public static double DefoliateCohort(ActiveSite site, ISpecies species, int cohortBiomass, int siteBiomass)
{
//PlugIn.ModelCore.UI.WriteLine(" Calculating insect defoliation...");
double totalDefoliation = 0.0; // Cohort total defoliation
foreach (IInsect insect in manyInsect)
{
if (!insect.ActiveOutbreak)
continue;
double defoliation = 0.0;
// Calculate biomass proportion of "protective" species
double protectBiomass = 0;
foreach (Landis.Library.BiomassCohorts.ISpeciesCohorts spp in SiteVars.Cohorts[site])
{
foreach (Landis.Library.BiomassCohorts.ICohort spp_cohort in spp)
{
if (insect.Susceptibility[spp_cohort.Species] == 4)
protectBiomass += spp_cohort.Biomass;
}
}
double protectProp = protectBiomass / (double)siteBiomass;
int suscIndex = insect.Susceptibility[species] - 1;
if (suscIndex < 0) suscIndex = 0;
if (suscIndex > 2) suscIndex = 2;
// Get the Neighborhood GrowthReduction Density
double meanNeighborhoodDefoliation = 0.0;
int neighborCnt = 0;
// If it is the first year, the neighborhood growth reduction
// will have been initialized in Outbreak.InitializeDefoliationPatches
if (insect.NeighborhoodDefoliation[site] > 0)
{
//PlugIn.ModelCore.UI.WriteLine(" First Year of Defoliation: Using initial patch defo={0:0.00}.", SiteVars.NeighborhoodDefoliation[site]);
meanNeighborhoodDefoliation = insect.NeighborhoodDefoliation[site];
}
// If not the first year, calculate mean neighborhood defoliation based on the
// previous year.
else
{
double sumNeighborhoodDefoliation = 0.0;
//PlugIn.ModelCore.UI.WriteLine("Look at the Neighbors... ");
foreach (RelativeLocation relativeLoc in insect.Neighbors)
{
Site neighbor = site.GetNeighbor(relativeLoc);
if (neighbor != null && neighbor.IsActive)
{
neighborCnt++;
// The previous year...
//if(SiteVars.DefoliationByYear[neighbor].ContainsKey(PlugIn.ModelCore.CurrentTime - 1))
// sumNeighborhoodDefoliation += SiteVars.DefoliationByYear[neighbor][PlugIn.ModelCore.CurrentTime - 1];
// BUG - This does not sum values in the nbrhd, just uses the last nbr value
//sumNeighborhoodDefoliation = Math.Min(1.0, insect.LastYearDefoliation[neighbor]);
// BUG FIX - BRM
sumNeighborhoodDefoliation += Math.Min(1.0, insect.LastYearDefoliation[neighbor]);
}
}
if (neighborCnt > 0.0)
meanNeighborhoodDefoliation = sumNeighborhoodDefoliation / (double)neighborCnt;
} //endif
if (meanNeighborhoodDefoliation > 1.0 || meanNeighborhoodDefoliation < 0)
{
PlugIn.ModelCore.UI.WriteLine("MeanNeighborhoodDefoliation={0}; NeighborCnt={1}.", meanNeighborhoodDefoliation, neighborCnt);
throw new ApplicationException("Error: Mean Neighborhood GrowthReduction is not between 1.0 and 0.0");
}
// First assume that there are no neighbors whatsoever:
DistributionType dist = insect.SusceptibleTable[suscIndex].Distribution_0.Name;
double value1 = insect.SusceptibleTable[suscIndex].Distribution_0.Value1;
double value2 = insect.SusceptibleTable[suscIndex].Distribution_0.Value2;
if (meanNeighborhoodDefoliation <= 1.0 && meanNeighborhoodDefoliation >= 0.8)
{
dist = insect.SusceptibleTable[suscIndex].Distribution_80.Name;
value1 = insect.SusceptibleTable[suscIndex].Distribution_80.Value1;
value2 = insect.SusceptibleTable[suscIndex].Distribution_80.Value2;
}
else if (meanNeighborhoodDefoliation < 0.8 && meanNeighborhoodDefoliation >= 0.6)
{
dist = insect.SusceptibleTable[suscIndex].Distribution_60.Name;
value1 = insect.SusceptibleTable[suscIndex].Distribution_60.Value1;
value2 = insect.SusceptibleTable[suscIndex].Distribution_60.Value2;
}
else if (meanNeighborhoodDefoliation < 0.6 && meanNeighborhoodDefoliation >= 0.4)
{
dist = insect.SusceptibleTable[suscIndex].Distribution_40.Name;
value1 = insect.SusceptibleTable[suscIndex].Distribution_40.Value1;
value2 = insect.SusceptibleTable[suscIndex].Distribution_40.Value2;
}
else if (meanNeighborhoodDefoliation < 0.4 && meanNeighborhoodDefoliation >= 0.2)
{
dist = insect.SusceptibleTable[suscIndex].Distribution_20.Name;
value1 = insect.SusceptibleTable[suscIndex].Distribution_20.Value1;
value2 = insect.SusceptibleTable[suscIndex].Distribution_20.Value2;
}
else if (meanNeighborhoodDefoliation < 0.2 && meanNeighborhoodDefoliation >= 0.0)
{
dist = insect.SusceptibleTable[suscIndex].Distribution_0.Name;
value1 = insect.SusceptibleTable[suscIndex].Distribution_0.Value1;
value2 = insect.SusceptibleTable[suscIndex].Distribution_0.Value2;
}
// Next, ensure that all cohorts of the same susceptibility class
// receive the same level of defoliation.
