private void Muster()
{
foreach (Ruminant ind in this.CurrentHerd(false))
{
// set new location ID
ind.Location = Pasture.Name;
this.SetStatusSuccess();
// 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>
/// A method to add the male attributes to the female attribute store at mating
/// </summary>
/// <param name="female">The female breeder successfully mated</param>
/// <param name="male">The mated male</param>
private void AddMalesAttributeDetails(RuminantFemale female, Ruminant male)
{
if (male != null)
{
foreach (var attribute in female.Attributes)
{
var maleAttribute = male.GetAttributeValue(attribute.Key);
if (maleAttribute != null)
{
if (attribute.Value.InheritanceStyle != maleAttribute.InheritanceStyle)
{
throw new ApsimXException(this, $"The inheritance style for attribute [{attribute.Key}] differs between the breeder and breeding male from the herd in [a={this.Name}]");
}
attribute.Value.storedMateValue = maleAttribute.storedValue;
}
else
{
attribute.Value.storedMateValue = null;
if (female.BreedParams.IsMandatoryAttribute(attribute.Key))
{
throw new ApsimXException(this, $"The attributes provided with the breeding male from the herd does not include the madatory attribute [{attribute.Key}] in [a={this.Name}]");
}
}
}
}
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="status">Change status</param>
/// <param name="female">Individual being reported</param>
/// <param name="dateTime">Current clock</param>
/// <param name="offspring">The offspring related to</param>
public ConceptionStatusChangedEventArgs(ConceptionStatus status, RuminantFemale female, DateTime dateTime, Ruminant offspring = null)
{
Status = status;
Female = female;
// Calculate conception date
switch (Status)
{
case ConceptionStatus.Conceived:
case ConceptionStatus.Failed:
case ConceptionStatus.Birth:
ConceptionDate = dateTime.AddMonths(-1 * Convert.ToInt32(female.Age - female.AgeAtLastConception, CultureInfo.InvariantCulture));
ConceptionDate = new DateTime(ConceptionDate.Year, ConceptionDate.Month, DateTime.DaysInMonth(ConceptionDate.Year, ConceptionDate.Month));
break;
case ConceptionStatus.Weaned:
if (offspring is null)
{
throw new ArgumentException("Code logice error: An offspring must be supplied in ConceptionStatusChangedEventArgs when status is Weaned");
}
ConceptionDate = dateTime.AddMonths(-1 * Convert.ToInt32(offspring.Age + female.BreedParams.GestationLength, CultureInfo.InvariantCulture));
ConceptionDate = new DateTime(ConceptionDate.Year, ConceptionDate.Month, DateTime.DaysInMonth(ConceptionDate.Year, ConceptionDate.Month));
break;
case ConceptionStatus.Unsuccessful:
case ConceptionStatus.NotMated:
case ConceptionStatus.NotReady:
ConceptionDate = dateTime;
break;
default:
break;
}
}
private void Move()
{
Status = ActivityStatus.NotNeeded;
// allow multiple filter groups for moving.
var filterGroups = FindAllChildren <RuminantGroup>();
foreach (RuminantGroup item in filterGroups)
{
foreach (Ruminant ind in item.Filter(CurrentHerd(false)))
{
// set new location ID
if (ind.Location != pastureName)
{
this.Status = ActivityStatus.Success;
ind.Location = pastureName;
// check if sucklings are to be moved with mother
if (MoveSucklings)
{
// if female
if (ind is RuminantFemale)
{
RuminantFemale female = ind as RuminantFemale;
// check if mother with sucklings
foreach (var suckling in female.SucklingOffspringList)
{
suckling.Location = pastureName;
}
}
}
}
}
}
}
/// <summary>
/// Set the milk production of the selected female given diet drymatter digesibility
/// </summary>
/// <param name="ind">Female individual</param>
/// <returns>energy of milk</returns>
private double CalculateMilkProduction(RuminantFemale ind)
{
double energyMetabolic = EnergyGross * (((ind.DietDryMatterDigestibility == 0)?50:ind.DietDryMatterDigestibility) / 100.0) * 0.81;
// Reference: SCA p.
double kl = ind.BreedParams.ELactationEfficiencyCoefficient * energyMetabolic / EnergyGross + ind.BreedParams.ELactationEfficiencyIntercept;
double milkTime = ind.DaysLactating;
double milkCurve = 0;
if (ind.SucklingOffspring.Count == 0 && ind.MilkingPerformed) // no suckling calf and milking has been performed
{
milkCurve = ind.BreedParams.MilkCurveNonSuckling;
}
else // suckling calf
{
milkCurve = ind.BreedParams.MilkCurveSuckling;
}
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
double energyMilk = milkProduction * 3.2 / kl;
// adjust last time step's energy balance
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));
// set milk production in lactating females for consumption.
