| public static GenerateRandomNum ( DistributionType dist, double parameter1, double parameter2 ) : double | ||
| dist | DistributionType | |
| parameter1 | double | |
| parameter2 | double | |
| return | double | |
//---------------------------------------------------------------------
// Initialize landscape with patches of defoliation during the first year
public static void InitializeDefoliationPatches(IInsect insect)
{
PlugIn.ModelCore.UI.WriteLine(" Initializing Defoliation Patches... ");
SiteVars.InitialOutbreakProb.ActiveSiteValues = 0.0;
insect.Disturbed.ActiveSiteValues = false;
insect.NeighborhoodDefoliation.ActiveSiteValues = 0.0;
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
double suscIndexSum = 0.0;
double sumBio = 0.0;
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
//foreach (ISpeciesCohorts speciesCohorts in (Landis.Library.BiomassCohorts.ISpeciesCohorts) SiteVars.Cohorts[site]) // Rob's suggestion. Raised an error...
{
foreach (ICohort cohort in speciesCohorts)
{
suscIndexSum += cohort.Biomass * (insect.SppTable[cohort.Species.Index].Susceptibility);
sumBio += cohort.Biomass;
}
}
// If no biomass, no chance of defoliation, go to the next site.
if (suscIndexSum <= 0 || sumBio <= 0)
{
SiteVars.InitialOutbreakProb[site] = 0.0;
continue;
}
int suscIndex = (int)Math.Round(suscIndexSum / sumBio) - 1;
if (suscIndex > 2.0 || suscIndex < 0)
{
PlugIn.ModelCore.UI.WriteLine("SuscIndex < 0 || > 2. Site R/C={0}/{1},suscIndex={2},suscIndexSum={3},sumBio={4}.", site.Location.Row, site.Location.Column, suscIndex, suscIndexSum, sumBio);
throw new ApplicationException("Error: SuscIndex is not between 2.0 and 0.0");
}
// Assume that there are no neighbors and draw initial defoliation from the most intense neighborhood distribution:
DistributionType dist = insect.SusceptibleTable[suscIndex].Distribution_80.Name;
// PlugIn.ModelCore.UI.WriteLine("suscIndex={0},suscIndexSum={1},cohortBiomass={2}.", suscIndex,suscIndexSum,sumBio);
double value1 = insect.SusceptibleTable[suscIndex].Distribution_80.Value1;
double value2 = insect.SusceptibleTable[suscIndex].Distribution_80.Value2;
double probability = Distribution.GenerateRandomNum(dist, value1, value2);
if (probability > 1.0 || probability < 0)
{
PlugIn.ModelCore.UI.WriteLine("Initial Defoliation Probility < 0 || > 1. Site R/C={0}/{1}.", site.Location.Row, site.Location.Column);
throw new ApplicationException("Error: Probability is not between 1.0 and 0.0");
}
// Try cleaning up defoliation patterns so areas outside main patches are less defoliated
// How about using Brian's patch shape calibrator here instead. Divide probability by susIndex * PSC, to tie initial patch probs. more closely to host abundance...
//SiteVars.InitialOutbreakProb[site] = probability;
SiteVars.InitialOutbreakProb[site] = probability / ((double)suscIndex + 1);
// PlugIn.ModelCore.UI.WriteLine("Susceptiblity index={0}. Outbreak Probability={1:0.00}. R/C={2}/{3}.", suscIndex, probability, site.Location.Row, site.Location.Column);
}
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
//get a random site from the stand
double randomNum = PlugIn.ModelCore.GenerateUniform();
double randomNum2 = PlugIn.ModelCore.GenerateUniform();
//Create random variability in outbreak area within a simulation so outbreaks are more variable.
double initialAreaCalibratorRandomNum = (randomNum2 - 0.5) * insect.InitialPatchOutbreakSensitivity / 2;
//Start spreading!
if (randomNum < SiteVars.InitialOutbreakProb[site] * (insect.InitialPatchOutbreakSensitivity + initialAreaCalibratorRandomNum))
{
//start with this site (if it's active)
ActiveSite currentSite = site;
//queue to hold sites to defoliate
Queue <ActiveSite> sitesToConsider = new Queue <ActiveSite>();
//put initial site on queue
sitesToConsider.Enqueue(currentSite);
DistributionType dist = insect.InitialPatchDistr;
double targetArea = Distribution.GenerateRandomNum(dist, insect.InitialPatchValue1, insect.InitialPatchValue2);
// PlugIn.ModelCore.UI.WriteLine(" Target Patch Area={0:0.0}.", targetArea);
double areaSelected = 0.0;
//loop through stand, defoliating patches of size target area
while (sitesToConsider.Count > 0 && areaSelected < targetArea)
{
currentSite = sitesToConsider.Dequeue();
// Because this is the first year, neighborhood defoliation is given a value.