if (insect.HostDefoliationByYear[site].ContainsKey(PlugIn.ModelCore.CurrentTime))
{
if (insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime][suscIndex] <= 0.00000000)
{
defoliation = Distribution.GenerateRandomNum(dist, value1, value2);
// Account for protective effect of Susc Class 4
if (protectProp > 0)
{
double slope = 1.0;
double protectReduce = 1 - (protectProp * slope);
if (protectReduce > 1)
protectReduce = 1;
if (protectReduce < 0)
protectReduce = 0;
defoliation = defoliation * protectReduce;
}
insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime][suscIndex] = defoliation;
}
else
{
defoliation = insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime][suscIndex];
}
}
else
{
insect.HostDefoliationByYear[site].Add(PlugIn.ModelCore.CurrentTime, new Double[3] { 0.0, 0.0, 0.0 });
defoliation = Distribution.GenerateRandomNum(dist, value1, value2);
//if (meanNeighborhoodDefoliation <= 0.0 && defoliation > 0.0)
// PlugIn.ModelCore.UI.WriteLine("THAT'S WEIRD!! meanNeighborhoodDefoliation = {0}, defoliation={1}.", meanNeighborhoodDefoliation, defoliation);
// Account for protective effect of Susc Class 4
if (protectProp > 0)
{
double slope = 1.0;
double protectReduce = 1 - (protectProp * slope);
if (protectReduce > 1)
protectReduce = 1;
if (protectReduce < 0)
protectReduce = 0;
defoliation = defoliation * protectReduce;
}
insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime][suscIndex] = defoliation;
}
// Alternatively, allow defoliation to vary even among cohorts and species with
// the same susceptibility.
if (defoliation > 1.0 || defoliation < 0)
{
PlugIn.ModelCore.UI.WriteLine("DEFOLIATION TOO BIG or SMALL: {0}, {1}, {2}, {3}.", dist, value1, value2, defoliation);
throw new ApplicationException("Error: New defoliation is not between 1.0 and 0.0");
}
//PlugIn.ModelCore.UI.WriteLine("Cohort age={0}, species={1}, suscIndex={2}, defoliation={3}.", cohort.Age, cohort.Species.Name, (suscIndex -1), defoliation);
// BUG - This is summed proportions across all cohorts (exceeds 1.0)
//insect.ThisYearDefoliation[site] += defoliation;
// BUG FIX - Weight site-level defoliation by cohort biomass
double weightedDefoliation = (defoliation * Math.Min(1.0, (double)cohortBiomass/(double) siteBiomass));
//PlugIn.ModelCore.UI.WriteLine("Cohort age={0}, species={1}, suscIndex={2}, cohortDefoliation={3}, weightedDefolation={4}.", cohort.Age, cohort.Species.Name, (suscIndex+1), defoliation, weightedDefoliation);
insect.ThisYearDefoliation[site] += weightedDefoliation;
totalDefoliation += defoliation; // Cohort total defoliation (summed across insects)
}
if (totalDefoliation > 1.0) // Cannot exceed 100% defoliation
totalDefoliation = 1.0;
if (totalDefoliation > 1.1 || totalDefoliation < 0)
{
PlugIn.ModelCore.UI.WriteLine("Cohort Total Defoliation = {0:0.00}. Site R/C={1}/{2}.", totalDefoliation, site.Location.Row, site.Location.Column);
throw new ApplicationException("Error: Total Defoliation is not between 1.1 and 0.0");
}
return totalDefoliation; // Cohort total defoliation proportion (summed across insects)
}
