//---------------------------------------------------------------------
/// <summary>
/// Objects and Lists must be initialized.
/// </summary>
public Agent(int sppCount, int ecoCount)
{
SppParameters = new ISppParameters[sppCount];
EcoParameters = new IEcoParameters[ecoCount];
//DistParameters = new IDistParameters[distCount];
disturbanceTypes = new List <IDisturbanceType>();
negSppList = new List <ISpecies>();
//advRegenSppList = new List<ISpecies>();
dispersalNeighbors = new List <RelativeLocation>();
resourceNeighbors = new List <RelativeLocationWeighted>();
severity = PlugIn.ModelCore.Landscape.NewSiteVar <byte>();
outbreakZone = PlugIn.ModelCore.Landscape.NewSiteVar <Zone>();
climateDataTable = new DataTable();
for (int i = 0; i < sppCount; i++)
{
SppParameters[i] = new SppParameters();
}
for (int i = 0; i < ecoCount; i++)
{
EcoParameters[i] = new EcoParameters();
}
//for (int i = 0; i < distCount; i++)
// DistParameters[i] = new DistParameters();
}
//---------------------------------------------------------------------
// DamageCohort is a filter to determine which cohorts are removed.
// Each cohort is passed into the function and tested whether it should
// be killed.
bool ICohortDisturbance.MarkCohortForDeath(ICohort cohort)
{
//PlugIn.ModelCore.Log.WriteLine("Cohort={0}, {1}, {2}.", cohort.Species.Name, cohort.Age, cohort.Species.Index);
bool killCohort = false;
bool BF = false;
ISppParameters sppParms = epidemicParms.SppParameters[cohort.Species.Index];
string mySpecies = cohort.Species.Name;
if (mySpecies == "abiebals")
{
BF = true;
}
if (BF && cohort.Age > this.bfAgeCutoff)
{
killCohort = true;
}
else
{
if (cohort.Age >= sppParms.ResistantHostAge)
{
if (this.random <= this.siteVulnerability * sppParms.ResistantHostVuln)
{
killCohort = true;
}
}
if (cohort.Age >= sppParms.TolerantHostAge)
{
if (this.random <= this.siteVulnerability * sppParms.TolerantHostVuln)
{
killCohort = true;
}
}
if (cohort.Age >= sppParms.VulnerableHostAge)
{
if (this.random <= this.siteVulnerability * sppParms.VulnerableHostVuln)
{
killCohort = true;
}
}
}
if (killCohort)
{
this.siteCohortsKilled++;
if (sppParms.CFSConifer)
{
this.siteCFSconifersKilled++;
}
}
return(killCohort);
}
//---------------------------------------------------------------------
/// <summary>
/// Objects and Lists must be initialized.
/// </summary>
public Agent(int sppCount, int ecoCount, int distCount)
{
SppParameters = new ISppParameters[sppCount];
EcoParameters = new IEcoParameters[ecoCount];
DistParameters = new IDistParameters[distCount];
negSppList = new List <ISpecies>();
dispersalNeighbors = new List <RelativeLocation>();
resourceNeighbors = new List <RelativeLocationWeighted>();
severity = Model.Core.Landscape.NewSiteVar <byte>();
outbreakZone = Model.Core.Landscape.NewSiteVar <Zone>();
for (int i = 0; i < sppCount; i++)
{
SppParameters[i] = new SppParameters();
}
}
//---------------------------------------------------------------------
// This is a filter to determine which cohorts are removed.