// The value is used in Defoliate.DefoliateCohort()
insect.NeighborhoodDefoliation[currentSite] = SiteVars.InitialOutbreakProb[currentSite];
areaSelected += PlugIn.ModelCore.CellArea;
//insect.Disturbed[currentSite] = true;
//Next, add site's neighbors to the list of
//sites to consider.
//loop through the site's neighbors enqueueing all the good ones.
//double maxNeighborProb = 0.0;
//Site maxNeighbor = currentSite;
//bool foundNewNeighbor = false;
foreach (RelativeLocation loc in all_neighbor_locations)
{
Site neighbor = currentSite.GetNeighbor(loc);
//get a neighbor site (if it's non-null and active)
if (neighbor != null &&
neighbor.IsActive &&
!sitesToConsider.Contains((ActiveSite)neighbor) &&
!insect.Disturbed[neighbor])
{
insect.Disturbed[currentSite] = true;
randomNum = PlugIn.ModelCore.GenerateUniform();
/*if (SiteVars.InitialOutbreakProb[neighbor] > maxNeighborProb)
* {
* maxNeighbor = currentSite.GetNeighbor(loc);
* maxNeighborProb = SiteVars.InitialOutbreakProb[neighbor];
* foundNewNeighbor = true;
* }*/
//check if it's a valid neighbor:
if (SiteVars.InitialOutbreakProb[neighbor] > randomNum)
{
sitesToConsider.Enqueue((ActiveSite)neighbor);
}
}
}
//if(foundNewNeighbor)
// sitesToConsider.Enqueue((ActiveSite) maxNeighbor);
}
// PlugIn.ModelCore.UI.WriteLine(" Initial Patch Area Selected={0:0.0}.", areaSelected);
}
}
}
//---------------------------------------------------------------------
///<summary>
/// Run Biomass Insects extension at a particular timestep.
///</summary>
public override void Run()
{
running = true;
PlugIn.ModelCore.UI.WriteLine(" Processing landscape for Biomass Insect events ...");
SiteVars.SiteDefoliation.ActiveSiteValues = 0;
foreach (IInsect insect in manyInsect)
{
//SiteVars.BiomassRemoved.ActiveSiteValues = 0;
//SiteVars.InitialOutbreakProb.ActiveSiteValues = 0.0;
if (insect.MortalityYear == PlugIn.ModelCore.CurrentTime)
{
Outbreak.Mortality(insect);
}
if (insect.MortalityYear != PlugIn.ModelCore.CurrentTime)
{
insect.LastBioRemoved = 0;
}
// Copy the data from current to last
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
double thisYearDefol = insect.ThisYearDefoliation[site];
insect.LastYearDefoliation[site] = thisYearDefol;
SiteVars.SiteDefoliation[site] += (int)Math.Round(thisYearDefol * 100);
if (thisYearDefol > 0)
{
SiteVars.TimeOfLastEvent[site] = PlugIn.ModelCore.CurrentTime - 1;
SiteVars.InsectName[site] = insect.Name;
}
}
insect.ThisYearDefoliation.ActiveSiteValues = 0.0;
insect.ActiveOutbreak = false;
insect.SingleOutbreakYear = false;
//PlugIn.ModelCore.NormalDistribution.Mu = 0.0;
//PlugIn.ModelCore.NormalDistribution.Sigma = 1.0;
//double randomNum = PlugIn.ModelCore.NormalDistribution.NextDouble();
//randomNum = PlugIn.ModelCore.NormalDistribution.NextDouble();
double randomNum = Distribution.GenerateRandomNum(DistributionType.Normal, 0.0, 1.0);
DistributionType distDuration = insect.DurationDistribution;
double randomNumE = Distribution.GenerateRandomNum(distDuration, insect.DurationParameter1, insect.DurationParameter2);
// First, has enough time passed since the last outbreak? This is calculated each year,
// but only used in last year of an outbreak to generate next outbreak characteristics.
double timeBetweenOutbreaks = insect.MeanTimeBetweenOutbreaks + (insect.StdDevTimeBetweenOutbreaks * randomNum);
double duration = System.Math.Round(randomNumE);
if (distDuration == DistributionType.Exponential || distDuration == DistributionType.Normal)
{
duration = System.Math.Max(duration + 1, 1); // Duration cannot be less than 1. Added to allow Normal distribution parameters.
