/// <summary>
/// Calculate conception rate for a female
/// </summary>
/// <param name="female">Female to calculate conception rate for</param>
/// <returns></returns>
private double ConceptionRate(RuminantFemale female)
{
double rate = 0;
switch (female.NumberOfBirths)
{
case 0:
// first mating
if (female.BreedParams.MinimumAge1stMating >= 24)
{
// 1st mated at 24 months or older
rate = female.BreedParams.ConceptionRateAsymptote[1] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[1] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[1]));
}
else if (female.BreedParams.MinimumAge1stMating >= 12)
{
// 1st mated between 12 and 24 months
double rate24 = female.BreedParams.ConceptionRateAsymptote[1] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[1] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[1]));
double rate12 = female.BreedParams.ConceptionRateAsymptote[0] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[0] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[0]));
rate = (rate12 + rate24) / 2;
// Not sure what the next code was doing in old version
//Concep_rate = ((730 - Anim_concep(rumcat)) * temp1 + (Anim_concep(rumcat) - 365) * temp2) / 365 ' interpolate between 12 & 24 months
}
break;
case 1:
// second offspring mother
rate = female.BreedParams.ConceptionRateAsymptote[2] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[2] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[2]));
break;
default:
// females who have had more then one birth (twins should could as one birth)
if (female.WeightAtConception > female.BreedParams.CriticalCowWeight * female.StandardReferenceWeight)
{
rate = female.BreedParams.ConceptionRateAsymptote[3] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[3] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[3]));
}
break;
}
return(rate);
}
private void Muster()
{
// get herd to muster
RuminantHerd ruminantHerd = Resources.RuminantHerd();
List <Ruminant> herd = ruminantHerd.Herd;
if (herd == null && herd.Count == 0)
{
return;
}
// get list from filters
foreach (Ruminant ind in herd.Filter(this))
{
// set new location ID
ind.Location = pasture.Name;
// check if sucklings are to be moved with mother
if (MoveSucklings)
{
// if female
if (ind.GetType() == typeof(RuminantFemale))
{
RuminantFemale female = ind as RuminantFemale;
// check if mother with sucklings
if (female.SucklingOffspring.Count > 0)
{
foreach (var suckling in female.SucklingOffspring)
{
suckling.Location = pasture.Name;
}
}
}
}
}
}
/// <summary>
/// Calculate conception rate for a female
/// </summary>
/// <param name="female">Female to calculate conception rate for</param>
/// <returns></returns>
private double ConceptionRate(RuminantFemale female)
{
double rate = 0;
switch (female.NumberOfBirths)
{
case 0:
// first mating
if(female.BreedParams.MinimumAge1stMating >= 24)
{
// 1st mated at 24 months or older
rate = female.BreedParams.ConceptionRateAsymptote[1] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[1] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[1]));
}
else if(female.BreedParams.MinimumAge1stMating >= 12)
{
// 1st mated between 12 and 24 months
double rate24 = female.BreedParams.ConceptionRateAsymptote[1] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[1] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[1]));
double rate12 = female.BreedParams.ConceptionRateAsymptote[0] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[0] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[0]));
rate = (rate12 + rate24) / 2;
// Not sure what the next code was doing in old version
//Concep_rate = ((730 - Anim_concep(rumcat)) * temp1 + (Anim_concep(rumcat) - 365) * temp2) / 365 ' interpolate between 12 & 24 months
}
break;
case 1:
// second offspring mother
rate = female.BreedParams.ConceptionRateAsymptote[2] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[2] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[2]));
break;
default:
// females who have had more then one birth (twins should could as one birth)
if(female.WeightAtConception > female.BreedParams.CriticalCowWeight * female.StandardReferenceWeight)
{
rate = female.BreedParams.ConceptionRateAsymptote[3] / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent[3] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept[3]));
}
break;
}
return rate;
}
private void OnWFAnimalManage(object sender, EventArgs e)
{
RuminantHerd ruminantHerd = Resources.RuminantHerd();
List<Ruminant> herd = ruminantHerd.Herd.Where(a => a.HerdName == HerdName).ToList();
RuminantType breedParams;
// get breedParams when no herd remaining
if (herd.Count() == 0)
{
breedParams = Resources.GetResourceItem("Ruminants", HerdName) as RuminantType;
}
else
{
breedParams = herd.FirstOrDefault().BreedParams;
}
// can sell off males any month as per NABSA
// if we don't need this monthly, then it goes into next if statement with herd declaration
// NABSA MALES - weaners, 1-2, 2-3 and 3-4 yo, we check for any male weaned and not a breeding sire.
