// Management events .......................................................
/// <summary>
/// Add animal cohorts
/// </summary>
/// <param name="CohortsInfo"></param>
/// <param name="iDOY"></param>
/// <param name="fLatitude"></param>
/// <param name="newGroups"></param>
public void AddCohorts(TCohortsInfo CohortsInfo, int iDOY, double fLatitude, List<int> newGroups)
{
TAnimalParamSet mainGenotype;
TAgeInfo[] AgeInfo;
TAnimalInits AnimalInits;
int iNoCohorts;
double fSurvival;
int iDaysSinceShearing;
double fMeanNormalWt;
double fMeanFleeceWt;
double fBaseWtScalar;
double fFleeceWtScalar;
int iTotalAnimals;
int iMateDOY;
double fLowCondition;
double fLowFoetuses;
double fHighCondition;
double fHighFoetuses;
double fCondition;
double fTrialFoetuses;
double[] fPregRate = new double[4]; //TConceptionArray;
int[] iShiftNumber = new int[4];
bool bLactationDone;
double fLowChill;
double fLowOffspring;
double fHighChill;
double fHighOffspring;
double fChillIndex;
double fTrialOffspring;
double[] fLactRate = new double[4];
int iCohort;
int iPreg;
int iLact;
int groupIndex;
if (CohortsInfo.iNumber > 0)
{
mainGenotype = getGenotype(CohortsInfo.sGenotype);
AgeInfo = new TAgeInfo[CohortsInfo.iMaxYears + 1];
for (int i = 0; i < CohortsInfo.iMaxYears + 1; i++)
AgeInfo[i] = new TAgeInfo();
iNoCohorts = CohortsInfo.iMaxYears - CohortsInfo.iMinYears + 1;
fSurvival = 1.0 - mainGenotype.AnnualDeaths(false);
if (mainGenotype.Animal == GrazType.AnimalType.Cattle)
iDaysSinceShearing = 0;
else if (bIsGiven(CohortsInfo.fMeanGFW) && (CohortsInfo.iFleeceDays == 0))
iDaysSinceShearing = Convert.ToInt32(Math.Truncate(365.25 * CohortsInfo.fMeanGFW / mainGenotype.PotentialGFW));
else
iDaysSinceShearing = CohortsInfo.iFleeceDays;
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
//Proportion of all stock in this age cohort
if (fSurvival >= 1.0)
AgeInfo[iCohort].fPropn = 1.0 / iNoCohorts;
else
AgeInfo[iCohort].fPropn = (1.0 - fSurvival) * Math.Pow(fSurvival, iCohort - CohortsInfo.iMinYears)
/ (1.0 - Math.Pow(fSurvival, iNoCohorts));
AgeInfo[iCohort].iAgeDays = Convert.ToInt32(Math.Truncate(365.25 * iCohort) + CohortsInfo.iAgeOffsetDays);
// Normal weight for age
AgeInfo[iCohort].fNormalBaseWt = GrowthCurve(AgeInfo[iCohort].iAgeDays, CohortsInfo.ReproClass, mainGenotype);
// Estimate a default fleece weight based on time since shearing
AgeInfo[iCohort].fFleeceWt = TAnimalParamSet.fDefaultFleece(mainGenotype,
AgeInfo[iCohort].iAgeDays,
CohortsInfo.ReproClass,
iDaysSinceShearing);
}
// Re-scale the fleece-free and fleece weights
fMeanNormalWt = 0.0;
fMeanFleeceWt = 0.0;
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
fMeanNormalWt = fMeanNormalWt + AgeInfo[iCohort].fPropn * AgeInfo[iCohort].fNormalBaseWt;
fMeanFleeceWt = fMeanFleeceWt + AgeInfo[iCohort].fPropn * AgeInfo[iCohort].fFleeceWt;
}
if ((CohortsInfo.fMeanGFW > 0.0) && (fMeanFleeceWt > 0.0))
fFleeceWtScalar = CohortsInfo.fMeanGFW / fMeanFleeceWt;
else
fFleeceWtScalar = 1.0;
if (!bIsGiven(CohortsInfo.fMeanGFW))
CohortsInfo.fMeanGFW = fMeanFleeceWt;
if (bIsGiven(CohortsInfo.fMeanLiveWt))
