/// <summary>Method to bring a new cohort of individuls to the specified LifeCyclePhase</summary>
/// <param name="InfestationInfo"></param>
public void Infest(SourceInfo InfestationInfo)
{
LifeCyclePhase InfestingPhase = FindChild <LifeCyclePhase>(InfestationInfo.LifeCyclePhase);
InfestingPhase.NewCohort(InfestationInfo);
mySummary.WriteMessage(this, "An infestation of " + InfestationInfo.Population + " " + FullPath + " " + InfestationInfo.LifeCyclePhase + "'s occured today, just now :-)");
}
/// <summary>Method to bring a new cohort of individuls to the specified LifeCyclePhase</summary>
/// <param name="Immigrants"></param>
public void Infest(Cohort Immigrants)
{
LifeCyclePhase InfestingPhase = Immigrants.BelongsToPhase;
InfestingPhase.NewCohort(Immigrants.Population, Immigrants.ChronologicalAge, Immigrants.PhysiologicalAge);
mySummary.WriteMessage(this, "An infestation of " + Immigrants.Population + " " + Apsim.FullPath(this) + " " + Immigrants.BelongsToPhase.Name + "'s occured today, just now :-)");
}
/// <summary>Loop through each cohort in this LifeCyclePhase to calculate development, mortality, graduation and reproduciton</summary>
public void Process()
{
if (Cohorts?.Count > 13000) //Check cohort number are not becomming silly
{
throw new Exception(FullPath + " has over 1500 cohorts which is to many really. This is why your simulation is slow and the data store is about to chuck it in. Check your " + this.Parent.Name.ToString() + " model to ensure development and mortality are sufficient.");
}
ZeorDeltas(); //Zero reporting properties for daily summing
if (Cohorts != null)
{
// Calculate daily deltas
foreach (Cohort c in Cohorts)
{
CurrentCohort = c;
c.ChronologicalAge += 1;
//Do development for each cohort
c.PhysiologicalAge = Math.Min(1.0, c.PhysiologicalAge + development.Value());
//Do mortality for each cohort
c.Mortalities = mortality.Value();
Mortalities += c.Mortalities;
c.Population = Math.Max(0.0, c.Population - c.Mortalities);
//Do reproduction for each cohort
c.Progeny = reproduction.Value();
Progeny += c.Progeny;
//Do migration for each cohort
c.Emigrants = migration.Value();
Emigrants += c.Emigrants;
c.Population = Math.Max(0.0, c.Population - c.Emigrants);
}
//Add Migrants into destination phase
if (Emigrants > 0)
{
double SumMigrantAge = 0;
double SumMigrantPAge = 0;
foreach (Cohort c in Cohorts)
{
if (c.Emigrants > 0)
{
SumMigrantAge += c.Emigrants * c.ChronologicalAge;
SumMigrantPAge += c.Emigrants * c.PhysiologicalAge;
}
}
double MeanMigrantAge = SumMigrantAge / Emigrants;
double MeanMigrantPAge = SumMigrantPAge / Emigrants;
if (MigrantDestinations.Count == 0)
{
throw new Exception(FullPath + " is predicting values for migration but has no MigrationDestinationPhase specified");
}
double MtotalProportion = 0;
foreach (MigrantDestinationPhase mdest in MigrantDestinations)
{
double destEmigrants = Emigrants * mdest.ProportionOfMigrants;
if ((MigrantDestinations.Count == 0) && (destEmigrants > 0))
{
throw new Exception(FullPath + " is predicting values for migration but has not MigrantDestinationPhase specified");
}
if (destEmigrants > 0)
{
IModel zone = Parent.FindAncestor <Zone>();
LifeCycle mDestinationCycle = zone.FindInScope <LifeCycle>(mdest.NameOfLifeCycleForMigrants);
if (mDestinationCycle == null)
{
throw new Exception(FullPath + " could not find a destination LifeCycle for migrants called " + mdest.NameOfLifeCycleForMigrants);
}
LifeCyclePhase mDestinationPhase = mDestinationCycle.FindChild <LifeCyclePhase>(mdest.NameOfPhaseForMigrants);
if (mDestinationPhase == null)
{
throw new Exception(FullPath + " could not find a destination LifeCyclePhase for migrants called " + mdest.NameOfPhaseForMigrants);
}
SourceInfo ImigrantInfo = new SourceInfo();
ImigrantInfo.LifeCycle = Parent.Name;
ImigrantInfo.LifeCyclePhase = this.Name;
ImigrantInfo.Type = SourceInfo.TypeOptions.Reproduction;