// check for sell age/weight of young males
// if SellYoungFemalesLikeMales then all apply to both sexes else only males.
foreach (var ind in herd.Where(a => a.Weaned & (SellFemalesLikeMales ? true : (a.Gender == Sex.Male)) & (a.Age >= SellingAge ^ a.Weight >= SellingWeight)))
{
bool sell = true;
if (ind.GetType() == typeof(RuminantMale))
{
// don't sell breeding sires.
sell = !((ind as RuminantMale).BreedingSire);
}
if (sell)
{
ind.SaleFlag = Common.HerdChangeReason.AgeWeightSale;
}
}
// if management month
if (Clock.Today.Month == ManagementMonth ^ MonthlyManagement)
{
// Perform weaning
foreach (var ind in herd.Where(a => a.Weaned == false))
{
if (ind.Age >= WeaningAge ^ ind.Weight >= WeaningWeight)
{
ind.Wean();
}
}
// check for maximum age (females and males have different cutoffs)
foreach (var ind in herd.Where(a => a.Age >= ((a.Gender == Sex.Female) ? MaximumBreederAge : MaximumBullAge)))
{
ind.SaleFlag = Common.HerdChangeReason.MaxAgeSale;
}
// MALES
// check for breeder bulls after sale of old individuals and buy/sell
int numberinherd = herd.Where(a => a.Gender == Sex.Male & a.SaleFlag == Common.HerdChangeReason.None).Cast<RuminantMale>().Where(a => a.BreedingSire).Count();
if (numberinherd > MaximumSiresKept)
{
// sell bulls
// What rule? oldest first as they may be lost soonest
int numberToRemove = MaximumSiresKept - numberinherd;
foreach (var male in herd.Where(a => a.Gender == Sex.Male).Cast<RuminantMale>().Where(a => a.BreedingSire).OrderByDescending(a => a.Age).Take(numberToRemove))
{
male.SaleFlag = Common.HerdChangeReason.ExcessBullSale;
}
}
else if(numberinherd < MaximumSiresKept)
{
// remove young bulls from sale herd to replace breed bulls (not those sold because too old)
foreach (RuminantMale male in herd.Where(a => a.Gender == Sex.Male & a.SaleFlag == Common.HerdChangeReason.AgeWeightSale).OrderByDescending(a => a.Weight))
{
male.SaleFlag = Common.HerdChangeReason.None;
male.BreedingSire = true;
numberinherd++;
if (numberinherd >= MaximumSiresKept) break;
}
// if still insufficient buy bulls.
if (numberinherd < MaximumSiresKept)
{
int numberToBuy = Convert.ToInt32((MaximumSiresKept - numberinherd) * 0.05);
for (int i = 0; i < numberToBuy; i++)
{
RuminantMale newbull = new RuminantMale();
newbull.Age = 48;
newbull.HerdName = HerdName;
newbull.BreedingSire = true;
newbull.BreedParams = breedParams;
newbull.Gender = Sex.Male;
newbull.ID = ruminantHerd.NextUniqueID;
newbull.Weight = 450;
newbull.HighWeight = newbull.Weight;
newbull.SaleFlag = Common.HerdChangeReason.SirePurchase;
// add to purchase request list and await purchase in Buy/ Sell
ruminantHerd.PurchaseIndividuals.Add(newbull);
}
}
}
// FEMALES
// check for maximum number of breeders remaining after sale and buy/sell
numberinherd = herd.Where(a => a.Gender == Sex.Female & a.Age >= a.BreedParams.MinimumAge1stMating & a.SaleFlag == Common.HerdChangeReason.None).Count();
if (numberinherd > MaximumBreedersKept)
{
// sell breeders
// What rule? oldest first as they may be lost soonest
// should keep pregnant females... and young...
// this will currently remove pregnant females and females with suckling calf
int numberToRemove = MaximumBreedersKept - numberinherd;
foreach (var female in herd.Where(a => a.Gender == Sex.Female & a.Age >= a.BreedParams.MinimumAge1stMating).OrderByDescending(a => a.Age).Take(numberToRemove))
{
female.SaleFlag = Common.HerdChangeReason.ExcessBreederSale;
}
}
else
{
// remove young females from sale herd to replace breeders (not those sold because too old)
foreach (RuminantFemale female in herd.Where(a => a.Gender == Sex.Female & a.SaleFlag == Common.HerdChangeReason.AgeWeightSale).OrderByDescending(a => a.Weight))
{
female.SaleFlag = Common.HerdChangeReason.None;
numberinherd++;
if (numberinherd >= MaximumBreedersKept) break;
}
// if still insufficient buy breeders.
if (numberinherd < MaximumBreedersKept)
{
int ageOfHeifer = 12;
double weightOfHeifer = 260;
int numberToBuy = Convert.ToInt32((MaximumBreedersKept - numberinherd) * 0.05);
for (int i = 0; i < numberToBuy; i++)
{
RuminantFemale newheifer = new RuminantFemale();
newheifer.Age = ageOfHeifer;
newheifer.HerdName = HerdName;
newheifer.BreedParams = breedParams;
newheifer.Gender = Sex.Female;
newheifer.ID = ruminantHerd.NextUniqueID;
newheifer.Weight = weightOfHeifer;
newheifer.HighWeight = newheifer.Weight;
newheifer.SaleFlag = Common.HerdChangeReason.HeiferPurchase;
// add to purchase request list and await purchase in Buy/ Sell
ruminantHerd.PurchaseIndividuals.Add(newheifer);
}
}
}
}
}
/// <summary>
/// Create the individual ruminant animals using the Cohort parameterisations.
