whether or not to preserve predator densities between model timesteps (true) or re-initialize with predator initial density (false).


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

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