/// <summary>
/// Mix of two genotypes (as at mating)
/// </summary>
/// <param name="sBreedName"></param>
/// <param name="damBreed"></param>
/// <param name="sireBreed"></param>
/// <param name="iGeneration"></param>
/// <returns>The new object</returns>
public static TAnimalParamSet CreateFactory(string sBreedName, TAnimalParamSet damBreed, TAnimalParamSet sireBreed, int iGeneration = 1)
{
TAnimalParamBlend[] aBlend = new TAnimalParamBlend[2];
aBlend[0].Breed = damBreed;
aBlend[0].fPropn = Math.Pow(0.5, iGeneration);
aBlend[1].Breed = sireBreed;
aBlend[1].fPropn = 1.0 - aBlend[0].fPropn;
return CreateFactory(sBreedName, aBlend);
}
/// <summary>
/// Default fleece weight as a function of age, sex and time since shearing
/// </summary>
/// <param name="Params"></param>
/// <param name="iAgeDays"></param>
/// <param name="Repr"></param>
/// <param name="iFleeceDays"></param>
/// <returns></returns>
public static double fDefaultFleece(TAnimalParamSet Params,
int iAgeDays,
GrazType.ReproType Repr,
int iFleeceDays)
{
double Result;
double fMeanAgeFactor;
iFleeceDays = Math.Min(iFleeceDays, iAgeDays);
if ((Params.Animal == GrazType.AnimalType.Sheep) && (iFleeceDays > 0))
{
fMeanAgeFactor = 1.0 - (1.0 - Params.WoolC[5])
* (Math.Exp(-Params.WoolC[12] * (iAgeDays - iFleeceDays)) - Math.Exp(-Params.WoolC[12] * iAgeDays))
/ (Params.WoolC[12] * iFleeceDays);
Result = Params.FleeceRatio * Params.fSexStdRefWt(Repr) * fMeanAgeFactor * iFleeceDays / 365.0;
}
else
Result = 0.0;
return Result;
}
/// <summary>
/// Copies a parameter set from AnimalParamsGlb
/// </summary>
/// <param name="sBreedName"></param>
public static TAnimalParamSet CreateFactory(string sBreedName)
{
TAnimalParamSet newObj = null;
TAnimalParamSet baseParams;
baseParams = (TAnimalParamSet)TGAnimalParams.AnimalParamsGlb().getNode(sBreedName);
if (baseParams != null)
newObj = new TAnimalParamSet(null, baseParams);
else
{
newObj = new TAnimalParamSet();
throw new Exception("Breed name \"" + sBreedName + "\" not recognised");
}
return newObj;
}
/// <summary>
/// Creates an object based on the parameters passed
/// </summary>
/// <param name="sBreedName"></param>
/// <param name="Blend"></param>
/// <returns></returns>
public static TAnimalParamSet CreateFactory(string sBreedName, TAnimalParamBlend[] Blend)
{
TAnimalParamSet newObj = null;
if (Blend.Length == 0) // No mixture of breeds provided, so
newObj = CreateFactory(sBreedName); // copy a breed from AnimalParamsGlb
else if (Blend.Length == 2) // Special case: optimized for speed
{
newObj = new TAnimalParamSet((TParameterSet)null, (TAnimalParamSet)null);
}
else
{
newObj = new TAnimalParamSet(null, Blend[0].Breed); // Sets the integer, string and Boolean
}
newObj.InitParameterSet(sBreedName, Blend);
return newObj;
}
/// <summary>
/// Construct an animal parameter set from a source one
/// </summary>
public TAnimalParamSet(TAnimalParamSet src)
: base(src)
{
for (int i = 0; i < ConceiveSigs.Length; i++)
ConceiveSigs[i] = new double[2];
ConstructCopy(src);
}
/// <summary>
/// Alternative copy constructor
/// </summary>
/// <param name="aParent"></param>
/// <param name="srcSet"></param>
public TAnimalParamSet(TParameterSet aParent, TAnimalParamSet srcSet)
: base(aParent/*, srcSet*/)
{
//create a new array
for (int i = 0; i < ConceiveSigs.Length; i++)
ConceiveSigs[i] = new double[2];
ConstructCopy(srcSet);
int Jdx;
if (srcSet != null)
{
if (srcSet.Animal == GrazType.AnimalType.Sheep)
setPotGFW(srcSet.PotentialGFW);
if (srcSet.bUseDairyCurve)
setPeakMilk(srcSet.PotMilkYield);
if (srcSet.FParentage.Length == 0)
{
Array.Resize(ref FParentage, 1);
FParentage[0].sBaseBreed = srcSet.sName;
FParentage[0].fPropn = 1.0;
}
else
{
Array.Resize(ref FParentage, srcSet.FParentage.Length);
for (Jdx = 0; Jdx <= FParentage.Length - 1; Jdx++)
{
FParentage[Jdx].sBaseBreed = srcSet.FParentage[Jdx].sBaseBreed;
FParentage[Jdx].fPropn = srcSet.FParentage[Jdx].fPropn;
}
}
}
}
/// <summary>
/// GrowthCurve calculates MaxNormalWt (see below) for an animal with the
/// default birth weight.