/// </summary>
/// <returns></returns>
public List <Ruminant> CreateIndividuals()
{
List <Ruminant> Individuals = new List <Ruminant>();
IModel parentNode = Apsim.Parent(this, typeof(IModel));
RuminantType parent = parentNode as RuminantType;
// get Ruminant Herd resource for unique ids
RuminantHerd ruminantHerd = Resources.RuminantHerd();
parent = this.Parent as RuminantType;
if (StartingNumber > 0)
{
//TODO: get random generator from global store with seed
Random rand = new Random();
for (int i = 1; i <= StartingNumber; i++)
{
object ruminantBase = null;
if (this.Gender == Sex.Male)
{
ruminantBase = new RuminantMale();
}
else
{
ruminantBase = new RuminantFemale();
}
Ruminant ruminant = ruminantBase as Ruminant;
ruminant.ID = ruminantHerd.NextUniqueID;
ruminant.BreedParams = parent;
ruminant.Breed = parent.Breed;
ruminant.HerdName = parent.Name;
ruminant.Gender = Gender;
ruminant.Age = StartingAge;
ruminant.SaleFlag = Common.HerdChangeReason.None;
if (Suckling)
{
ruminant.SetUnweaned();
}
double u1 = rand.NextDouble();
double u2 = rand.NextDouble();
double randStdNormal = Math.Sqrt(-2.0 * Math.Log(u1)) *
Math.Sin(2.0 * Math.PI * u2);
ruminant.Weight = StartingWeight + StartingWeightSD * randStdNormal;
ruminant.PreviousWeight = ruminant.Weight;
if (this.Gender == Sex.Female)
{
RuminantFemale ruminantFemale = ruminantBase as RuminantFemale;
ruminantFemale.DryBreeder = true;
ruminantFemale.WeightAtConception = this.StartingWeight;
ruminantFemale.NumberOfBirths = 0;
}
Individuals.Add(ruminantBase as Ruminant);
}
}
return(Individuals);
}
private void OnWFAnimalManage(object sender, EventArgs e)
{
RuminantHerd ruminantHerd = Resources.RuminantHerd();
List <Ruminant> herd = ruminantHerd.Herd.Where(a => a.HerdName == HerdName).ToList();
RuminantType breedParams;
// get breedParams when no herd remaining
if (herd.Count() == 0)
{
breedParams = Resources.GetResourceItem("Ruminants", HerdName) as RuminantType;
}
else
{
breedParams = herd.FirstOrDefault().BreedParams;
}
// can sell off males any month as per NABSA
// if we don't need this monthly, then it goes into next if statement with herd declaration
// NABSA MALES - weaners, 1-2, 2-3 and 3-4 yo, we check for any male weaned and not a breeding sire.
// check for sell age/weight of young males
// if SellYoungFemalesLikeMales then all apply to both sexes else only males.
foreach (var ind in herd.Where(a => a.Weaned & (SellFemalesLikeMales ? true : (a.Gender == Sex.Male)) & (a.Age >= SellingAge ^ a.Weight >= SellingWeight)))
{
bool sell = true;
if (ind.GetType() == typeof(RuminantMale))
{
// don't sell breeding sires.
sell = !((ind as RuminantMale).BreedingSire);
}
if (sell)
{
ind.SaleFlag = Common.HerdChangeReason.AgeWeightSale;
}
}
// if management month
if (Clock.Today.Month == ManagementMonth ^ MonthlyManagement)
{
// Perform weaning
foreach (var ind in herd.Where(a => a.Weaned == false))
{
if (ind.Age >= WeaningAge ^ ind.Weight >= WeaningWeight)
{
ind.Wean();
}
}
// check for maximum age (females and males have different cutoffs)
foreach (var ind in herd.Where(a => a.Age >= ((a.Gender == Sex.Female) ? MaximumBreederAge : MaximumBullAge)))
{
ind.SaleFlag = Common.HerdChangeReason.MaxAgeSale;
}
// MALES
// check for breeder bulls after sale of old individuals and buy/sell
int numberinherd = herd.Where(a => a.Gender == Sex.Male & a.SaleFlag == Common.HerdChangeReason.None).Cast <RuminantMale>().Where(a => a.BreedingSire).Count();
if (numberinherd > MaximumSiresKept)
{
// sell bulls
// What rule? oldest first as they may be lost soonest
int numberToRemove = MaximumSiresKept - numberinherd;
foreach (var male in herd.Where(a => a.Gender == Sex.Male).Cast <RuminantMale>().Where(a => a.BreedingSire).OrderByDescending(a => a.Age).Take(numberToRemove))
{
male.SaleFlag = Common.HerdChangeReason.ExcessBullSale;
}
}
else if (numberinherd < MaximumSiresKept)
{
// remove young bulls from sale herd to replace breed bulls (not those sold because too old)
foreach (RuminantMale male in herd.Where(a => a.Gender == Sex.Male & a.SaleFlag == Common.HerdChangeReason.AgeWeightSale).OrderByDescending(a => a.Weight))
{
male.SaleFlag = Common.HerdChangeReason.None;
male.BreedingSire = true;
numberinherd++;
if (numberinherd >= MaximumSiresKept)
{
break;
}
}
// if still insufficient buy bulls.
