Substrate Dependent Seed Survival - Version 1.1. More...
#include <SubstrateDepSeedSurvival.h>
Public Member Functions | |
| clSubstrateDepSeedSurvival (clSimManager *p_oSimManager) | |
| Constructor. More... | |
| ~clSubstrateDepSeedSurvival () | |
| Destructor. More... | |
| void | GetData (xercesc::DOMDocument *p_oDoc) |
| Performs setup. More... | |
| void | Action () |
| Assesses seed survival. More... | |
| void | SetNameData (std::string sNameString) |
| Captures the behavior name passed from the parameter file. More... | |
 Public Member Functions inherited from clBehaviorBase | |
| virtual float | GetBehaviorVersion () |
| Gets the behavior version number. More... | |
| clBehaviorBase (clSimManager *p_oSimManager) | |
| Constructor. More... | |
| virtual | ~clBehaviorBase () |
| Destructor. More... | |
| virtual short int | ValidateVersionNumber (float fTestVersion) |
| Makes sure that the version number of a file passed is between the minimum and current version numbers. More... | |
| virtual void | RegisterTreeDataMembers () |
| Registers tree data members. More... | |
| virtual void | SetSpeciesTypeCombos (short int iNumCombos, stcSpeciesTypeCombo *p_whatCombos) |
| Sets the species/type combos for a behavior. More... | |
| virtual short int | GetNewTreeInts () |
| Gets the number of new tree integer data members this behavior wants to register. More... | |
| virtual short int | GetNewTreeFloats () |
| Gets the number of new tree float data members this behavior wants to register. More... | |
| virtual short int | GetNewTreeChars () |
| Gets the number of new tree character data members this behavior wants to register. More... | |
| virtual short int | GetNewTreeBools () |
| Gets the number of new tree bool data members this behavior wants to register. More... | |
| virtual short int | GetNumSpeciesTypeCombos () |
| Gets the number of species/type combos to which this behavior applies. More... | |
| virtual short int | GetNumBehaviorSpecies () |
| Gets the number of unique tree species to which this behavior applies. More... | |
| struct stcSpeciesTypeCombo | GetSpeciesTypeCombo (short int iIndex) |
| Gets one of this behavior's type/species combos. More... | |
| virtual short int | GetBehaviorSpecies (short int iIndex) |
| Gets one of the behavior's species. More... | |
| short int | GetBehaviorListNumber () |
| Gets the behavior list number for this behavior, which differentiates between multiple copies of the behavior in the behavior list. More... | |
| void | SetBehaviorListNumber (short int iNumber) |
| Sets the behavior list number for this behavior, which differentiates between multiple copies of the behavior in the behavior list. More... | |
| std::string | FormatSpeciesTypeQueryString () |
| Formats the string for species/types query. More... | |
| virtual DOMElement * | GetParentParametersElement (xercesc::DOMDocument *p_oDoc) |
| This will get the correct set of parameters for this behavior based on the behavior list position number. More... | |
| Public Member Functions inherited from clWorkerBase | |
| clWorkerBase (clSimManager *p_oSimManager) | |
| Constructor. More... | |
| virtual | ~clWorkerBase () |
| Destructor. More... | |
| std::string | GetName () |
| Gets the object's namestring. More... | |
| clSimManager * | GetSimManager () |
| void | DoObjectSetup (xercesc::DOMDocument *p_oDoc, fileType iFileType) |
| Triggers the setup process. More... | |
| virtual void | TimestepCleanup () |
| Performs any necessary cleanup operations at the end of a timestep. More... | |
| virtual void | EndOfRunCleanup () |
| Performs any necessary cleanup operations at the end of a run. More... | |
Protected Member Functions | |
| void | GetParameterFileData (xercesc::DOMDocument *p_oDoc) |
| Declares arrays and fills them with parameter file data. More... | |
| void | CalculateSubstrateFavorabilityIndex () |
| For each grid cell in the substrate favorability grid, determines its substrate favorability index. More... | |
| void | SetupGrids () |
| Sets up the grids. More... | |
| Protected Member Functions inherited from clWorkerBase | |
| void | AssembleFileCode (int iFileType, int iFileVersion, char *cCode) |
| Creates the proper identifying filecode for an XML file. More... | |
Protected Attributes | |
| clGrid * | mp_oSubstrateGrid |
| Pointer to "Substrate" grid, created by clSubstrate. More... | |
| clGrid * | mp_oSubstrateFavGrid |
| The grid called "Substrate Favorability" will have a cell resolution matching the "Substrate" grid. More... | |
| clGrid * | mp_oSeedGrid |
| Pointer to the "Dispersed Seeds" grid created by disperse behaviors. More... | |
| double * | mp_fCanGroundScarSoilFav |
| Canopy / ground scarified soil favorability - one per behavior species. More... | |
| double * | mp_fCanGroundTipUpFav |