}
else
{
duration = System.Math.Max(duration, 1); // Duration cannot be less than 1.
}
// Apply optional maximum - if not used maxDur = Inf
if (duration > insect.MaxDuration)
{
duration = insect.MaxDuration;
}
double timeAfterDuration = timeBetweenOutbreaks - duration;
// Users can parameterize model to have overlapping outbreaks, but then patches will not initialize correctly.
// Do below to prevent overlapping outbreaks of same insect. This will affect the realized distribution of time between outbreaks somewhat.
while (timeAfterDuration <= 1.0)
{
PlugIn.ModelCore.UI.WriteLine("CAUTION: Time Between Outbreaks TOO SMALL (< 1), you may need to adjust timing parameters: {0}.", timeAfterDuration);
timeBetweenOutbreaks = timeBetweenOutbreaks + 1;
timeAfterDuration = timeBetweenOutbreaks - duration;
}
//PlugIn.ModelCore.UI.WriteLine("Calculated time between = {0:0.00}. inputMeanTime={1:0.00}, inputStdTime={2:0.00}., timeAftDur={3:0.00}.", timeBetweenOutbreaks, insect.MeanTimeBetweenOutbreaks, insect.StdDevTimeBetweenOutbreaks, timeAfterDuration);
// The logic below determines whether an outbreak is active. And sets a new outbreak duration and timeBetweenOutbreaks
// for the next outbreak if is the last year of an outbreak.
// The very first outbreak is set first.
if (PlugIn.ModelCore.CurrentTime == 1)
{
PlugIn.ModelCore.UI.WriteLine(" Year 1: Setting initial start and stop times.");
double randomNum1 = PlugIn.ModelCore.GenerateUniform();
//insect.OutbreakStartYear = (int) (timeBetweenOutbreaks / 2.0) + 1;
insect.OutbreakStartYear = Math.Max(2, (int)(randomNum1 * timeBetweenOutbreaks + 1)); // New, try making 1st start year more random. 1st outbreak has to occur > year1 to for InitializeDefoliationPatches to work properly.
insect.OutbreakStartYear = Math.Max(insect.OutbreakStartYear, insect.StartYear); // BRM - optional start year (first outbreak can't be before StartYear)
insect.OutbreakStopYear = insect.OutbreakStartYear + (int)duration - 1;
// PlugIn.ModelCore.UI.WriteLine(" {0} is not active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
}
else if (insect.OutbreakStartYear <= PlugIn.ModelCore.CurrentTime &&
insect.OutbreakStopYear > PlugIn.ModelCore.CurrentTime) // first year of a multiyear outbreak
{
// PlugIn.ModelCore.UI.WriteLine(" An outbreak starts or continues. Start and stop time do not change.");
insect.ActiveOutbreak = true;
PlugIn.ModelCore.UI.WriteLine(" {0} is active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
insect.MortalityYear = PlugIn.ModelCore.CurrentTime + 1;
insect.LastStartYear = insect.OutbreakStartYear; // Added here for Brian's log file.
insect.LastStopYear = insect.OutbreakStopYear; // Added here for Brian's log file.
}
//Special case for single year outbreak.
else if (insect.OutbreakStartYear == PlugIn.ModelCore.CurrentTime &&
insect.OutbreakStopYear == PlugIn.ModelCore.CurrentTime)
{
insect.ActiveOutbreak = true;
PlugIn.ModelCore.UI.WriteLine(" {0} is active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
if (insect.OutbreakStartYear == insect.OutbreakStopYear) // shouldn't need this. JRF
{
insect.SingleOutbreakYear = true;
}
insect.MortalityYear = PlugIn.ModelCore.CurrentTime + 1;
insect.LastStartYear = insect.OutbreakStartYear; // Added here for Brian's log file.
insect.LastStopYear = insect.OutbreakStopYear; // Added here for Brian's log file.
insect.OutbreakStartYear = PlugIn.ModelCore.CurrentTime + (int)timeBetweenOutbreaks;
insect.OutbreakStopYear = insect.OutbreakStartYear + (int)duration - 1;
}
else if (insect.OutbreakStopYear <= PlugIn.ModelCore.CurrentTime &&
timeAfterDuration > PlugIn.ModelCore.CurrentTime - insect.OutbreakStopYear)
{
// PlugIn.ModelCore.UI.WriteLine(" In between outbreaks, reset start and stop times.");
insect.ActiveOutbreak = true;
PlugIn.ModelCore.UI.WriteLine(" {0} is active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
insect.MortalityYear = PlugIn.ModelCore.CurrentTime + 1;
insect.LastStartYear = insect.OutbreakStartYear; // Added here for Brian's log file.
