/// <summary>
/// Applies each function in this Lifestage process to a cohort item that is owned by a Lifestage
/// </summary>
/// <param name="cohortItem"></param>
public void ProcessCohort(Cohort cohortItem)
{
//apply the functions from the function list to this cohort
foreach (IFunction func in FunctionList)
{
if (FecundityFunc != null && ProgenyFunc != null)
{
if (cohortItem.Fecundity < 0)
cohortItem.Fecundity = FecundityFunc.Value;
double progenyrate = ProgenyFunc.Value;
if (cohortItem.Fecundity > 0)
{
//number of Progeny produced per individual per timestep
double progenyRate = Math.Max(0.0, Math.Min(cohortItem.Fecundity, progenyrate));
if (progenyRate > 0)
{
double numberToCreate = cohortItem.Count * progenyRate;
if (numberToCreate > 0)
{
//transfer magic here
Lifestage destStage = cohortItem.OwningStage.OwningCycle.ChildStages.Find(s => s.Name == TransferTo);
cohortItem.OwningStage.Reproduce(cohortItem, destStage, numberToCreate);
}
cohortItem.Fecundity -= progenyRate;
}
}
}
else
{
throw new Exception("Fecundity and Progeny functions must be configured for " + this.Name + " lifestage");
}
}
}
/// <summary>
/// Applies each function in this Lifestage process to a cohort item that is owned by a Lifestage
/// </summary>
/// <param name="cohortItem"></param>
public void ProcessCohort(Cohort cohortItem)
{
//apply the functions from the function list to this cohort
foreach (IFunction func in FunctionList)
{
if (func == ProgenyFunc) // assume there is only one of these for the process
{
if (FecundityFunc != null && ProgenyFunc != null)
{
if (cohortItem.Fecundity < 0)
{
cohortItem.Fecundity = FecundityFunc.Value();
}
double progenyrate = ProgenyFunc.Value();
if (cohortItem.Fecundity > 0)
{
//number of Progeny produced per individual per timestep
double progenyRate = Math.Max(0.0, Math.Min(cohortItem.Fecundity, progenyrate));
if (progenyRate > 0)
{
double numberToCreate = cohortItem.Count * progenyRate;
if (numberToCreate > 0)
{
//transfer magic here
Lifestage destStage = cohortItem.OwningStage.OwningCycle.ChildStages.Find(s => s.Name == TransferTo);
cohortItem.OwningStage.Reproduce(cohortItem, destStage, numberToCreate);
}
cohortItem.Fecundity -= progenyRate;
}
}
}
else
{
throw new Exception("Fecundity and Progeny functions must be configured for " + this.Name + " lifestage");
}
}
else
{
//execute another function
}
}
}
private void OnStartOfSimulation(object sender, EventArgs e)
{
ChildStages = new List <Lifestage>();
foreach (Lifestage stage in Apsim.Children(this, typeof(Lifestage)))
{
stage.OwningCycle = this;
ChildStages.Add(stage);
}
int i = 0;
//create new cohorts from the InitialPopulation[]
foreach (Lifestage stage in ChildStages)
{
if (InitialPopulation.Length > i)
{
Cohort newCohort = stage.NewCohort();
newCohort.Count = InitialPopulation[i];
}
i++;
}
}
/// <summary>
///
/// </summary>
/// <param name="aCohort"></param>
public void Remove(Cohort aCohort)
{
CohortList.Remove(aCohort);
}
/// <summary>
/// Applies each function in this Lifestage process to a cohort item that is owned by a Lifestage
/// </summary>
/// <param name="cohortItem"></param>
public void ProcessCohort(Cohort cohortItem)
{
//apply the functions from the function list to this cohort
foreach (IFunction func in FunctionList)
{
if (ProcessAction == ProcessType.PhysiologicalGrowth)
{
cohortItem.PhysiologicalAge += func.Value;
}
else if (ProcessAction == ProcessType.Transfer)
{
double numberToMove = cohortItem.Count * func.Value;
if (numberToMove > 0)
{
//transfer magic here
Lifestage destStage = cohortItem.OwningStage.OwningCycle.ChildStages.Find(s => s.Name == TransferTo);
cohortItem.OwningStage.PromoteGraduates(cohortItem, destStage, numberToMove);
}
}
else if (ProcessAction == ProcessType.Mortality)
{
//kill some creatures
cohortItem.Count = cohortItem.Count * (1 - func.Value);
}
}
}
/// <summary>
/// The source cohort reproduces and sends count creatures to the destination stage.
/// </summary>
/// <param name="srcCohort"></param>
/// <param name="destStage"></param>
/// <param name="count"></param>
public void Reproduce(Cohort srcCohort, Lifestage destStage, double count)
{
if (destStage != null)
{
// move the count creatures into a new cohort
Cohort newCohort = null;
// find a cohort in the destStage that has PhenoAge = 0
int i = 0;
while (i < destStage.CohortList.Count)
{
if (destStage.CohortList[i].PhenoAge == 0)
{
newCohort = destStage.CohortList[i];
i = destStage.CohortList.Count; // terminate loop
}
i++;
}
if (newCohort == null)
newCohort = destStage.NewCohort();
newCohort.ChronoAge = 0;
newCohort.PhenoAge = 0;
newCohort.PhysiologicalAge = 0;
newCohort.Count += count;
}
else
{
throw new Exception("Destination stage is incorrectly specified");
}
}
/// <summary>
///
/// </summary>
/// <param name="aCohort"></param>
public void Remove(Cohort aCohort)
{
CohortList.Remove(aCohort);
}
/// <summary>
/// Move cohort on to the next stage
/// </summary>
public void PromoteGraduates(Cohort srcCohort, Lifestage destStage, double count)
{
if (destStage != null)
{
//move the count creatures into a new cohort
Cohort newCohort = destStage.NewCohort();
newCohort.ChronoAge = srcCohort.ChronoAge;
newCohort.PhenoAge = 0;
newCohort.PhysiologicalAge = 0;
newCohort.Count = count;
srcCohort.Count = srcCohort.Count - count;
}
else
{
throw new Exception("Destination stage is incorrectly specified");
}
}
/// <summary>
/// Construct a new cohort, add it to the list and return a reference to it.
/// </summary>
/// <returns></returns>
public Cohort NewCohort()
{
if (CohortList == null)
CohortList = new List<Cohort>();
Cohort a = new Cohort(this);
CohortList.Add(a);
return a;
}