// Each cohort is passed into the function and tested whether it should
// be killed.
bool ICohortDisturbance.MarkCohortForDeath(ICohort cohort)
{
bool killCohort = false;
ISppParameters sppParms = epidemicParms.SppParameters[cohort.Species.Index];
if (cohort.Age >= sppParms.LowVulnHostAge)
{
if (random <= sppParms.LowVulnHostMortProb)
{
killCohort = true;
}
}
if (cohort.Age >= sppParms.MediumVulnHostAge)
{
if (random <= sppParms.MediumVulnHostMortProb)
{
killCohort = true;
}
}
if (cohort.Age >= sppParms.HighVulnHostAge)
{
if (random <= sppParms.HighVulnHostMortProb)
{
killCohort = true;
}
}
if (killCohort)
{
siteCohortsKilled++;
if (sppParms.CFSConifer)
{
siteCFSconifersKilled++;
}
if (sppParms.MortSppFlag)
{
siteMortSppKilled++;
}
}
return(killCohort);
}
//---------------------------------------------------------------------
// DamageCohort is a filter to determine which cohorts are removed.
// Each cohort is passed into the function and tested whether it should
// be killed.
bool AgeCohort.ICohortDisturbance.Damage(AgeCohort.ICohort cohort)
{
bool killCohort = false;
ISppParameters sppParms = epidemicParms.SppParameters[cohort.Species.Index];
if (sppParms == null)
{
return(killCohort);
}
if (this.siteSeverity == 1)
{
if (cohort.Age >= sppParms.VulnerableHostAge)
{
killCohort = true;
}
}
if (this.siteSeverity == 2)
{
if (cohort.Age >= sppParms.TolerantHostAge)
{
killCohort = true;
}
}
if (this.siteSeverity == 3)
{
if (cohort.Age >= sppParms.ResistantHostAge)
{
killCohort = true;
}
}
if (killCohort)
{
this.siteCohortsKilled++;
if (sppParms.CFSConifer)
{
this.siteCFSconifersKilled++;
}
}
return(killCohort);
}
//---------------------------------------------------------------------
// DamageCohort is a filter to determine which cohorts are removed.
// Each cohort is passed into the function and tested whether it should
// be killed.
bool ICohortDisturbance.MarkCohortForDeath(ICohort cohort)
{
//PlugIn.ModelCore.UI.WriteLine("Cohort={0}, {1}, {2}.", cohort.Species.Name, cohort.Age, cohort.Species.Index);
bool killCohort = false;
ISppParameters sppParms = epidemicParms.SppParameters[cohort.Species.Index];
if (this.siteSeverity == 1)
{
if (cohort.Age >= sppParms.VulnerableHostAge)
{
killCohort = true;
}
}
if (this.siteSeverity == 2)
{
if (cohort.Age >= sppParms.TolerantHostAge)
{
killCohort = true;
}
}
if (this.siteSeverity == 3)
{
if (cohort.Age >= sppParms.ResistantHostAge)
{
killCohort = true;
}
}
if (killCohort)
{
this.siteCohortsKilled++;
if (sppParms.CFSConifer)
{
this.siteCFSconifersKilled++;
}
}
return(killCohort);
}
//---------------------------------------------------------------------
/// <summary>
/// Objects and Lists must be initialized.
/// </summary>
public AgentParameters(int sppCount, int ecoCount)
{
SppParameters = new ISppParameters[sppCount];
EcoParameters = new IEcoParameters[ecoCount];
EcoWeatherIndexNormal = new double[ecoCount];
disturbanceTypes = new List <IDisturbanceType>();
negSppList = new List <ISpecies>();
climateVarDefn = new List <IClimateVariableDefinition>();
derivedClimateVars = new List <IDerivedClimateVariable>();
weatherIndexVars = new List <string>();
climateDataTable = new DataTable();
for (int i = 0; i < sppCount; i++)
{
SppParameters[i] = new SppParameters();
}
for (int i = 0; i < ecoCount; i++)
{
EcoParameters[i] = new EcoParameters();
}
}
//---------------------------------------------------------------------
/// <summary>
/// Objects and Lists must be initialized.