/// </summary>
/// <param name="SRW"></param>
/// <param name="BW"></param>
/// <param name="AgeDays"></param>
/// <param name="Params"></param>
/// <returns></returns>
private double MaxNormWtFunc(double SRW, double BW, int AgeDays, TAnimalParamSet Params)
{
double GrowthRate;
GrowthRate = Params.GrowthC[1] / Math.Pow(SRW, Params.GrowthC[2]);
return SRW - (SRW - BW) * Math.Exp(-GrowthRate * AgeDays);
}
/// <summary>
/// Calculate the growth from the standard growth curve
/// </summary>
/// <param name="iAgeDays"></param>
/// <param name="Repr"></param>
/// <param name="Params"></param>
/// <returns></returns>
public double GrowthCurve(int iAgeDays, GrazType.ReproType Repr, TAnimalParamSet Params)
{
double SRW;
SRW = Params.BreedSRW;
if ((Repr == GrazType.ReproType.Male) || (Repr == GrazType.ReproType.Castrated))
SRW = SRW * Params.SRWScalars[(int)Repr];
return MaxNormWtFunc(SRW, Params.StdBirthWt(1), iAgeDays, Params);
}
/// <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;
}
/// <summary>
/// Makes a copy of TAnimalParamsGlb and modifies it according to sConstFile
/// </summary>
/// <param name="sConstFile"></param>
/// <returns></returns>
private TAnimalParamSet MakeParamSet(string sConstFile)
{
TAnimalParamSet Result = new TAnimalParamSet((TAnimalParamSet)null);
Result.CopyAll(TGAnimalParams.AnimalParamsGlb());
if (sConstFile != "")
TGParamFactory.ParamXMLFactory().readFromFile(sConstFile, Result, true);
Result.sCurrLocale = GrazLocale.sDefaultLocale();
return Result;
}
private double[] getOffspringRates(TAnimalParamSet Params,
double fLatitude,
int iMateDOY,
int iAgeDays,
double fMatingSize,
double fCondition,
double fChillIndex = 0.0)
{
const double NO_CYCLES = 2.5;
const double STD_LATITUDE = -35.0; // Latitude (in degrees) for which the
// DayLengthConst[] parameters are set
double[] Result;
double[] Conceptions = new double[4];
double fEmptyPropn;
double fDLFactor;
double fPropn;
double fExposureOdds;
double fDeathRate;
int N;
fDLFactor = (1.0 - Math.Sin(GrazEnv.DAY2RAD * (iMateDOY + 10)))
* Math.Sin(GrazEnv.DEG2RAD * fLatitude) / Math.Sin(GrazEnv.DEG2RAD * STD_LATITUDE);
for (N = 1; N <= Params.MaxYoung; N++)
{
if ((iAgeDays > Params.Puberty[0]) && (Params.ConceiveSigs[N][0] < 5.0)) //Puberty[false]
fPropn = StdMath.DIM(1.0, Params.DayLengthConst[N] * fDLFactor)
* StdMath.SIG(fMatingSize * fCondition, Params.ConceiveSigs[N]);
else
fPropn = 0.0;
if (N == 1)
Conceptions[N] = fPropn;
else
{
Conceptions[N] = fPropn * Conceptions[N - 1];
Conceptions[N - 1] = Conceptions[N - 1] - Conceptions[N];
}
}
fEmptyPropn = 1.0;
for (N = 1; N <= Params.MaxYoung; N++)
fEmptyPropn = fEmptyPropn - Conceptions[N];
Result = new double[4];
if (fEmptyPropn < 1.0)
for (N = 1; N <= Params.MaxYoung; N++)
Result[N] = Conceptions[N] * (1.0 - Math.Pow(fEmptyPropn, NO_CYCLES)) / (1.0 - fEmptyPropn);