insect.LastStopYear = insect.OutbreakStopYear; // Added here for Brian's log file.
insect.OutbreakStartYear = PlugIn.ModelCore.CurrentTime + (int)timeBetweenOutbreaks;
insect.OutbreakStopYear = insect.OutbreakStartYear + (int)duration - 1;
}
PlugIn.ModelCore.UI.WriteLine(" Insect Start Time = {0}, Stop Time = {1}.", insect.OutbreakStartYear, insect.OutbreakStopYear);
// Now that logic determining when an outbreak will be active is done, tell model what to do when outbreak is occurring.
if (insect.ActiveOutbreak)
{
// PlugIn.ModelCore.UI.WriteLine(" OutbreakStartYear={0}.", insect.OutbreakStartYear);
if (insect.OutbreakStartYear == PlugIn.ModelCore.CurrentTime || insect.SingleOutbreakYear)
{
// Initialize neighborhoodGrowthReduction with patches
Outbreak.InitializeDefoliationPatches(insect);
}
else
{
insect.NeighborhoodDefoliation.ActiveSiteValues = 0;
}
}
// Now report on the previous year's defoliation, that which has been processed
// through biomass succession. Calculations for logfile.
double sumDefoliation = 0.0;
double meanDefoliation = 0.0;
int numSites0_33 = 0;
int numSites33_66 = 0;
int numSites66_100 = 0;
int numInitialSites = 0;
int numSitesActive = 0; // Just get a sum of all active sites to calculate mean defoliation accurately for log file.
// ONly calculate for log file when outbreak or mortality is active <- Modified, JRF, add to log file each year.
if (insect.ActiveOutbreak || insect.SingleOutbreakYear || (insect.LastStopYear + 1 >= PlugIn.ModelCore.CurrentTime) || (insect.LastBioRemoved > 0))
{
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
sumDefoliation += insect.LastYearDefoliation[site];
if (insect.LastYearDefoliation[site] > 0.0 && insect.LastYearDefoliation[site] <= 0.33)
{
numSites0_33++;
}
if (insect.LastYearDefoliation[site] > 0.33 && insect.LastYearDefoliation[site] <= 0.66)
{
numSites33_66++;
}
if (insect.LastYearDefoliation[site] > 0.66 && insect.LastYearDefoliation[site] <= 1.0)
{
numSites66_100++;
}
if (insect.Disturbed[site] && SiteVars.InitialOutbreakProb[site] > 0)
{
numInitialSites++;
}
numSitesActive++;
}
if (insect.OutbreakStartYear == PlugIn.ModelCore.CurrentTime)
{
insect.InitialSites = numInitialSites;
}
if (numSites0_33 + numSites33_66 + numSites66_100 > 0)
{
meanDefoliation = sumDefoliation / (double)numSitesActive;
}
//PlugIn.ModelCore.UI.WriteLine(" sumDefoliation={0}, numSites={1}.", sumDefoliation, numSites0_33 + numSites33_66 + numSites66_100);
}
int totalBioRemoved = 0;
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
totalBioRemoved += SiteVars.BiomassRemoved[site]; // kg across all defoliated sites
}
insect.LastBioRemoved = totalBioRemoved; //Assign variables for the logfile
// PlugIn.ModelCore.UI.WriteLine(" totalBioRemoved={0}.", totalBioRemoved);
// ONly add to log & output maps during outbreak <- Modified, JRF, add to log file each year.