if (numberinherd < MaximumSiresKept)
{
int numberToBuy = Convert.ToInt32((MaximumSiresKept - numberinherd) * 0.05);
for (int i = 0; i < numberToBuy; i++)
{
RuminantMale newbull = new RuminantMale();
newbull.Age = 48;
newbull.HerdName = HerdName;
newbull.BreedingSire = true;
newbull.BreedParams = breedParams;
newbull.Gender = Sex.Male;
newbull.ID = ruminantHerd.NextUniqueID;
newbull.Weight = 450;
newbull.HighWeight = newbull.Weight;
newbull.SaleFlag = Common.HerdChangeReason.SirePurchase;
// add to purchase request list and await purchase in Buy/ Sell
ruminantHerd.PurchaseIndividuals.Add(newbull);
}
}
}
// FEMALES
// check for maximum number of breeders remaining after sale and buy/sell
numberinherd = herd.Where(a => a.Gender == Sex.Female & a.Age >= a.BreedParams.MinimumAge1stMating & a.SaleFlag == Common.HerdChangeReason.None).Count();
if (numberinherd > MaximumBreedersKept)
{
// sell breeders
// What rule? oldest first as they may be lost soonest
// should keep pregnant females... and young...
// this will currently remove pregnant females and females with suckling calf
int numberToRemove = MaximumBreedersKept - numberinherd;
foreach (var female in herd.Where(a => a.Gender == Sex.Female & a.Age >= a.BreedParams.MinimumAge1stMating).OrderByDescending(a => a.Age).Take(numberToRemove))
{
female.SaleFlag = Common.HerdChangeReason.ExcessBreederSale;
}
}
else
{
// remove young females from sale herd to replace breeders (not those sold because too old)
foreach (RuminantFemale female in herd.Where(a => a.Gender == Sex.Female & a.SaleFlag == Common.HerdChangeReason.AgeWeightSale).OrderByDescending(a => a.Weight))
{
female.SaleFlag = Common.HerdChangeReason.None;
numberinherd++;
if (numberinherd >= MaximumBreedersKept)
{
break;
}
}
// if still insufficient buy breeders.
if (numberinherd < MaximumBreedersKept)
{
int ageOfHeifer = 12;
double weightOfHeifer = 260;
int numberToBuy = Convert.ToInt32((MaximumBreedersKept - numberinherd) * 0.05);
for (int i = 0; i < numberToBuy; i++)
{
RuminantFemale newheifer = new RuminantFemale();
newheifer.Age = ageOfHeifer;
newheifer.HerdName = HerdName;
newheifer.BreedParams = breedParams;
newheifer.Gender = Sex.Female;
newheifer.ID = ruminantHerd.NextUniqueID;
newheifer.Weight = weightOfHeifer;
newheifer.HighWeight = newheifer.Weight;
newheifer.SaleFlag = Common.HerdChangeReason.HeiferPurchase;
// add to purchase request list and await purchase in Buy/ Sell
ruminantHerd.PurchaseIndividuals.Add(newheifer);
}
}
}
}
}
private void CalculatePotentialIntake(Ruminant ind)
{
// calculate daily potential intake for the selected individual/cohort
double standardReferenceWeight = ind.StandardReferenceWeight;
ind.NormalisedAnimalWeight = standardReferenceWeight - ((1 - ind.BreedParams.SRWBirth) * standardReferenceWeight) * Math.Exp(-(ind.BreedParams.AgeGrowthRateCoefficient * (ind.Age * 30.4)) / (Math.Pow(standardReferenceWeight, ind.BreedParams.SRWGrowthScalar)));
double liveWeightForIntake = ind.NormalisedAnimalWeight;
ind.HighWeight = Math.Max(ind.HighWeight, ind.Weight);
if (ind.HighWeight < ind.NormalisedAnimalWeight)
{
liveWeightForIntake = ind.HighWeight;
}
// Calculate potential intake based on current weight compared to SRW and previous highest weight
double potentialIntake = 0;
// calculate milk intake shortfall for sucklings
if (!ind.Weaned)
{
// potential milk intake/animal/day
double potentialMilkIntake = ind.BreedParams.MilkIntakeIntercept + ind.BreedParams.IntakeCoefficient * ind.Weight;
// get mother
ind.MilkIntake = Math.Min(potentialMilkIntake, ind.MothersMilkAvailable);
// if milk supply low, calf will subsitute forage up to a specified % of bodyweight (R_C60)
if (ind.MilkIntake < ind.Weight * ind.BreedParams.MilkLWTFodderSubstitutionProportion)
{
potentialIntake = Math.Max(0.0, ind.Weight * ind.BreedParams.MaxJuvenileIntake - ind.MilkIntake * ind.BreedParams.ProportionalDiscountDueToMilk);
}
// This has been removed and replaced with prop of LWT based on milk supply.