if ((fChillIndex > 0) && (Params.Animal == GrazType.AnimalType.Sheep))
{
for (N = 1; N <= Params.MaxYoung; N++)
{
fExposureOdds = Params.ExposureConsts[0] - Params.ExposureConsts[1] * fCondition + Params.ExposureConsts[2] * fChillIndex;
if (N > 1)
fExposureOdds = fExposureOdds + Params.ExposureConsts[3];
fDeathRate = Math.Exp(fExposureOdds) / (1.0 + Math.Exp(fExposureOdds));
Result[N] = (1.0 - fDeathRate) * Result[N];
}
}
return Result;
}
/// <summary>
///
/// </summary>
/// <param name="mainParams"></param>
/// <param name="Inits"></param>
/// <param name="sName"></param>
/// <param name="iSearchBefore"></param>
/// <returns></returns>
private TAnimalParamSet findGenotype(TAnimalParamSet mainParams, TSingleGenotypeInits[] Inits, string sName, int iSearchBefore)
{
TAnimalParamSet Result;
TAnimalParamSet foundParams;
int Idx;
Idx = 0;
while ((Idx < iSearchBefore) && (sName.ToLower() != Inits[Idx].sGenotypeName.ToLower()))
Idx++;
if (Idx < iSearchBefore)
Result = ParamsFromGenotypeInits(mainParams, Inits, Idx);
else
{
foundParams = mainParams.Match(sName);
if (foundParams != null)
Result = new TAnimalParamSet(null, foundParams);
else
throw new Exception("Breed name \"" + sName + "\" not recognised");
}
return Result;
}
/// <summary>
/// Always makes a copy
/// </summary>
/// <param name="mainParams"></param>
/// <param name="Inits"></param>
/// <param name="iGenotype"></param>
/// <returns></returns>
public TAnimalParamSet ParamsFromGenotypeInits(TAnimalParamSet mainParams,
TSingleGenotypeInits[] Inits,
int iGenotype)
{
TAnimalParamSet Result;
//bool bWeaner;
if (Inits[iGenotype].sDamBreed == String.Empty)
Result = findGenotype(mainParams, Inits, Inits[iGenotype].sGenotypeName, 0);
else if (Inits[iGenotype].iGeneration == 0)
Result = findGenotype(mainParams, Inits, Inits[iGenotype].sDamBreed, 0);
else
Result = TAnimalParamSet.CreateFactory(Inits[iGenotype].sGenotypeName,
findGenotype(mainParams, Inits, Inits[iGenotype].sDamBreed, iGenotype),
findGenotype(mainParams, Inits, Inits[iGenotype].sSireBreed, iGenotype));
Result.sName = Inits[iGenotype].sGenotypeName;
if (bIsGiven(Inits[iGenotype].SRW))
Result.BreedSRW = Inits[iGenotype].SRW;
if (bIsGiven(Inits[iGenotype].PotFleeceWt))
Result.PotentialGFW = Inits[iGenotype].PotFleeceWt;
if (bIsGiven(Inits[iGenotype].MaxFibreDiam))
Result.MaxMicrons = Inits[iGenotype].MaxFibreDiam;
if (bIsGiven(Inits[iGenotype].FleeceYield))
Result.FleeceYield = Inits[iGenotype].FleeceYield;
if (bIsGiven(Inits[iGenotype].PeakMilk))
Result.PotMilkYield = Inits[iGenotype].PeakMilk;
for (int iWeaner = 0; iWeaner <= 1; iWeaner++)
{
if (Inits[iGenotype].DeathRate[iWeaner] != StdMath.DMISSING) // A zero death rate is permissible
Result.SetAnnualDeaths(iWeaner == 1, Inits[iGenotype].DeathRate[iWeaner]);
}
if (bIsGiven(Inits[iGenotype].Conceptions[1]))