//if ((insect.ActiveOutbreak && insect.OutbreakStartYear < PlugIn.ModelCore.CurrentTime) || (meanDefoliation > 0) || (insect.LastBioRemoved > 0))
//{
/* Old code for log file
* if (meanDefoliation > 0)
* {
*
* log.Write("{0},{1},{2},{3},{4:0.0000},{5},{6},{7},{8},{9}",
* PlugIn.ModelCore.CurrentTime-1, //0
* insect.Name, //1
* insect.LastStartYear, //2
* insect.LastStopYear, //3
* meanDefoliation, //4
* numSites0_33, //5
* numSites33_66, //6
* numSites66_100, //7
* insect.InitialSites, //8
* insect.LastBioRemoved //9
* );
* }
*
* else
* {
* log.Write("{0},{1},{2},{3},{4:0.0000},{5},{6},{7},{8},{9}",
* PlugIn.ModelCore.CurrentTime - 1, //0
* insect.Name, //1
* 0, //2
* 0, //3
* meanDefoliation, //4
* numSites0_33, //5
* numSites33_66, //6
* numSites66_100, //7
* 0, //8
* insect.LastBioRemoved //9
* );
* }
*
*
* //foreach (IEcoregion ecoregion in Ecoregions.Dataset)
* // log.Write(",{0}", 1);
*
* log.WriteLine("");
*/
eventLog.Clear();
EventsLog el = new EventsLog();
el.Time = PlugIn.ModelCore.CurrentTime - 1;
el.InsectName = insect.Name;
el.MeanDefoliation = meanDefoliation;
el.NumSitesDefoliated0_33 = numSites0_33;
el.NumSitesDefoliated33_66 = numSites33_66;
el.NumSitesDefoliated66_100 = numSites66_100;
el.NumOutbreakInitialSites = insect.InitialSites;
el.MortalityBiomass = insect.LastBioRemoved;
if (insect.ActiveOutbreak)
{
el.StartYear = insect.OutbreakStartYear;
el.StopYear = insect.OutbreakStopYear;
}
else
{
el.StartYear = insect.LastStartYear;
el.StopYear = insect.LastStopYear;
}
eventLog.AddObject(el);
eventLog.WriteToFile();
//----- Write Insect Defoliation/GrowthReduction maps --------
string path = MapNames.ReplaceTemplateVars(mapNameTemplate, insect.Name, PlugIn.ModelCore.CurrentTime - 1);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (short)(insect.LastYearDefoliation[site] * 100.0);
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
//----- Write Initial Patch maps --------
string path2 = MapNames.ReplaceTemplateVars(mapNameTemplate, ("InitialPatchMap" + insect.Name), PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path2, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
if (insect.Disturbed[site])
{
pixel.MapCode.Value = (short)(SiteVars.InitialOutbreakProb[site] * 100);
}
else
{
pixel.MapCode.Value = 0;
}
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
//Zero out the InitialOutbreakProb after output maps are written.
SiteVars.InitialOutbreakProb[site] = 0;
}
}
//----- Write Biomass Reduction maps --------
string path3 = MapNames.ReplaceTemplateVars(mapNameTemplate, ("BiomassRemoved" + insect.Name), PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path3, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
if (SiteVars.BiomassRemoved[site] > 0)
{
pixel.MapCode.Value = Math.Max((short)1, (short)(SiteVars.BiomassRemoved[site] / 100)); // convert to Mg/ha
}
else
{
pixel.MapCode.Value = 0;
}
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
//Zero out the BiomassRemoved after the last insect mortality event in a given year.
SiteVars.BiomassRemoved[site] = 0;
}
}
//}
//insect.ThisYearDefoliation.ActiveSiteValues = 0.0; //reset this year to 0 for all sites, this was already done at the top of loop to initialize defoliation patchs, Outbreak.cs
}
}
//---------------------------------------------------------------------
// This method replaces the delegate method. It is called every year when
// ACT_ANPP is calculated, for each cohort. Therefore, this method is operating at
// an ANNUAL time step and separate from the normal extension time step.
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)
}
//---------------------------------------------------------------------
// This method replaces the delegate method. It is called every year when
// ACT_ANPP is calculated, for each cohort. Therefore, this method is operating at
// an ANNUAL time step and separate from the normal extension time step.
public static double DefoliateCohort(ICohort cohort, ActiveSite site, int siteBiomass)
{
// PlugIn.ModelCore.UI.WriteLine(" Calculating insect defoliation...");
int sppIndex = cohort.Species.Index;
double totalDefoliation = 0.0;
foreach (IInsect insect in manyInsect)
{
if (!insect.ActiveOutbreak)
{
continue;
}
double defoliation = 0.0;
double weightedDefoliation = 0.0;
int suscIndex = insect.SppTable[sppIndex].Susceptibility - 1;
if (suscIndex < 0)
{
suscIndex = 0;
}
// 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];
sumNeighborhoodDefoliation += 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);
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);
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);
// For first insect in a given year, actual defoliation equals the potential defoliation drawn from insect distributions.
// For second insect in a given year, actual defoliation can only be as high as the amount of canopy foliage left by first insect.
// This change makes sure next year's neighborhoodDefoliation will reflect actual defoliation, rather than "potential" defoliation.