fBaseWtScalar = (CohortsInfo.fMeanLiveWt - CohortsInfo.fMeanGFW) / fMeanNormalWt;
else if (bIsGiven(CohortsInfo.fCondScore))
fBaseWtScalar = TAnimalParamSet.CondScore2Condition(CohortsInfo.fCondScore);
else
fBaseWtScalar = 1.0;
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
AgeInfo[iCohort].fBaseWeight = AgeInfo[iCohort].fNormalBaseWt * fBaseWtScalar;
AgeInfo[iCohort].fFleeceWt = AgeInfo[iCohort].fFleeceWt * fFleeceWtScalar;
}
// Numbers in each age cohort
iTotalAnimals = 0;
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
AgeInfo[iCohort].iNumbers[0, 0] = Convert.ToInt32(Math.Truncate(AgeInfo[iCohort].fPropn * CohortsInfo.iNumber));
iTotalAnimals += AgeInfo[iCohort].iNumbers[0, 0];
}
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
if (iTotalAnimals < CohortsInfo.iNumber)
{
AgeInfo[iCohort].iNumbers[0, 0]++;
iTotalAnimals++;
}
// Pregnancy and lactation
if ((CohortsInfo.ReproClass == GrazType.ReproType.Empty) || (CohortsInfo.ReproClass == GrazType.ReproType.EarlyPreg) || (CohortsInfo.ReproClass == GrazType.ReproType.LatePreg))
{
// Numbers with each number of foetuses
if ((CohortsInfo.iDaysPreg > 0) && (CohortsInfo.fFoetuses > 0.0))
{
iMateDOY = 1 + (iDOY - CohortsInfo.iDaysPreg + 364) % 365;
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
AgeInfo[iCohort].iAgeAtMating = AgeInfo[iCohort].iAgeDays - CohortsInfo.iDaysPreg;
AgeInfo[iCohort].fSizeAtMating = GrowthCurve(AgeInfo[iCohort].iAgeAtMating,
CohortsInfo.ReproClass,
mainGenotype) / mainGenotype.fSexStdRefWt(CohortsInfo.ReproClass);
}
// binary search for the body condition at mating that yields the desired pregnancy rate
fLowCondition = 0.60;
fLowFoetuses = getReproRate(CohortsInfo, mainGenotype, AgeInfo, fLatitude, iMateDOY, fLowCondition, 0);
fHighCondition = 1.40;
fHighFoetuses = getReproRate(CohortsInfo, mainGenotype, AgeInfo, fLatitude, iMateDOY, fHighCondition, 0);
if (fLowFoetuses > CohortsInfo.fFoetuses)
fCondition = fLowCondition;
else if (fHighFoetuses < CohortsInfo.fFoetuses)
fCondition = fHighCondition;
else
{
do
{
fCondition = 0.5 * (fLowCondition + fHighCondition);
fTrialFoetuses = getReproRate(CohortsInfo, mainGenotype, AgeInfo, fLatitude, iMateDOY, fCondition, 0);
if (fTrialFoetuses < CohortsInfo.fFoetuses)
fLowCondition = fCondition;
else
fHighCondition = fCondition;
}
while (Math.Abs(fTrialFoetuses - CohortsInfo.fFoetuses) >= 1.0E-5); //until (Abs(fTrialFoetuses-CohortsInfo.fFoetuses) < 1.0E-5);
}
// Compute final pregnancy rates and numbers
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
fPregRate = getOffspringRates(mainGenotype, fLatitude, iMateDOY,
AgeInfo[iCohort].iAgeAtMating,
AgeInfo[iCohort].fSizeAtMating,
fCondition);
for (iPreg = 1; iPreg <= 3; iPreg++)
iShiftNumber[iPreg] = Convert.ToInt32(Math.Round(fPregRate[iPreg] * AgeInfo[iCohort].iNumbers[0, 0]));
for (iPreg = 1; iPreg <= 3; iPreg++)
{
AgeInfo[iCohort].iNumbers[iPreg, 0] += iShiftNumber[iPreg];
AgeInfo[iCohort].iNumbers[0, 0] -= iShiftNumber[iPreg];
}
}
} // if (iDaysPreg > 0) and (fFoetuses > 0.0)
// Numbers with each number of suckling young