ImigrantInfo.Population = Emigrants;
ImigrantInfo.ChronologicalAge = MeanMigrantAge;
ImigrantInfo.PhysiologicalAge = MeanMigrantPAge;
mDestinationPhase?.NewCohort(ImigrantInfo);
MtotalProportion += mdest.ProportionOfMigrants;
}
}
if ((MtotalProportion > 1.001) && (Emigrants > 0))
{
throw new Exception("The sum of ProportionOfMigrants values in " + FullPath + " ProgenyDestinationPhases is greater than 1.0");
}
}
// Add progeny into destination phases
if (Progeny > 0)
{
if ((ProgenyDestinations.Count == 0) && (Progeny > 0))
{
throw new Exception(FullPath + " is predicting values for reproduction but has no ProgenyDestinationPhase specified");
}
double PtotalProportion = 0;
foreach (ProgenyDestinationPhase pdest in ProgenyDestinations)
{
double arrivals = Progeny * pdest.ProportionOfProgeny;
if (arrivals > 0)
{
IModel zone = Parent.FindAncestor <Zone>();
LifeCycle pDestinationCylce = zone.FindInScope <LifeCycle>(pdest.NameOfLifeCycleForProgeny);
if (pDestinationCylce == null)
{
throw new Exception(FullPath + " could not find a destination LifeCycle for progeny called " + pdest.NameOfLifeCycleForProgeny);
}
LifeCyclePhase pDestinationPhase = pDestinationCylce.FindChild <LifeCyclePhase>(pdest.NameOfPhaseForProgeny);
if (pDestinationPhase == null)
{
throw new Exception(FullPath + " could not find a destination LifeCyclePhase for progeny called " + pdest.NameOfPhaseForProgeny);
}
SourceInfo ArivalsInfo = new SourceInfo();
ArivalsInfo.LifeCycle = Parent.Name;
ArivalsInfo.LifeCyclePhase = this.Name;
ArivalsInfo.Type = SourceInfo.TypeOptions.Reproduction;
ArivalsInfo.Population = arrivals;
ArivalsInfo.ChronologicalAge = 0;
ArivalsInfo.PhysiologicalAge = 0;
pDestinationPhase?.NewCohort(ArivalsInfo);
PtotalProportion += pdest.ProportionOfProgeny;
}
}
if (((PtotalProportion < 0.999) || (PtotalProportion > 1.001)) && (Progeny > 0))
{
throw new Exception("The sum of ProportionOfProgeny values in " + FullPath + " ProgenyDestinationPhases does not equal 1.0");
}
}
// Move garduates to destination phase
foreach (Cohort c in Cohorts.ToArray())
{
if (c.PhysiologicalAge >= 1.0) //Members ready to graduate or die
{
if (LifeCyclePhaseForGraduates != null)
{
Graduates += c.Population; //Members graduate
}
else
{
Mortalities += c.Population; //Members die
}
Cohorts.Remove(c); //Remove mature cohort
}
if (c.Population < 0.001) //Remove cohort if all members dead
{
Cohorts.Remove(c);
}
}
if (Graduates > 0) //Promote graduates to cohort in next LifeCyclePhase
{
SourceInfo GraduateInfo = new SourceInfo();
GraduateInfo.LifeCycle = Parent.Name;
GraduateInfo.LifeCyclePhase = this.Name;
GraduateInfo.Type = SourceInfo.TypeOptions.Graduation;
GraduateInfo.Population = Graduates;
GraduateInfo.ChronologicalAge = 0;
GraduateInfo.PhysiologicalAge = 0;
LifeCyclePhaseForGraduates?.NewCohort(GraduateInfo);
}
}
}
/// <summary>Loop through each cohort in this LifeCyclePhase to calculate development, mortality, graduation and reproduciton</summary>
public void Process()
{
if (Cohorts?.Count > 500) //Check cohort number are not becomming silly
{
throw new Exception(Apsim.FullPath(this) + " has over 500 cohorts which is to many really. This is why your simulation is slow and the data store is about to chuck it in. Check your " + this.Parent.Name.ToString() + " model to ensure development and mortality are sufficient.");
}
ZeorDeltas(); //Zero reporting properties for daily summing
foreach (ProgenyDestinationPhase pdest in ProgenyDestinations)
{
pdest.ProgenyToDestination = 0;
}
if (Cohorts != null)
{
// Calculate daily deltas
foreach (Cohort c in Cohorts)
{
CurrentCohort = c;
c.ChronologicalAge += 1;
//Do development for each cohort
c.PhysiologicalAge = Math.Min(1.0, c.PhysiologicalAge + development.Value());
//Do mortality for each cohort
c.Mortalities = mortality.Value();
Mortalities += c.Mortalities;
c.Population = Math.Max(0.0, c.Population - c.Mortalities);