// Reference: SCA Metabolic LWTs
//potentialIntake = ind.BreedParams.IntakeCoefficient * standardReferenceWeight * (Math.Pow(liveWeightForIntake, 0.75) / Math.Pow(standardReferenceWeight, 0.75)) * (ind.BreedParams.IntakeIntercept - (Math.Pow(liveWeightForIntake, 0.75) / Math.Pow(standardReferenceWeight, 0.75)));
}
else
{
// Reference: SCA based actual LWTs
potentialIntake = ind.BreedParams.IntakeCoefficient * liveWeightForIntake * (ind.BreedParams.IntakeIntercept - liveWeightForIntake / standardReferenceWeight);
if (ind.Gender == Sex.Female)
{
RuminantFemale femaleind = ind as RuminantFemale;
// Increase potential intake for lactating breeder
if (femaleind.IsLactating)
{
double dayOfLactation = Math.Max((ind.Age - femaleind.AgeAtLastBirth) * 30.4, 0);
if (dayOfLactation > ind.BreedParams.MilkingDays)
{
// Reference: Intake multiplier for lactating cow (M.Freer)
// TODO: Need to look at equation to fix Math.Pow() ^ issue
// double intakeMilkMultiplier = 1 + 0.57 * Math.Pow((dayOfLactation / 81.0), 0.7) * Math.Exp(0.7 * (1 - (dayOfLactation / 81.0)));
double intakeMilkMultiplier = 1 + ind.BreedParams.LactatingPotentialModifierConstantA * Math.Pow((dayOfLactation / ind.BreedParams.LactatingPotentialModifierConstantB), ind.BreedParams.LactatingPotentialModifierConstantC) * Math.Exp(ind.BreedParams.LactatingPotentialModifierConstantC * (1 - (dayOfLactation / ind.BreedParams.LactatingPotentialModifierConstantB)));
// To make this flexible for sheep and goats, added three new Ruminant Coeffs
// Feeding standard values for Beef, Dairy suck, Dairy non-suck and sheep are:
// For 0.57 (A) use .42, .58, .85 and .69; for 0.7 (B) use 1.7, 0.7, 0.7 and 1.4, for 81 (C) use 62, 81, 81, 28
// added LactatingPotentialModifierConstantA, LactatingPotentialModifierConstantB and LactatingPotentialModifierConstantC
potentialIntake *= intakeMilkMultiplier;
}
}
}
//TODO: option to restrict potential further due to stress (e.g. heat, cold, rain)
// get monthly intake
potentialIntake *= 30.4;
}
ind.PotentialIntake = potentialIntake;
}
/// <summary>
/// Function to calculate energy from intake and subsequent growth
/// </summary>
/// <param name="ind">Ruminant individual class</param>
/// <param name="methaneProduced">Sets output variable to value of methane produced</param>
/// <returns></returns>
private void CalculateEnergy(Ruminant ind, out double methaneProduced)
{
// Sme 1 for females and castrates
// TODO: castrates not implemented
double Sme = 1;
// Sme 1.15 for all males.
if (ind.Gender == Sex.Male)
{
Sme = 1.15;
}
double energyDiet = EnergyGross * ind.DietDryMatterDigestibility / 100.0;
// Reference: Nutrient Requirements of domesticated ruminants (p7)
double energyMetabolic = energyDiet * 0.81;
double energyMetablicFromIntake = energyMetabolic * ind.Intake;
double km = ind.BreedParams.EMaintCoefficient * energyMetabolic / EnergyGross + ind.BreedParams.EMaintIntercept;
// Reference: SCA p.49
double kg = ind.BreedParams.EGrowthCoefficient * energyMetabolic / EnergyGross + ind.BreedParams.EGrowthIntercept;
double energyPredictedBodyMassChange = 0;
double energyMaintenance = 0;
if (!ind.Weaned)
{
// old code
// dum = potential milk intake daily
// dumshort = potential intake. check that it isnt monthly
// average energy efficiency for maintenance
double kml = ((ind.MilkIntake * 0.7) + (ind.PotentialIntake * km)) / (ind.MilkIntake + ind.PotentialIntake);
// average energy efficiency for growth
double kgl = ((ind.MilkIntake * 0.7) + (ind.PotentialIntake * kg)) / (ind.MilkIntake + ind.PotentialIntake);
double energyMilkConsumed = ind.MilkIntake * 3.2;
// limit calf intake of milk per day
energyMilkConsumed = Math.Min(ind.BreedParams.MilkIntakeMaximum * 3.2, energyMilkConsumed);
energyMaintenance = (ind.BreedParams.EMaintCoefficient * Math.Pow(ind.Weight, 0.75) / kml) * Math.Exp(-ind.BreedParams.EMaintExponent * ind.Age);
ind.EnergyBalance = energyMilkConsumed - energyMaintenance + energyMetablicFromIntake;
double feedingValue = 0;
if (ind.EnergyBalance > 0)
{
feedingValue = 2 * 0.7 * ind.EnergyBalance / (kgl * energyMaintenance) - 1;
}
else
{
//(from Hirata model)
feedingValue = 2 * ind.EnergyBalance / (0.85 * energyMaintenance) - 1;
}
double energyEmptyBodyGain = ind.BreedParams.GrowthEnergyIntercept1 + feedingValue + (ind.BreedParams.GrowthEnergyIntercept2 - feedingValue) / (1 + Math.Exp(-6 * (ind.Weight / ind.NormalisedAnimalWeight - 0.4)));
energyPredictedBodyMassChange = ind.BreedParams.GrowthEfficiency * 0.7 * ind.EnergyBalance / energyEmptyBodyGain;
}
else
{
//all weaned individuals
double energyMilk = 0;
double energyFoetus = 0;
if (ind.Gender == Sex.Female)
{
RuminantFemale femaleind = ind as RuminantFemale;
// calculate energy for lactation
if (femaleind.IsLactating)
{
// Reference: SCA p.