// Different logic for sheep and cattle:
// - for sheep, first assume average body condition at conception and vary
// the chill index. If that doesn't work, fix the chill index & vary the
// body condition
// - for cattle, fix the chill index & vary the body condition
if ((CohortsInfo.iDaysLact > 0) && (CohortsInfo.fOffspring > 0.0))
{
bLactationDone = false;
fCondition = 1.0;
fChillIndex = 0;
iMateDOY = 1 + (iDOY - CohortsInfo.iDaysLact - mainGenotype.Gestation + 729) % 365;
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
AgeInfo[iCohort].iAgeAtMating = AgeInfo[iCohort].iAgeDays - CohortsInfo.iDaysLact - mainGenotype.Gestation;
AgeInfo[iCohort].fSizeAtMating = GrowthCurve(AgeInfo[iCohort].iAgeAtMating,
CohortsInfo.ReproClass,
mainGenotype) / mainGenotype.fSexStdRefWt(CohortsInfo.ReproClass);
}
if (mainGenotype.Animal == GrazType.AnimalType.Sheep)
{
// binary search for the chill index at birth that yields the desired proportion of lambs
fLowChill = 500.0;
fLowOffspring = getReproRate(CohortsInfo, mainGenotype, AgeInfo, fLatitude, iMateDOY, 1.0, fLowChill);
fHighChill = 2500.0;
fHighOffspring = getReproRate(CohortsInfo, mainGenotype, AgeInfo, fLatitude, iMateDOY, 1.0, fHighChill);
// this is a monotonically decreasing function...
if ((fHighOffspring < CohortsInfo.fOffspring) && (fLowOffspring > CohortsInfo.fOffspring))
{
do
{
fChillIndex = 0.5 * (fLowChill + fHighChill);
fTrialOffspring = getReproRate(CohortsInfo, mainGenotype, AgeInfo, fLatitude, iMateDOY, 1.0, fChillIndex);
if (fTrialOffspring > CohortsInfo.fOffspring)
fLowChill = fChillIndex;
else
fHighChill = fChillIndex;
} while (Math.Abs(fTrialOffspring - CohortsInfo.fOffspring) >= 1.0E-5); //until (Abs(fTrialOffspring-CohortsInfo.fOffspring) < 1.0E-5);
bLactationDone = true;
}
} // fitting lactation rate to a chill index
if (!bLactationDone)
{
fChillIndex = 800.0;
// binary search for the body condition at mating that yields the desired proportion of lambs or calves
fLowCondition = 0.60;
fLowOffspring = getReproRate(CohortsInfo, mainGenotype, AgeInfo, fLatitude, iMateDOY, fLowCondition, fChillIndex);
fHighCondition = 1.40;
fHighOffspring = getReproRate(CohortsInfo, mainGenotype, AgeInfo, fLatitude, iMateDOY, fHighCondition, fChillIndex);
if (fLowOffspring > CohortsInfo.fOffspring)
fCondition = fLowCondition;
else if (fHighOffspring < CohortsInfo.fOffspring)
fCondition = fHighCondition;
else
{
do
{
fCondition = 0.5 * (fLowCondition + fHighCondition);
fTrialOffspring = getReproRate(CohortsInfo, mainGenotype, AgeInfo, fLatitude, iMateDOY, fCondition, fChillIndex);
if (fTrialOffspring < CohortsInfo.fOffspring)
fLowCondition = fCondition;
else
fHighCondition = fCondition;
} while (Math.Abs(fTrialOffspring - CohortsInfo.fOffspring) >= 1.0E-5); //until (Abs(fTrialOffspring-CohortsInfo.fOffspring) < 1.0E-5);
}
} // fitting lactation rate to a condition
// Compute final offspring rates and numbers
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
fLactRate = getOffspringRates(mainGenotype, fLatitude, iMateDOY,
AgeInfo[iCohort].iAgeAtMating,