Result.Conceptions = Inits[iGenotype].Conceptions;
return Result;
}
/// <summary>
/// Default fibre diameter as a function of age, sex, time since shearing and fleece weight
/// </summary>
/// <param name="Params"></param>
/// <param name="iAgeDays"></param>
/// <param name="Repr"></param>
/// <param name="iFleeceDays"></param>
/// <param name="fGFW"></param>
/// <returns></returns>
public static double fDefaultMicron(TAnimalParamSet Params, int iAgeDays, GrazType.ReproType Repr, int iFleeceDays, double fGFW)
{
double fPotFleece;
if ((iFleeceDays > 0) && (fGFW > 0.0))
{
fPotFleece = fDefaultFleece(Params, iAgeDays, Repr, iFleeceDays);
return Params.MaxMicrons * Math.Pow(fGFW / fPotFleece, Params.WoolC[13]);
}
else
return Params.MaxMicrons;
}
private void setParamFile(string sFileName)
{
FBaseParams = null;
FBaseParams = MakeParamSet(sFileName);
FParamFile = sFileName;
}
/// <summary>
/// Returns TRUE i.f.f. all parameters other than the breed name are identical
/// </summary>
/// <param name="otherSet"></param>
/// <returns></returns>
public bool bFunctionallySame(TAnimalParamSet otherSet)
{
int iCount;
TParameterDefinition Defn;
string sTag;
int iPrm;
bool result = true;
iCount = this.iParamCount();
iPrm = 0;
while ((iPrm < iCount) && result)
{
Defn = this.getParam(iPrm);
if (Defn != null)
{
sTag = Defn.sFullName;
if (this.bIsDefined(sTag))
{
switch (Defn.paramType)
{
case ptyText: result = (result && (this.sParam(sTag) == otherSet.sParam(sTag)));
break;
case ptyReal: result = (result && (this.fParam(sTag) == otherSet.fParam(sTag)));
break;
case ptyInt: result = (result && (this.iParam(sTag) == otherSet.iParam(sTag)));
break;
case ptyBool: result = (result && (this.bParam(sTag) == otherSet.bParam(sTag)));
break;
}
}
else
result = (result && !otherSet.bIsDefined(Defn.sFullName));
}
else
result = false;
iPrm++;
}
return result;
}
/// <summary>
/// Locate a genotype in FGenotypes. If this fails, try searching for it in the
/// main parameter set and adding it to FGenotypes.
/// </summary>
/// <param name="sName"></param>
/// <returns></returns>
public TAnimalParamSet getGenotype(string sName)
{
int Idx;
TAnimalParamSet srcParamSet;
TAnimalParamSet Result = null;
if ((sName == "") && (FGenotypes.Length >= 1)) // Null string is a special case
Result = FGenotypes[0];
else
{
Idx = 0;
while ((Idx < FGenotypes.Length) && (sName.ToLower() != FGenotypes[Idx].sName.ToLower()))
Idx++;
if (Idx < FGenotypes.Length)
Result = FGenotypes[Idx];
else
{
srcParamSet = FBaseParams.Match(sName);
if (srcParamSet != null)
{
Result = new TAnimalParamSet(null, srcParamSet);
Idx = FGenotypes.Length;
Array.Resize(ref FGenotypes, Idx + 1);
FGenotypes[Idx] = Result;
}
}
}
if (Result == null)
throw new Exception("Genotype name \"" + sName + "\" not recognised");
return Result;
}