| Canopy / ground tip-up mounds favorability - one per behavior species. More... | |
| double * | mp_fCanGroundFreshLogFav |
| Canopy / ground fresh logs favorability - one per behavior species. More... | |
| double * | mp_fCanGroundDecLogFav |
| Canopy / ground decayed logs favorability - one per behavior species. More... | |
| double * | mp_fCanGroundForFlLitterFav |
| Canopy / ground forest floor litter favorability - one per behavior species. More... | |
| double * | mp_fCanGroundForFlMossFav |
| Canopy / ground forest floor moss favorability - one per behavior species. More... | |
| double * | mp_fGapMoundScarSoilFav |
| Gap / mound scarified soil favorability - one per behavior species. More... | |
| double * | mp_fGapMoundTipUpFav |
| Gap / mound tip-up mounds favorability - one per behavior species. More... | |
| double * | mp_fGapMoundFreshLogFav |
| Gap / mound fresh logs favorability - one per behavior species. More... | |
| double * | mp_fGapMoundDecLogFav |
| Gap / mound decayed logs favorability - one per behavior species. More... | |
| double * | mp_fGapMoundForFlLitterFav |
| Gap / mound forest floor litter favorability - one per behavior species. More... | |
| double * | mp_fGapMoundForFlMossFav |
| Gap / mound forest floor moss favorability - one per behavior species. More... | |
| short int * | mp_iIndexes |
| Speeds access to favorability arrays. More... | |
| short int * | mp_iSubstrFavCode |
| Data member codes for substrate grid for favorability index. More... | |
| short int * | mp_iSeedGridCode |
| Data member codes for seed grid for number of seeds. More... | |
| double | m_fMoundProp |
| Proportion of plot that is mound, if using microtopography - 0 - 1. More... | |
| short int | m_iIsGapCode |
| Data member code for gap status in dispersed seed grid. More... | |
| short int | m_iScarifiedSoilCode |
| Data member code - float - scarsoil grid data member. More... | |
| short int | m_iForestFloorLitterCode |
| Data member code - float - fflitter grid data member. More... | |
| short int | m_iForestFloorMossCode |
| Data member code - float - ffmoss grid data member. More... | |
| short int | m_iTipUpCode |
| Data member code - float - tipup grid data member. More... | |
| short int | m_iFreshLogCode |
| Data member code - float - freshlog grid data member. More... | |
| short int | m_iDecayedLogCode |
| Data member code - float - declog grid data member. More... | |
| bool | m_bUsesGap |
| Whether or not gap status is used by this behavior. More... | |
| bool | m_bUsesMicro |
| Whether or not microtopography is used. More... | |
| Protected Attributes inherited from clBehaviorBase | |
| short int | m_iNumSpeciesTypeCombos |
| How many type/species combos a behavior will act on. More... | |
| short int | m_iNumBehaviorSpecies |
| How many distinct species are in the combo list - important for filling species-specific values from parameter file. More... | |
| short int * | mp_iWhatSpecies |
| List of distinct species - for filling species-specific values from parameter file. More... | |
| stcSpeciesTypeCombo * | mp_whatSpeciesTypeCombos |
| Array of species/type combos that the behavior will act on. More... | |
| short int | m_iNewTreeInts |
| The number of new tree integer data members this behavior wants to add. More... | |
| short int | m_iNewTreeFloats |
| The number of new tree float data members this behavior wants to add. More... | |
| short int | m_iNewTreeChars |
| The number of new tree character data members this behavior wants to add. More... | |
| short int | m_iNewTreeBools |
| The number of new tree boolean data members this behavior wants to add. More... | |
| short int | m_iBehaviorListNumber |
| The number of this behavior in the behavior list, to differentiate between possible multiple copies of this behavior. More... | |
| float | m_fVersionNumber |
| Version number - this will be rounded to 2 digits after the decimal place. More... | |
| std::string | m_sXMLRoot |
| XML root that encloses the parameters for this behavior. More... | |
| float | m_fMinimumVersionNumber |
| Minimum version number - this behavior will run parameter data for a file marked between this number and the current version number, inclusive. More... | |
| Protected Attributes inherited from clWorkerBase | |
| std::string | m_sNameString |
| If a behavior has registered a command line command with the sim manager, this allows it to be called. More... | |
| clSimManager * | mp_oSimManager |
| Pointer to the simulation manager object. More... | |
| int * | mp_iAllowedFileTypes |
| List of the input file types this object can handle. More... | |
| int | m_iNumAllowedTypes |
| Number of input file types this object can handle. More... | |
Detailed Description
Substrate Dependent Seed Survival - Version 1.1.