// It should also ensure that the sum of defoliation maps for all insects adds up to 1 for a given year.
weightedDefoliation = (Math.Min((1 - totalDefoliation), defoliation) * ((double)cohort.Biomass / (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;
}
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);
}
//---------------------------------------------------------------------
// This method replaces the delegate method. It is called every year when
// ACT_ANPP is calculated, for each cohort. Therefore, this method is operating at
// an ANNUAL time step and separate from the normal extension time step.
//static int LastYearDefoliationCohortWasCalled = int.MinValue; // Add this for error capture. Ensure timestep for succession is annual. Previous method doesn't work with new biomass library.
//static bool TimeStepChecked = false;
public static double DefoliateCohort(ActiveSite site,
ISpecies species,
int cohortBiomass,
int siteBiomass)
{
// if (TimeStepChecked == false)
// {
// if (LastYearDefoliationCohortWasCalled > 0 && PlugIn.ModelCore.CurrentTime - LastYearDefoliationCohortWasCalled > 1)
// {
// throw new System.Exception(" CAUTION! If using Biomass Insects, Succession Extension should be operating at an ANNUAL time step.");
// }
// LastYearDefoliationCohortWasCalled = PlugIn.ModelCore.CurrentTime;
// TimeStepChecked = true;
// }
//public static double DefoliateCohort(ICohort cohort, ActiveSite site, int siteBiomass)
//{
// PlugIn.ModelCore.UI.WriteLine(" Calculating insect defoliation...");
int sppIndex = species.Index;
double totalDefoliation = 0.0;
foreach (IInsect insect in manyInsect)
//foreach (IInsect insect in PlugIn.ManyInsect) // This the construction used by GrowthReduction and PartialDisturbance, why was above different? Defoliation seems to calculate out of order...
{
if (!insect.ActiveOutbreak)
{
continue;
}
double defoliation = 0.0;
double weightedDefoliation = 0.0;
int suscIndex = insect.SppTable[sppIndex].Susceptibility - 1;
if (suscIndex < 0)
{
suscIndex = 0;
}
// Get the Neighborhood Mean Defoliation surrounding current site.
//This needs to be reset to zero here at the start of a new outbreak.
double meanNeighborhoodDefoliation = 0.0;
int neighborCnt = 0;
// If it is the first year, the neighborhood defoliation
// 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++;
sumNeighborhoodDefoliation += 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 Defoliation 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, draw defoliation value and apply to all cohorts of the same susceptibility class on current site.
// If a defoliation has happened on the site...
if (insect.HostDefoliationByYear[site].ContainsKey(PlugIn.ModelCore.CurrentTime))
{
// These cases depend on Beta distribution always drawing a positive, non-zero value even if very small. Trying to zero-out defoliation here causes problems.
// If no value for defoliation of this susceptibility class has been drawn yet, draw one here from correct distribution...
if (insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime][suscIndex] <= 0.00000000)
{
defoliation = Distribution.GenerateRandomNum(dist, value1, value2);
// Need this here and in each else statement: To correct for error reporting Mean Neighborhood Defoliation < 0. Bug arises when tested with 3+ insects.
// Looping over multiple insects in same year could produce totalDefoliation > 1. If this year's total defoliation = 1, next insect can't defoliate more.
defoliation = Math.Min((1 - totalDefoliation), defoliation);
defoliation = Math.Max(0.0001, defoliation);
insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime][suscIndex] = defoliation;
}
//If a value for this susceptibility class already exists, use already drawn value.
else
{
defoliation = insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime][suscIndex];
}
// Not sure why below is needed, but somehow higher defoliation is getting assigned to insect.HostDefoliationByYear[site][suscIndex] with 3rd insect.
defoliation = Math.Min((1 - totalDefoliation), defoliation);
defoliation = Math.Max(0.0001, defoliation);
insect.HostDefoliationByYear[site][PlugIn.ModelCore.CurrentTime][suscIndex] = defoliation;
//if (defoliation <= 0.0)
//PlugIn.ModelCore.UI.WriteLine("THAT'S WEIRD!! meanNeighborhoodDefoliation = {0}, defoliation={1}.", meanNeighborhoodDefoliation, defoliation);
}
// Else if no defoliation for this SITE has been drawn yet, draw the SITE-LEVEL defoliation value...then draw and assign the SUSCEPTIBILITY CLASS value.
else
{
insect.HostDefoliationByYear[site].Add(PlugIn.ModelCore.CurrentTime, new Double[3] {
0.0, 0.0, 0.0
});
defoliation = Distribution.GenerateRandomNum(dist, value1, value2);
// Need this here and in each else statement: To correct for error reporting Mean Neighborhood Defoliation < 0. Bug arises when tested with 3+ insects.