AgeInfo[iCohort].fSizeAtMating,
fCondition, fChillIndex);
for (iPreg = 0; iPreg <= 3; iPreg++)
{
for (iLact = 1; iLact <= 3; iLact++)
iShiftNumber[iLact] = Convert.ToInt32(Math.Round(fLactRate[iLact] * AgeInfo[iCohort].iNumbers[iPreg, 0]));
for (iLact = 1; iLact <= 3; iLact++)
{
AgeInfo[iCohort].iNumbers[iPreg, iLact] += iShiftNumber[iLact];
AgeInfo[iCohort].iNumbers[iPreg, 0] -= iShiftNumber[iLact];
}
}
}
} //_ lactating animals _
} //_ female animals
// Construct the animal groups from the numbers and cohort-specific information
AnimalInits.sGenotype = CohortsInfo.sGenotype;
AnimalInits.sMatedTo = CohortsInfo.sMatedTo;
AnimalInits.Sex = CohortsInfo.ReproClass;
AnimalInits.Birth_CS = StdMath.DMISSING;
AnimalInits.Paddock = "";
AnimalInits.Tag = 0;
AnimalInits.Priority = 0;
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
for (iPreg = 0; iPreg <= 3; iPreg++)
{
for (iLact = 0; iLact <= 3; iLact++)
{
if (AgeInfo[iCohort].iNumbers[iPreg, iLact] > 0)
{
AnimalInits.Number = AgeInfo[iCohort].iNumbers[iPreg, iLact];
AnimalInits.AgeDays = AgeInfo[iCohort].iAgeDays;
AnimalInits.Weight = AgeInfo[iCohort].fBaseWeight + AgeInfo[iCohort].fFleeceWt;
AnimalInits.MaxPrevWt = StdMath.DMISSING; // compute from cond_score
AnimalInits.Fleece_Wt = AgeInfo[iCohort].fFleeceWt;
AnimalInits.Fibre_Diam = TAnimalParamSet.fDefaultMicron(mainGenotype,
AnimalInits.AgeDays,
AnimalInits.Sex,
iDaysSinceShearing,
AnimalInits.Fleece_Wt);
if (iPreg > 0)
{
AnimalInits.Pregnant = CohortsInfo.iDaysPreg;
AnimalInits.No_Foetuses = iPreg;
}
else
{
AnimalInits.Pregnant = 0;
AnimalInits.No_Foetuses = 0;
}
if ((iLact > 0)
|| ((mainGenotype.Animal == GrazType.AnimalType.Cattle) && (CohortsInfo.iDaysLact > 0) && (CohortsInfo.fOffspring == 0.0)))
{
AnimalInits.Lactating = CohortsInfo.iDaysLact;
AnimalInits.No_Suckling = iLact;
AnimalInits.Young_GFW = CohortsInfo.fLambGFW;
AnimalInits.Young_Wt = CohortsInfo.fOffspringWt;
}
else
{
AnimalInits.Lactating = 0;
AnimalInits.No_Suckling = 0;
AnimalInits.Young_GFW = 0.0;
AnimalInits.Young_Wt = 0.0;
}
groupIndex = Add(AnimalInits);
if (newGroups != null)
{
newGroups.Add(groupIndex);
}
}
}
}
}
} // if CohortsInfo.iNumber > 0
}
/// <summary>
///
/// </summary>
/// <param name="CohortsInfo"></param>
/// <param name="mainGenotype"></param>
/// <param name="AgeInfo"></param>
/// <param name="fLatitude"></param>
/// <param name="iMateDOY"></param>
/// <param name="fCondition"></param>
/// <param name="fChill"></param>
/// <returns></returns>
private double getReproRate(TCohortsInfo CohortsInfo, TAnimalParamSet mainGenotype, TAgeInfo[] AgeInfo, double fLatitude, int iMateDOY, double fCondition, double fChill)
{
double Result = 0.0;
double[] fPregRate = new double[4];
int iCohort;
int N;
for (iCohort = CohortsInfo.iMinYears; iCohort <= CohortsInfo.iMaxYears; iCohort++)
{
fPregRate = getOffspringRates(mainGenotype, fLatitude, iMateDOY,
AgeInfo[iCohort].iAgeAtMating,
AgeInfo[iCohort].fSizeAtMating,
fCondition, fChill);
for (N = 1; N <= 3; N++)
Result = Result + AgeInfo[iCohort].fPropn * fPregRate[N];
}
return Result;
}