//Do reproduction for each cohort
Progeny += reproduction.Value();
foreach (ProgenyDestinationPhase dest in ProgenyDestinations)
{
dest.ProgenyToDestination += reproduction.Value() * dest.ProportionOfProgeny;
}
//Do migration for each cohort
Migrants += migration.Value();
if (Migrants > 0)
{
if (MigrantDestinations.Count == 0)
{
throw new Exception(Apsim.FullPath(this) + " is predicting values for migration but has no MigrationDestinationPhase specified");
}
double MtotalProportion = 0;
foreach (MigrantDestinationPhase mdest in MigrantDestinations)
{
double cohortMigrants = migration.Value() * mdest.ProportionOfMigrants;
if ((MigrantDestinations.Count == 0) && (cohortMigrants > 0))
{
throw new Exception(Apsim.FullPath(this) + " is predicting values for migration but has not MigrantDestinationPhase specified");
}
if (cohortMigrants > 0)
{
IModel zone = Apsim.Parent(this.Parent, typeof(Zone));
LifeCycle mDestinationCycle = Apsim.Find(zone, mdest.NameOfLifeCycleForMigrants) as LifeCycle;
if (mDestinationCycle == null)
{
throw new Exception(Apsim.FullPath(this) + " could not find a destination LifeCycle for migrants called " + mdest.NameOfLifeCycleForMigrants);
}
LifeCyclePhase mDestinationPhase = Apsim.Child(mDestinationCycle, mdest.NameOfPhaseForMigrants) as LifeCyclePhase;
if (mDestinationPhase == null)
{
throw new Exception(Apsim.FullPath(this) + " could not find a destination LifeCyclePhase for migrants called " + mdest.NameOfPhaseForMigrants);
}
mDestinationPhase.NewCohort(cohortMigrants, c.ChronologicalAge, c.PhysiologicalAge);
MtotalProportion += mdest.ProportionOfMigrants;
}
}
if ((MtotalProportion > 1.001) && (Migrants > 0))
{
throw new Exception("The sum of ProportionOfMigrants values in " + Apsim.FullPath(this) + " ProgenyDestinationPhases is greater than 1.0");
}
}
}
// Add progeny into destination phase
if ((ProgenyDestinations.Count == 0) && (Progeny > 0))
{
throw new Exception(Apsim.FullPath(this) + " is predicting values for reproduction but has no ProgenyDestinationPhase specified");
}
double PtotalProportion = 0;
foreach (ProgenyDestinationPhase pdest in ProgenyDestinations)
{
if (pdest.ProgenyToDestination > 0)
{
IModel zone = Apsim.Parent(this.Parent, typeof(Zone));
LifeCycle pDestinationCylce = Apsim.Find(zone, pdest.NameOfLifeCycleForProgeny) as LifeCycle;
if (pDestinationCylce == null)
{
throw new Exception(Apsim.FullPath(this) + " could not find a destination LifeCycle for progeny called " + pdest.NameOfLifeCycleForProgeny);
}
LifeCyclePhase pDestinationPhase = Apsim.Child(pDestinationCylce, pdest.NameOfPhaseForProgeny) as LifeCyclePhase;
if (pDestinationPhase == null)
{
throw new Exception(Apsim.FullPath(this) + " could not find a destination LifeCyclePhase for progeny called " + pdest.NameOfPhaseForProgeny);
}
pDestinationPhase.NewCohort(pdest.ProgenyToDestination, 0, 0);
PtotalProportion += pdest.ProportionOfProgeny;
}
}
if (((PtotalProportion < 0.999) || (PtotalProportion > 1.001)) && (Progeny > 0))
{
throw new Exception("The sum of ProportionOfProgeny values in " + Apsim.FullPath(this) + " ProgenyDestinationPhases does not equal 1.0");
}
// Move garduates to destination phase
foreach (Cohort c in Cohorts.ToArray())
{
if (c.PhysiologicalAge >= 1.0) //Members ready to graduate or die
{
if (LifeCyclePhaseForGraduates != null)
{
Graduates += c.Population; //Members graduate
}
else
{
Mortalities += c.Population; //Members die
}
Cohorts.Remove(c); //Remove mature cohort
}
if (c.Population < 0.001) //Remove cohort if all members dead
{
Cohorts.Remove(c);
}
}
if (Graduates > 0) //Promote graduates to cohort in next LifeCyclePhase
{
LifeCyclePhaseForGraduates?.NewCohort(Graduates, 0.0, 0.0);
}
}
}
/// <summary> Construct and store reference to owner.</summary>
/// <param name="belongsTo"></param>
public Cohort(LifeCyclePhase belongsTo)
{
BelongsToPhase = belongsTo;
}