// Looping over multiple insects in same year could produce totalDefoliation > 1. If this year's total defoliation = 1, next insect can't defoliate more.
defoliation = Math.Min((1 - totalDefoliation), defoliation);
defoliation = Math.Max(0.0001, defoliation);
//if (meanNeighborhoodDefoliation <= 0.0 && defoliation > 0.0)
// PlugIn.ModelCore.UI.WriteLine("THAT'S WEIRD!! meanNeighborhoodDefoliation = {0}, defoliation={1}.", meanNeighborhoodDefoliation, defoliation);
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}, {1:0.00000000}, {2:0.000000000}, {3:0.000000000}, {4:0.000000000},{5:0.000000000}.", dist, value1, value2, defoliation, meanNeighborhoodDefoliation, totalDefoliation);
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);
// For first insect in a given year, actual defoliation equals the potential defoliation drawn from insect distributions.
// For second insect in a given year, actual defoliation can only be as high as the amount of canopy foliage left by first insect.
// This change makes sure next year's neighborhoodDefoliation will reflect actual defoliation, rather than "potential" defoliation.
// It should also ensure that the sum of defoliation maps for all insects adds up to 1 for a given year.
// Maybe need this here: To correct for error reporting Mean Neighborhood Defoliation < 0.
// Looping over multiple insects in same year could produce totalDefoliation > 1. If this year's total defoliation = 1, next insect can't defoliate more.
// This needs to be moved within each if-else statement above before assigning defoliation to HostDefoliationByYear...Doing now...
//defoliation = Math.Min((1 - totalDefoliation),defoliation);
// Then:
weightedDefoliation = defoliation * ((double)cohortBiomass / (double)siteBiomass);
//weightedDefoliation = (Math.Min((1 - totalDefoliation), defoliation) * ((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;
if (totalDefoliation > 1.1)
{
PlugIn.ModelCore.UI.WriteLine("suscIndex={0}, cohortDefoliation={1}, weightedDefolation={2},insect={3}, totalDefoliation={4}.", (suscIndex + 1), defoliation, weightedDefoliation, insect.Name, totalDefoliation);
}
}
if (totalDefoliation > 1.0) // Cannot exceed 100% defoliation.
{
totalDefoliation = 1.0;
}
if (totalDefoliation > 1.0 || 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 1.0 and 0.0");
}
return(totalDefoliation);
}
//---------------------------------------------------------------------
// Initialize landscape with patches of defoliation during the first year
public static void InitializeDefoliationPatches(IInsect insect)
{
PlugIn.ModelCore.UI.WriteLine(" Initializing Defoliation Patches... ");
insect.InitialOutbreakProb.ActiveSiteValues = 0.0;
insect.Disturbed.ActiveSiteValues = false;
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
double suscIndexSum = 0.0;
double sumBio = 0.0;
double protectBiomass = 0.0;
Landis.Library.BiomassCohorts.ISiteCohorts siteCohorts = SiteVars.Cohorts[site];
foreach (ISpeciesCohorts speciesCohorts in siteCohorts)
{
foreach (ICohort cohort in speciesCohorts)
{
int sppSuscIndex = insect.Susceptibility[cohort.Species];
if (sppSuscIndex == 4)
{
protectBiomass += cohort.Biomass;
sppSuscIndex = 3;
}
suscIndexSum += cohort.Biomass * (sppSuscIndex);
sumBio += cohort.Biomass;
}
}
// If no biomass, no chance of defoliation, go to the next site.