/// </summary>
public Agent(int sppCount, int ecoCount)
{
SppParameters = new ISppParameters[sppCount];
EcoParameters = new IEcoParameters[ecoCount];
//DistParameters = new IDistParameters[distCount];
disturbanceTypes = new List<IDisturbanceType>();
negSppList = new List<ISpecies>();
//advRegenSppList = new List<ISpecies>();
dispersalNeighbors = new List<RelativeLocation>();
resourceNeighbors = new List<RelativeLocationWeighted>();
severity = PlugIn.ModelCore.Landscape.NewSiteVar<byte>();
outbreakZone = PlugIn.ModelCore.Landscape.NewSiteVar<Zone>();
for (int i = 0; i < sppCount; i++)
SppParameters[i] = new SppParameters();
for (int i = 0; i < ecoCount; i++)
EcoParameters[i] = new EcoParameters();
//for (int i = 0; i < distCount; i++)
// DistParameters[i] = new DistParameters();
}
//---------------------------------------------------------------------
///<summary>
///Calculate the Site Resource Dominance (SRD) for all active sites.
///The SRD averages the resources for each species as defined in the
///BDA species table.
///SRD ranges from 0 - 1.
///</summary>
//---------------------------------------------------------------------
public static void SiteResourceDominance(IAgent agent, int ROS)
{
PlugIn.ModelCore.UI.WriteLine(" Calculating BDA Site Resource Dominance.");
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
double sumValue = 0.0;
double maxValue = 0.0;
int ageOldestCohort = 0;
int numValidSpp = 0;
double speciesHostValue = 0;
foreach (ISpecies species in PlugIn.ModelCore.Species)
{
ageOldestCohort = Util.GetMaxAge(SiteVars.Cohorts[site][species]);
ISppParameters sppParms = agent.SppParameters[species.Index];
if (sppParms == null)
{
continue;
}
bool negList = false;
foreach (ISpecies negSpp in agent.NegSppList)
{
if (species == negSpp)
{
negList = true;
}
}
if ((ageOldestCohort > 0) && (!negList))
{
numValidSpp++;
speciesHostValue = 0.0;
if (ageOldestCohort >= sppParms.MinorHostAge)
{
//speciesHostValue = 0.33;
speciesHostValue = sppParms.MinorHostSRD;
}
if (ageOldestCohort >= sppParms.SecondaryHostAge)
{
//speciesHostValue = 0.66;
speciesHostValue = sppParms.SecondaryHostSRD;
}
if (ageOldestCohort >= sppParms.PrimaryHostAge)
{
//speciesHostValue = 1.0;
speciesHostValue = sppParms.PrimaryHostSRD;
}
sumValue += speciesHostValue;
maxValue = System.Math.Max(maxValue, speciesHostValue);
}
}
if (agent.SRDmode == SRDmode.mean)
{
SiteVars.SiteResourceDom[site] = sumValue / (double)numValidSpp;
}
if (agent.SRDmode == SRDmode.max)
{
SiteVars.SiteResourceDom[site] = maxValue;
}
}
} //end siteResourceDom
//---------------------------------------------------------------------
/// <summary>
/// Objects and Lists must be initialized.
/// </summary>
public Agent(int sppCount, int ecoCount, int distCount)
{
SppParameters = new ISppParameters[sppCount];
EcoParameters = new IEcoParameters[ecoCount];
DistParameters = new IDistParameters[distCount];
negSppList = new List<ISpecies>();
dispersalNeighbors = new List<RelativeLocation>();
resourceNeighbors = new List<RelativeLocationWeighted>();
severity = Model.Core.Landscape.NewSiteVar<byte>();
outbreakZone = Model.Core.Landscape.NewSiteVar<Zone>();
for(int i=0; i<sppCount; i++)
SppParameters[i] = new SppParameters();
}
//---------------------------------------------------------------------
// DamageCohort is a filter to determine which cohorts are removed.