double kl = ind.BreedParams.ELactationCoefficient * energyMetabolic / EnergyGross + ind.BreedParams.ELactationIntercept;
double milkTime = Math.Max(0.0, (ind.Age - femaleind.AgeAtLastBirth + 1) * 30.4);
if (milkTime <= ind.BreedParams.MilkingDays)
{
double milkCurve = 0;
if (femaleind.DryBreeder) // no suckling calf
{
milkCurve = ind.BreedParams.MilkCurveNonSuckling;
}
else // suckling calf
{
milkCurve = ind.BreedParams.MilkCurveSuckling;
}
//TODO: check this equation that I redefined it correctly.
double milkProduction = ind.BreedParams.MilkPeakYield * ind.Weight / ind.NormalisedAnimalWeight * (Math.Pow(((milkTime + ind.BreedParams.MilkOffsetDay) / ind.BreedParams.MilkPeakDay), milkCurve)) * Math.Exp(milkCurve * (1 - (milkTime + ind.BreedParams.MilkOffsetDay) / ind.BreedParams.MilkPeakDay));
milkProduction = Math.Max(milkProduction, 0.0);
// Reference: Potential milk prodn, 3.2 MJ/kg milk - Jouven et al 2008
energyMilk = milkProduction * 3.2 / kl;
if (ind.EnergyBalance < (-0.5936 / 0.322 * energyMilk))
{
ind.EnergyBalance = (-0.5936 / 0.322 * energyMilk);
}
milkProduction = Math.Max(0.0, milkProduction * (0.5936 + 0.322 * ind.EnergyBalance / energyMilk));
// Reference: Adjusted milk prodn, 3.2 MJ/kg milk - Jouven et al 2008
energyMilk = milkProduction * 3.2 / kl;
}
}
// Determine energy required for foetal development
if (femaleind.IsPregnant)
{
double standardReferenceWeight = ind.StandardReferenceWeight;
// Potential birth weight
// Reference: Freer
double potentialBirthWeight = ind.BreedParams.SRWBirth * standardReferenceWeight * (1 - 0.33 * (1 - ind.Weight / standardReferenceWeight));
double foetusAge = (femaleind.Age - femaleind.AgeAtLastConception + 1) * 30.4;
//TODO: Check foetus gage correct
energyFoetus = potentialBirthWeight * 349.16 * 0.000058 * Math.Exp(345.67 - 0.000058 * foetusAge - 349.16 * Math.Exp(-0.000058 * foetusAge)) / 0.13;
}
}
//TODO: add draft energy requirement
// set maintenance age to maximum of 6 years
double maintenanceAge = Math.Min(ind.Age * 30.4, 2190);
// Reference: SCA p.24
// Regference p19 (1.20). Does not include MEgraze or Ecold, also skips M,
// 0.000082 is -0.03 Age in Years/365 for days
energyMaintenance = ind.BreedParams.Kme * Sme * (0.26 * Math.Pow(ind.Weight, 0.75) / km) * Math.Exp(-0.000082 * maintenanceAge) + (0.09 * energyMetablicFromIntake);
ind.EnergyBalance = energyMetablicFromIntake - energyMaintenance - energyMilk - energyFoetus; // milk will be zero for non lactating individuals.
// Reference: Feeding_value = Ajustment for rate of loss or gain (SCA p.43, ? different from Hirata model)
double feedingValue = 0;
if (ind.EnergyBalance > 0)
{
feedingValue = 2 * ((kg * ind.EnergyBalance) / (km * energyMaintenance) - 1);
}
else
{
feedingValue = 2 * (ind.EnergyBalance / (0.8 * energyMaintenance) - 1); //(from Hirata model)
}
double weightToReferenceRatio = Math.Min(1.0, ind.Weight / ind.StandardReferenceWeight);
// Reference: MJ of Energy required per kg Empty body gain (SCA p.43)
double energyEmptyBodyGain = ind.BreedParams.GrowthEnergyIntercept1 + feedingValue + (ind.BreedParams.GrowthEnergyIntercept1 - feedingValue) / (1 + Math.Exp(-6 * (weightToReferenceRatio - 0.4)));
// Determine Empty body change from Eebg and Ebal, and increase by 9% for LW change
energyPredictedBodyMassChange = 0;
if (ind.EnergyBalance > 0)
{
energyPredictedBodyMassChange = ind.BreedParams.GrowthEfficiency * kg * ind.EnergyBalance / energyEmptyBodyGain;
}
else
{
// Reference: from Hirata model
energyPredictedBodyMassChange = ind.BreedParams.GrowthEfficiency * km * ind.EnergyBalance / (0.8 * energyEmptyBodyGain);
}
}
energyPredictedBodyMassChange *= 30.4; // Convert to monthly
ind.PreviousWeight = ind.Weight;
ind.Weight += energyPredictedBodyMassChange;
ind.Weight = Math.Max(0.0, ind.Weight);
ind.Weight = Math.Min(ind.Weight, ind.StandardReferenceWeight * ind.BreedParams.MaximumSizeOfIndividual);
// Function to calculate approximate methane produced by animal, based on feed intake
// Function based on Freer spreadsheet
methaneProduced = 0.02 * ind.Intake * ((13 + 7.52 * energyMetabolic) + energyMetablicFromIntake / energyMaintenance * (23.7 - 3.36 * energyMetabolic)); // MJ per day
methaneProduced /= 55.28 * 1000; // grams per day
}
private void OnWFAnimalBreeding(object sender, EventArgs e)
{
RuminantHerd ruminantHerd = Resources.RuminantHerd();
List<Ruminant> herd = ruminantHerd.Herd.Where(a => a.BreedParams.Name == HerdName).ToList();
// get list of all individuals of breeding age and condition
// grouped by location
var breeders = from ind in herd
where
(ind.Gender == Sex.Male & ind.Age >= ind.BreedParams.MinimumAge1stMating) ^
(ind.Gender == Sex.Female &
ind.Age >= ind.BreedParams.MinimumAge1stMating &
ind.Weight >= (ind.BreedParams.MinimumSize1stMating * ind.StandardReferenceWeight)
)
group ind by ind.Location into grp
select grp;
// for each location where parts of this herd are located
foreach (var location in breeders)
{
// check for births of all pregnant females.