if (suscIndexSum <= 0 || sumBio <= 0)
{
insect.InitialOutbreakProb[site] = 0.0;
continue;
}
int siteSuscIndex = (int)Math.Round(suscIndexSum / sumBio) - 1;
double protectProp = protectBiomass / sumBio;
if (siteSuscIndex > 2.0 || siteSuscIndex < 0)
{
PlugIn.ModelCore.UI.WriteLine("SuscIndex < 0 || > 2. Site R/C={0}/{1},suscIndex={2},suscIndexSum={3},sumBio={4}.", site.Location.Row, site.Location.Column, siteSuscIndex, suscIndexSum, sumBio);
throw new ApplicationException("Error: SuscIndex is not between 2.0 and 0.0");
}
// Assume that there are no neighbors whatsoever:
DistributionType dist = insect.SusceptibleTable[siteSuscIndex].Distribution_80.Name;
//PlugIn.ModelCore.UI.WriteLine("suscIndex={0},suscIndexSum={1},cohortBiomass={2}.", suscIndex,suscIndexSum,sumBio);
double value1 = insect.SusceptibleTable[siteSuscIndex].Distribution_80.Value1;
double value2 = insect.SusceptibleTable[siteSuscIndex].Distribution_80.Value2;
double probability = 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;
}
probability = probability * protectReduce;
}
if (probability > 1.0 || probability < 0)
{
PlugIn.ModelCore.UI.WriteLine("Initial Defoliation Probility < 0 || > 1. Site R/C={0}/{1}.", site.Location.Row, site.Location.Column);
throw new ApplicationException("Error: Probability is not between 1.0 and 0.0");
}
insect.InitialOutbreakProb[site] = probability; // This probability reflects the protective effects
//PlugIn.ModelCore.UI.WriteLine("Susceptiblity index={0}. Outbreak Probability={1:0.00}. R/C={2}/{3}.", suscIndex, probability, site.Location.Row, site.Location.Column);
}
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
//get a random site from the stand
double randomNum = PlugIn.ModelCore.GenerateUniform();
double randomNum2 = PlugIn.ModelCore.GenerateUniform();
//Create random variability in outbreak area within a simulation so outbreaks are more variable.
double initialAreaCalibratorRandomNum = (randomNum2 - 0.5) * insect.InitialPatchOutbreakSensitivity / 2;
//Start spreading!
if (randomNum < insect.InitialOutbreakProb[site] * (insect.InitialPatchOutbreakSensitivity + initialAreaCalibratorRandomNum))
//if(randomNum < SiteVars.InitialOutbreakProb[site] * insect.InitialPatchOutbreakSensitivity)
{
//start with this site (if it's active)
ActiveSite currentSite = site;
//queue to hold sites to defoliate
Queue <ActiveSite> sitesToConsider = new Queue <ActiveSite>();
//put initial site on queue
sitesToConsider.Enqueue(currentSite);
DistributionType dist = insect.InitialPatchDistr;
double targetArea = Distribution.GenerateRandomNum(dist, insect.InitialPatchValue1, insect.InitialPatchValue2);
//PlugIn.ModelCore.UI.WriteLine(" Target Patch Area={0:0.0}.", targetArea);
double areaSelected = 0.0;
//loop through stand, defoliating patches of size target area
while (sitesToConsider.Count > 0 && areaSelected < targetArea)
{
currentSite = sitesToConsider.Dequeue();
// Because this is the first year, neighborhood defoliaiton is given a value.
// The value is used in Defoliate.DefoliateCohort()
insect.NeighborhoodDefoliation[currentSite] = insect.InitialOutbreakProb[currentSite];
areaSelected += PlugIn.ModelCore.CellArea;
insect.Disturbed[currentSite] = true;
//Next, add site's neighbors to the list of
//sites to consider.
//loop through the site's neighbors enqueueing all the good ones.
//double maxNeighborProb = 0.0;
//Site maxNeighbor = currentSite;
//bool foundNewNeighbor = false;
foreach (RelativeLocation loc in all_neighbor_locations)
{
Site neighbor = currentSite.GetNeighbor(loc);
//get a neighbor site (if it's non-null and active)
if (neighbor != null &&
neighbor.IsActive &&
!sitesToConsider.Contains((ActiveSite)neighbor) &&
!insect.Disturbed[neighbor])
{
//insect.Disturbed[currentSite] = true;
randomNum = PlugIn.ModelCore.GenerateUniform();
/*if (SiteVars.InitialOutbreakProb[neighbor] > maxNeighborProb)
* {
* maxNeighbor = currentSite.GetNeighbor(loc);
* maxNeighborProb = SiteVars.InitialOutbreakProb[neighbor];
* foundNewNeighbor = true;
* }*/
//check if it's a valid neighbor:
if (insect.InitialOutbreakProb[neighbor] * insect.InitialPatchShapeCalibrator > randomNum)
{
sitesToConsider.Enqueue((ActiveSite)neighbor);
}
}
}
//if(foundNewNeighbor)
// sitesToConsider.Enqueue((ActiveSite) maxNeighbor);
}
//PlugIn.ModelCore.UI.WriteLine(" Initial Patch Area Selected={0:0.0}.", areaSelected);
}
}
}