This behavior assesses seed survival as a function of substrate composition. This behavior can be used in three different configurations: with gap status, without gap status, and with microtopography.
This uses the information in the "Substrate" grid (created and populated by clSubstrate) to determine how favorable a location is for seed survival. The "Substrate" grid contains, in each cell, the proportion of each of the six substrate types. For each species, this behavior knows, on a scale from 0 to 1, how favorable a substrate type is to seeds of that species. The behavior calculates a "favorability index" for each grid cell for each species by multiplying the proportion of each substrate by its favorability and summing the results. This index is the proportion of seeds of that species that survive at that location.
If this is used with gap status, then there are two possible favorabilities for each species for each substrate type: the favorability in a gap cell and the favorability in a canopy cell. This behavior uses the appropriate favorabilities for the gap status of the cell.
If this is used with microtopography, then there are twelve substrate types: each of the basic six on the ground and on a mound. Each substrate type is split into mound and ground based on the fixed proportion of each specified by the user. A favorability index is created from these twelve types the same way it is created with six, above.
To keep track of seed favorabilities, this behavior creates a grid called "Substrate Favorability".
In order to translate between different grid cell sizes in the "Substrate" and "Dispersed Seeds" grids, each seed is assigned a temporary random location within its "Dispersed Seeds" grid cell. A random number is compared to the favorability at that location and the seed either survives or dies. The number of surviving seeds in a "Dispersed Seeds" grid cell is assigned back to that cell.
A fatal error is thrown if: there are no disperse behaviors for the run, if gap status establishment is used without gap status disperse, or if substrate establishment is used without substrate.
The namestring for this class is "Substrate Dependent Seed Survival". Call this from the parameter file using either "NoGapSubstrateSeedSurvival", "GapSubstrateSeedSurvival", or "MicrotopographicSubstrateSeedSurvival". Apply this behavior to species; use any type, since it will be ignored.
Copyright 2011 Charles D. Canham.
Edit history:
--------------—
October 20, 2011 - Wiped the slate clean for SORTIE 7.0 (LEM)
Constructor & Destructor Documentation
◆ clSubstrateDepSeedSurvival()
| clSubstrateDepSeedSurvival::clSubstrateDepSeedSurvival | ( | clSimManager * | p_oSimManager | ) |
Constructor.
- Parameters
-
p_oSimManager Sim Manager object.
◆ ~clSubstrateDepSeedSurvival()
| clSubstrateDepSeedSurvival::~clSubstrateDepSeedSurvival | ( | ) |
Destructor.
Member Function Documentation
◆ Action()
|
virtual |
Assesses seed survival.
This calculates the favorability index for each grid cell. For each grid cell, the favorability index is the sum of the proportions of each substrate multiplied by the favorability of that substrate for the cover condition of that grid cell (canopy or gap).
Then, for each cell in the seeds grid, each seed's probability of survival is assessed. It will be given a random location within the grid cell of the "Dispersed Seeds" grid from which it comes. Then a random number is compared to the substrate favorability at that location to see if the seed survives or not. This allows us to translate easily between different grid cell resolutions in the "Dispersed Seeds" and "Substrate" grids.
Reimplemented from clBehaviorBase.
◆ CalculateSubstrateFavorabilityIndex()
|
protected |
For each grid cell in the substrate favorability grid, determines its substrate favorability index.
If m_bUsesGap is true, then the gap status is retrieved from the seed grid and the favorability matches the gap status; otherwise, the favorability is calculated with the canopy parameters.
For each grid cell, the favorability index is the sum of the proportions of each substrate multiplied by the favorability of that substrate for the cover condition of that grid cell (canopy or gap).
◆ GetData()
|
virtual |
Performs setup.
This calls GetParameterFileData() and SetupGrids().
- Parameters
-
p_oDoc DOM tree of parsed input file.
Implements clWorkerBase.
◆ GetParameterFileData()
|
protected |
Declares arrays and fills them with parameter file data.
If m_bUsesGap is true, all gap substrate favorabilities are also retrieved.
- Parameters
-
p_oDoc Parsed parameter file.