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast<RuminantFemale>().ToList())
{
if (female.BirthDue)
{
int numberOfNewborn = (female.CarryingTwins) ? 2 : 1;
for (int i = 0; i < numberOfNewborn; i++)
{
// Determine if the offspring died during pregancy from conception to after birth
// This is currently only performed at time of birth rather than monthly during pregnancy
// and so does not reflect changes in female intake etc after dead of foetus.
// this now occurs monthly at the ned of this breeding method.
//if (randomGenerator.RandNo > female.BreedParams.PrenatalMortality)
//{
object newCalf = null;
bool isMale = (randomGenerator.RandNo > 0.5);
if (isMale)
{
newCalf = new RuminantMale();
}
else
{
newCalf = new RuminantFemale();
}
Ruminant newCalfRuminant = newCalf as Ruminant;
newCalfRuminant.Age = 0;
newCalfRuminant.HerdName = female.HerdName;
newCalfRuminant.BreedParams = female.BreedParams;
newCalfRuminant.Gender = (isMale) ? Sex.Male : Sex.Female;
newCalfRuminant.ID = ruminantHerd.NextUniqueID;
newCalfRuminant.Location = female.Location;
newCalfRuminant.Mother = female;
// newCalfRuminant.Number = 1;
newCalfRuminant.SetUnweaned();
// calf weight from Freer
newCalfRuminant.Weight = female.BreedParams.SRWBirth * female.StandardReferenceWeight * (1 - 0.33 * (1 - female.Weight / female.StandardReferenceWeight));
newCalfRuminant.HighWeight = newCalfRuminant.Weight;
newCalfRuminant.SaleFlag = Common.HerdChangeReason.Born;
ruminantHerd.AddRuminant(newCalfRuminant);
// add to sucklings
female.SucklingOffspring.Add(newCalfRuminant);
//}
}
female.UpdateBirthDetails();
}
}
// Conception
// check if males and females of breeding condition are together
if (location.GroupBy(a => a.Gender).Count() == 2)
{
// servicing rate
int maleCount = location.Where(a => a.Gender == Sex.Male).Count();
int femaleCount = location.Where(a => a.Gender == Sex.Female).Count();
double matingsPossible = maleCount * location.FirstOrDefault().BreedParams.MaximumMaleMatingsPerDay * 30;
double maleLimiter = Math.Max(1.0, matingsPossible/ femaleCount);
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast<RuminantFemale>().ToList())
{
//TODO: ensure enough time since last calf
if (!female.IsPregnant & !female.IsLactating)
{
// calculate conception
double conceptionRate = ConceptionRate(female) * maleLimiter;
if (randomGenerator.RandNo <= conceptionRate)
{
female.UpdateConceptionDetails(randomGenerator.RandNo > female.BreedParams.TwinRate, conceptionRate);
}
}
}
}
// determine all foetus and newborn mortality.
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast<RuminantFemale>().ToList())
{
if (female.IsPregnant)
{
// calculate foetus and newborn mortality
// total mortality / gestation months to get monthly mortality
// TODO: check if need to be done before births to get last month mortality
if(randomGenerator.RandNo > female.BreedParams.PrenatalMortality/female.BreedParams.GestationLength)
{
female.OneOffspringDies();
}
}
}
}
}
private void OnWFAnimalBreeding(object sender, EventArgs e)
{
RuminantHerd ruminantHerd = Resources.RuminantHerd();
List <Ruminant> herd = ruminantHerd.Herd.Where(a => a.BreedParams.Name == HerdName).ToList();
// get list of all individuals of breeding age and condition
// grouped by location
var breeders = from ind in herd
where
(ind.Gender == Sex.Male & ind.Age >= ind.BreedParams.MinimumAge1stMating) ^
(ind.Gender == Sex.Female &
ind.Age >= ind.BreedParams.MinimumAge1stMating &
ind.Weight >= (ind.BreedParams.MinimumSize1stMating * ind.StandardReferenceWeight)
)
group ind by ind.Location into grp
select grp;
// for each location where parts of this herd are located
foreach (var location in breeders)
{
// check for births of all pregnant females.