// Each cohort is passed into the function and tested whether it should
// be killed.
bool ICohortDisturbance.MarkCohortForDeath(ICohort cohort)
{
//PlugIn.ModelCore.Log.WriteLine("Cohort={0}, {1}, {2}.", cohort.Species.Name, cohort.Age, cohort.Species.Index);
bool killCohort = false;
// bool advRegenSpp = false;
ISppParameters sppParms = epidemicParms.SppParameters[cohort.Species.Index];
//foreach (ISpecies mySpecies in epidemicParms.AdvRegenSppList)
//{
// if (cohort.Species == mySpecies)
// {
// advRegenSpp = true;
// break;
// }
//}
if (cohort.Age >= sppParms.ResistantHostAge)
{
if (this.random <= this.siteVulnerability * sppParms.ResistantHostVuln)
{
//if (advRegenSpp && cohort.Age <= this.advRegenAgeCutoff)
// killCohort = false;
//else
killCohort = true;
}
}
if (cohort.Age >= sppParms.TolerantHostAge)
{
if (this.random <= this.siteVulnerability * sppParms.TolerantHostVuln)
{
//if (advRegenSpp && cohort.Age <= this.advRegenAgeCutoff)
// killCohort = false;
//else
killCohort = true;
}
}
if (cohort.Age >= sppParms.VulnerableHostAge)
{
if (this.random <= this.siteVulnerability * sppParms.VulnerableHostVuln)
{
//if (advRegenSpp && cohort.Age <= this.advRegenAgeCutoff)
// killCohort = false;
//else
killCohort = true;
}
}
if (killCohort)
{
this.siteCohortsKilled++;
if (sppParms.CFSConifer)
{
this.siteCFSconifersKilled++;
}
}
return(killCohort);
}
//---------------------------------------------------------------------
///<summary>
///Calculate the Site Host Index (SHI) for all active sites.
///The SHI averages the host value for each species as defined in the
///EDA species table.
///SHI ranges from 0 - 1.
///</summary>
//---------------------------------------------------------------------
public static void SiteHostIndexCompute(IAgent agent)
{
PlugIn.ModelCore.UI.WriteLine(" Calculating EDA Total Site Host Index.");
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
double sumValue = 0.0;
double maxValue = 0.0;
int ageOldestCohort = 0;
int numValidSpp = 0;
double speciesHostValue = 0;
foreach (ISpecies species in PlugIn.ModelCore.Species)
{
//get age of oldest cohort: maybe change this to use ALL cohort ages. How to do so?
ageOldestCohort = Util.GetMaxAge(SiteVars.Cohorts[site][species]);
ISppParameters sppParms = agent.SppParameters[species.Index];
if (sppParms == null)
{
continue;
}
//this chunk of code check if the current species in the current active site
//is part of the ignored species list. If any of the species are in that list, then negList --> true
bool negList = false;
foreach (ISpecies negSpp in agent.NegSppList)
{
if (species == negSpp)
{
negList = true;
}
}
if ((ageOldestCohort > 0) && (!negList))
{
numValidSpp++;
speciesHostValue = 0.0;
if (ageOldestCohort >= sppParms.LowHostAge)
{
//speciesHostValue = 0.33; VALUES ARE READ IN FROM THE EDA Spp Param Table
speciesHostValue = sppParms.LowHostScore;
}
if (ageOldestCohort >= sppParms.MediumHostAge)
{
//speciesHostValue = 0.66; VALUES ARE READ IN FROM THE EDA Spp Param Table
speciesHostValue = sppParms.MediumHostScore;
}
if (ageOldestCohort >= sppParms.HighHostAge)
{
//speciesHostValue = 1.0; VALUES ARE READ IN FROM THE EDA Spp Param Table
speciesHostValue = sppParms.HighHostScore;
}
sumValue += speciesHostValue;
maxValue = System.Math.Max(maxValue, speciesHostValue);
}
}
if (agent.SHImode == SHImode.mean)
{
SiteVars.SiteHostIndex[site] = sumValue / numValidSpp; //division will be (double) because sumValue was initialized to 0.0
}
if (agent.SHImode == SHImode.max)
{
SiteVars.SiteHostIndex[site] = maxValue;
}
}
} //end SiteHostIndexCompute