- Exceptions
-
modelErr if any of the substrate favorabilities are not between 0 and 1, or if the mound proportion is not between 0 and 1.
◆ SetNameData()
|
virtual |
Captures the behavior name passed from the parameter file.
If the name called from the parameter file is "NoGapSubstrateSeedSurvival", then m_bUsesGap is set to false. If the name called is "Gap Substrate Seed Survival", then m_bUsesGap is set to true. If the name called is "MicrotopographicSubstrateSeedSurvival", then m_bUsesGap is set to false and m_bUsesMicro is set to true.
- Parameters
-
sNameString Behavior name from parameter file.
Reimplemented from clBehaviorBase.
◆ SetupGrids()
|
protected |
Sets up the grids.
This creates the substrate favorability grid and retrieves a pointer to the dispersed seeds grid.
- Exceptions
-
modelErr If the "Substrate" grid doesn't exist, or if the "Dispersed Seeds" grid doesn't exist.
Member Data Documentation
◆ m_bUsesGap
|
protected |
Whether or not gap status is used by this behavior.
◆ m_bUsesMicro
|
protected |
Whether or not microtopography is used.
◆ m_fMoundProp
|
protected |
Proportion of plot that is mound, if using microtopography - 0 - 1.
◆ m_iDecayedLogCode
|
protected |
Data member code - float - declog grid data member.
◆ m_iForestFloorLitterCode
|
protected |
Data member code - float - fflitter grid data member.
◆ m_iForestFloorMossCode
|
protected |
Data member code - float - ffmoss grid data member.
◆ m_iFreshLogCode
|
protected |
Data member code - float - freshlog grid data member.
◆ m_iIsGapCode
|
protected |
Data member code for gap status in dispersed seed grid.
◆ m_iScarifiedSoilCode
|
protected |
Data member code - float - scarsoil grid data member.
◆ m_iTipUpCode
|
protected |
Data member code - float - tipup grid data member.
◆ mp_fCanGroundDecLogFav
|
protected |
Canopy / ground decayed logs favorability - one per behavior species.
◆ mp_fCanGroundForFlLitterFav
|
protected |
Canopy / ground forest floor litter favorability - one per behavior species.
◆ mp_fCanGroundForFlMossFav
|
protected |
Canopy / ground forest floor moss favorability - one per behavior species.
◆ mp_fCanGroundFreshLogFav
|
protected |
Canopy / ground fresh logs favorability - one per behavior species.
◆ mp_fCanGroundScarSoilFav
|
protected |
Canopy / ground scarified soil favorability - one per behavior species.
◆ mp_fCanGroundTipUpFav
|
protected |
Canopy / ground tip-up mounds favorability - one per behavior species.
◆ mp_fGapMoundDecLogFav
|
protected |
Gap / mound decayed logs favorability - one per behavior species.
◆ mp_fGapMoundForFlLitterFav
|
protected |
Gap / mound forest floor litter favorability - one per behavior species.
◆ mp_fGapMoundForFlMossFav
|
protected |
Gap / mound forest floor moss favorability - one per behavior species.
◆ mp_fGapMoundFreshLogFav
|
protected |
Gap / mound fresh logs favorability - one per behavior species.
◆ mp_fGapMoundScarSoilFav
|
protected |
Gap / mound scarified soil favorability - one per behavior species.
◆ mp_fGapMoundTipUpFav
|
protected |
Gap / mound tip-up mounds favorability - one per behavior species.
◆ mp_iIndexes
|
protected |
Speeds access to favorability arrays.
◆ mp_iSeedGridCode
|
protected |
Data member codes for seed grid for number of seeds.
Array size is # total species.
◆ mp_iSubstrFavCode
|
protected |
Data member codes for substrate grid for favorability index.
Array size is # total species.
◆ mp_oSeedGrid
|
protected |
Pointer to the "Dispersed Seeds" grid created by disperse behaviors.
◆ mp_oSubstrateFavGrid
|
protected |
The grid called "Substrate Favorability" will have a cell resolution matching the "Substrate" grid.
It will contain the substrate favorability index. The grid cell record will consist of (# species) float data members, "Favorability IndexX". It will have a member for each species even if the creating behavior does not apply to all, because another behavior in this run may apply to different species.
It is possible that a grid map will have been read in for this grid; it will be ignored, and any grid created with such a map will be overwritten.
◆ mp_oSubstrateGrid
|
protected |
Pointer to "Substrate" grid, created by clSubstrate.
The documentation for this class was generated from the following file:
