//---------------------------------------------------------------------
int IDisturbance.ReduceOrKillMarkedCohort(ICohort cohort)
{
int currentDefol = 0;
if (PlugIn.Parameters.SBWHost[cohort.Species] && (cohort.Age >= PlugIn.Parameters.MinSusceptibleAge))
{
// assign defoliation to cohorts skewed by species and age (12a)
// These species names are hard-wired
// FIXME
double sppConvert = 0.0;
if (cohort.Species.Name == "abiebals")
{
sppConvert = 1.0;
}
else if (cohort.Species.Name == "piceglau")
{
sppConvert = 0.75;
}
else if (cohort.Species.Name == "picemari")
{
sppConvert = 0.375;
}
double cohortDefol = SiteVars.PctDefoliation[currentSite] * sppConvert * cohort.Age / SiteVars.MaxHostAge[currentSite];
if (cohortDefol > 100)
{
cohortDefol = 100;
}
cohort.UpdateDefoliationHistory(cohortDefol / 100.0);
currentDefol = (int)Math.Round((cohort.CurrentFoliage * (cohortDefol / 100))); // Assumes all defoliation comes out of current year foliage, convert percentage to proportion
SiteVars.TotalDefoliation[currentSite] += currentDefol;
}
if (currentDefol > cohort.Biomass || currentDefol < 0)
{
PlugIn.ModelCore.UI.WriteLine("Cohort Total Mortality={0}. Cohort Biomass={1}. Site R/C={2}/{3}.", currentDefol, cohort.Biomass, currentSite.Location.Row, currentSite.Location.Column);
throw new System.ApplicationException("Error: Total Mortality is not between 0 and cohort biomass");
}
double cohortPctMortality = Impacts.CohortMortality(cohort);
int cohortMortality = (int)(cohortPctMortality * (cohort.Biomass - currentDefol));
int totalBiomassReduction = currentDefol + cohortMortality;
SiteVars.BiomassRemoved[currentSite] += totalBiomassReduction;
return(totalBiomassReduction);
}
//---------------------------------------------------------------------
/// <summary>
/// Initializes the plug-in with a data file.
/// </summary>
/// <param name="dataFile">
/// Path to the file with initialization data.
/// </param>
/// <param name="startTime">
/// Initial timestep (year): the timestep that will be passed to the
/// first call to the component's Run method.
/// </param>
public override void Initialize()
{
Timestep = parameters.Timestep;
SiteVars.Initialize(parameters);
Impacts.Initialize();
Outputs.Initialize();
Dispersal.Initialize();
/*
* //Debug distribution
* StreamWriter randLog = Landis.Data.CreateTextFile("G:/Budworm_model/TEST/E_TEST/rand.csv");
* randLog.AutoFlush = true;
* randLog.WriteLine("Rand1, Rand2");
* //Troschuetz.Random.NormalDistribution r1 = new Troschuetz.Random.NormalDistribution();
* for (int i = 0; i < 10000; i++)
* {
*
* r1.Mu = 1;
* r1.Sigma = 0.01;
* double rand = r1.NextDouble();
* rand = r1.NextDouble();
*
* r1.Mu = 2;
* r1.Sigma = 0.01;
* double rand2 = r1.NextDouble();
* rand2 = r1.NextDouble();
*
* PlugIn.ModelCore.NormalDistribution.Mu = 1;
* PlugIn.ModelCore.NormalDistribution.Sigma = 0.01;
* double rand = PlugIn.ModelCore.NormalDistribution.NextDouble();
* //rand = PlugIn.ModelCore.NormalDistribution.NextDouble();
*
* PlugIn.ModelCore.NormalDistribution.Mu = 2;
* PlugIn.ModelCore.NormalDistribution.Sigma = 0.01;
* double rand2 = PlugIn.ModelCore.NormalDistribution.NextDouble();
* //rand2 = PlugIn.ModelCore.NormalDistribution.NextDouble();
*
* randLog.Write("{0:0.000}, {1:0.000}",
* rand,rand2);
* randLog.WriteLine("");
* }
*/
}
//---------------------------------------------------------------------
/// <summary>
/// Calculate cohort mortality (proportion)
/// </summary>
/// <param name="cohort"></param>
/// <returns></returns>
public static double CohortMortality(Landis.Library.BiomassCohorts.ICohort cohort)
{
// Calculate cumulative defoliation (13)
// Cumulative Annual Weighted Defoliation (Hennigar)
double annWtDefol0 = cohort.DefoliationHistory[0] * 0.28;
double annWtDefol1 = cohort.DefoliationHistory[1] * 0.26;
double annWtDefol2 = cohort.DefoliationHistory[2] * 0.22;
double annWtDefol3 = cohort.DefoliationHistory[3] * 0.13;
double annWtDefol4 = cohort.DefoliationHistory[4] * 0.08;
double annWtDefol5 = cohort.DefoliationHistory[5] * 0.03;
double cumAnnWtDefol = annWtDefol0 + annWtDefol1 + annWtDefol2 + annWtDefol3 + annWtDefol4 + annWtDefol5;
// Allocate impacts to cohorts (10a)
// Mortality
// Hennigar method
double percentMortality = 0;
const double CD_ScaleFactor = 0.952;
double periodicDefoliation = cumAnnWtDefol * CD_ScaleFactor;
percentMortality = Impacts.GetMortalityRate_AGE(cohort.Species, periodicDefoliation, cohort.Age);
return(percentMortality);
}