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().ToList())
{
if (female.BirthDue)
{
int numberOfNewborn = (female.CarryingTwins) ? 2 : 1;
for (int i = 0; i < numberOfNewborn; i++)
{
// Determine if the offspring died during pregancy from conception to after birth
// This is currently only performed at time of birth rather than monthly during pregnancy
// and so does not reflect changes in female intake etc after dead of foetus.
// this now occurs monthly at the ned of this breeding method.
//if (randomGenerator.RandNo > female.BreedParams.PrenatalMortality)
//{
object newCalf = null;
bool isMale = (randomGenerator.RandNo > 0.5);
if (isMale)
{
newCalf = new RuminantMale();
}
else
{
newCalf = new RuminantFemale();
}
Ruminant newCalfRuminant = newCalf as Ruminant;
newCalfRuminant.Age = 0;
newCalfRuminant.HerdName = female.HerdName;
newCalfRuminant.BreedParams = female.BreedParams;
newCalfRuminant.Gender = (isMale) ? Sex.Male : Sex.Female;
newCalfRuminant.ID = ruminantHerd.NextUniqueID;
newCalfRuminant.Location = female.Location;
newCalfRuminant.Mother = female;
// newCalfRuminant.Number = 1;
newCalfRuminant.SetUnweaned();
// calf weight from Freer
newCalfRuminant.Weight = female.BreedParams.SRWBirth * female.StandardReferenceWeight * (1 - 0.33 * (1 - female.Weight / female.StandardReferenceWeight));
newCalfRuminant.HighWeight = newCalfRuminant.Weight;
newCalfRuminant.SaleFlag = Common.HerdChangeReason.Born;
ruminantHerd.AddRuminant(newCalfRuminant);
// add to sucklings
female.SucklingOffspring.Add(newCalfRuminant);
//}
}
female.UpdateBirthDetails();
}
}
// Conception
// check if males and females of breeding condition are together
if (location.GroupBy(a => a.Gender).Count() == 2)
{
// servicing rate
int maleCount = location.Where(a => a.Gender == Sex.Male).Count();
int femaleCount = location.Where(a => a.Gender == Sex.Female).Count();
double matingsPossible = maleCount * location.FirstOrDefault().BreedParams.MaximumMaleMatingsPerDay * 30;
double maleLimiter = Math.Max(1.0, matingsPossible / femaleCount);
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().ToList())
{
//TODO: ensure enough time since last calf
if (!female.IsPregnant & !female.IsLactating)
{
// calculate conception
double conceptionRate = ConceptionRate(female) * maleLimiter;
if (randomGenerator.RandNo <= conceptionRate)
{
female.UpdateConceptionDetails(randomGenerator.RandNo > female.BreedParams.TwinRate, conceptionRate);
}
}
}
}
// determine all foetus and newborn mortality.
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().ToList())
{
if (female.IsPregnant)
{
// calculate foetus and newborn mortality
// total mortality / gestation months to get monthly mortality
// TODO: check if need to be done before births to get last month mortality
if (randomGenerator.RandNo > female.BreedParams.PrenatalMortality / female.BreedParams.GestationLength)
{
female.OneOffspringDies();
}
}
}
}
}
/// <summary>
/// Create the individual ruminant animals using the Cohort parameterisations.
/// </summary>
/// <returns></returns>
public List<Ruminant> CreateIndividuals()
{
List<Ruminant> Individuals = new List<Ruminant>();
IModel parentNode = Apsim.Parent(this, typeof(IModel));
RuminantType parent = parentNode as RuminantType;
// get Ruminant Herd resource for unique ids
RuminantHerd ruminantHerd = Resources.RuminantHerd();
parent = this.Parent as RuminantType;
if (StartingNumber > 0)
{
//TODO: get random generator from global store with seed
Random rand = new Random();
for (int i = 1; i <= StartingNumber; i++)
{
object ruminantBase = null;
if(this.Gender == Sex.Male)
{
ruminantBase = new RuminantMale();
}
else
{
ruminantBase = new RuminantFemale();
}
Ruminant ruminant = ruminantBase as Ruminant;
ruminant.ID = ruminantHerd.NextUniqueID;
ruminant.BreedParams = parent;
ruminant.Breed = parent.Breed;
ruminant.HerdName = parent.Name;
ruminant.Gender = Gender;
ruminant.Age = StartingAge;
ruminant.SaleFlag = Common.HerdChangeReason.None;
if (Suckling) ruminant.SetUnweaned();
double u1 = rand.NextDouble();
double u2 = rand.NextDouble();
double randStdNormal = Math.Sqrt(-2.0 * Math.Log(u1)) *
Math.Sin(2.0 * Math.PI * u2);
ruminant.Weight = StartingWeight + StartingWeightSD * randStdNormal;
ruminant.PreviousWeight = ruminant.Weight;
if(this.Gender == Sex.Female)
{
RuminantFemale ruminantFemale = ruminantBase as RuminantFemale;
ruminantFemale.DryBreeder = true;
ruminantFemale.WeightAtConception = this.StartingWeight;
ruminantFemale.NumberOfBirths = 0;
}
Individuals.Add(ruminantBase as Ruminant);
}
}
return Individuals;
}