ind.MilkProduction = milkProduction;
ind.MilkAmount = ind.MilkProduction * 30.4;
return(milkProduction * 3.2 / kl);
}
/// <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;
bool isConceptionReady = false;
if (female.Age >= female.BreedParams.MinimumAge1stMating && female.NumberOfBirths == 0)
{
isConceptionReady = true;
}
else
{
double currentIPI = female.BreedParams.InterParturitionIntervalIntercept * Math.Pow((female.Weight / female.StandardReferenceWeight), female.BreedParams.InterParturitionIntervalCoefficient) * 30.64;
// calculate inter-parturition interval
currentIPI = Math.Max(currentIPI, female.BreedParams.GestationLength * 30.4 + female.BreedParams.MinimumDaysBirthToConception); // 2nd param was 61
double ageNextConception = female.AgeAtLastConception + (currentIPI / 30.4);
isConceptionReady = (female.Age >= ageNextConception);
}
// if first mating and of age or suffcient time since last birth/conception
if (isConceptionReady)
{
// Get conception rate from conception model associated with the Ruminant Type parameters
if (female.BreedParams.ConceptionModel == null)
{
throw new ApsimXException(this, String.Format("No conception details were found for [r={0}]\nPlease add a conception component below the [r=RuminantType]", female.BreedParams.Name));
}
return(female.BreedParams.ConceptionModel.ConceptionRate(female));
}
return(rate / 100);
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="status">Change status</param>
/// <param name="female">Individual being reported</param>
/// <param name="dateTime">Current clock</param>
public ConceptionStatusChangedEventArgs(ConceptionStatus status, RuminantFemale female, DateTime dateTime)
{
Status = status;
Female = female;
// Calculate conception date
switch (Status)
{
case ConceptionStatus.Conceived:
case ConceptionStatus.Failed:
case ConceptionStatus.Birth:
case ConceptionStatus.Weaned:
ConceptionDate = dateTime.AddMonths(-1 * Convert.ToInt32(female.Age - female.AgeAtLastConception, CultureInfo.InvariantCulture));
ConceptionDate = new DateTime(ConceptionDate.Year, ConceptionDate.Month, DateTime.DaysInMonth(ConceptionDate.Year, ConceptionDate.Month));
break;
case ConceptionStatus.Unsuccessful:
case ConceptionStatus.NotMated:
case ConceptionStatus.NotReady:
ConceptionDate = dateTime;
break;
default:
break;
}
}
private void Muster()
{
Status = ActivityStatus.NotNeeded;
foreach (Ruminant ind in this.CurrentHerd(false))
{
// set new location ID
if (ind.Location != pastureName)
{
this.Status = ActivityStatus.Success;
}
ind.Location = pastureName;
// 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.SucklingOffspringList.Count > 0)
{
foreach (var suckling in female.SucklingOffspringList)
{
suckling.Location = pastureName;
}
}
}
}
}
}
/// <summary>
/// A method to add the available male attributes to the female store at mating using attributes supplied by controlled mating
/// </summary>
/// <param name="female">The female breeder successfully mated</param>
/// <param name="maleAttributes">a list of available male attributes setters</param>
/// <param name="newMale">Create new instance (T) or use last created (F)</param>
private void AddMalesAttributeDetails(RuminantFemale female, List <ISetAttribute> maleAttributes, bool newMale = true)
{
foreach (var attribute in female.Attributes.Items)
{
var maleAttribute = maleAttributes.FirstOrDefault(a => a.AttributeName == attribute.Key);
SetFemaleMateAttributes(female, attribute, maleAttribute?.GetAttribute(newMale));
}
}
/// <summary>
/// A method to add the available male attributes to the female store at mating using attributes supplied by controlled mating
/// </summary>
/// <param name="female">The female breeder successfully mated</param>
/// <param name="maleAttributes">a list of available male attributes setters</param>
/// <param name="newMale">Create new instance (T) or use last created (F)</param>
private void AddMalesAttributeDetails(RuminantFemale female, List <SetAttributeWithValue> maleAttributes, bool newMale = true)
{
foreach (var attribute in female.Attributes.Items)
{
var maleAttribute = maleAttributes.Where(a => a.AttributeName == attribute.Key).FirstOrDefault();
if (maleAttribute != null)
{
var calculatedAttribute = maleAttribute.GetAttribute(newMale);
if (attribute.Value != null && attribute.Value.InheritanceStyle != calculatedAttribute.InheritanceStyle)
{
throw new ApsimXException(this, $"The inheritance style for attribute [{attribute.Key}] differs between the breeder and attributes supplied by controlled mating in [a={this.Name}]");
}
if (attribute.Value != null)
{
attribute.Value.StoredMateValue = calculatedAttribute.StoredValue;
}
}
else
{
// if there are random herd attributes available
if (randomHerdAttributes.Any())
{
if (!randomHerdAttributes.TryGetValue(attribute.Key, out IIndividualAttribute randomAttribute))
{
throw new ApsimXException(this, $"Unable to assign mandatory attribute from random herd selection for [a={this.Name}] and madatory attribute [{attribute.Key}]");
}
else
{
if (attribute.Value != null && attribute.Value.InheritanceStyle != randomAttribute.InheritanceStyle)
{
throw new ApsimXException(this, $"The inheritance style for attribute [{attribute.Key}] differs between the breeder and attributes supplied by random herd selection in [a={this.Name}]");
}
if (attribute.Value != null)
{
attribute.Value.StoredMateValue = randomAttribute.StoredValue;
}
}
}
else
{
if (attribute.Value != null)
{
attribute.Value.StoredMateValue = null;
}
if (female.BreedParams.IsMandatoryAttribute(attribute.Key))
{
throw new ApsimXException(this, $"The sire attributes provided for [a={this.Name}] do not include the madatory attribute [{attribute.Key}]");
}
}
}
}
}
/// <summary>
/// A method to add the male attributes to the female attribute store at mating
/// </summary>
/// <param name="female">The female breeder successfully mated</param>
/// <param name="male">The mated male</param>
private void AddMalesAttributeDetails(RuminantFemale female, Ruminant male)
{
if (male is null)
{
return;
}
foreach (var attribute in female.Attributes.Items)
{
var maleAttribute = male.Attributes.GetValue(attribute.Key);
SetFemaleMateAttributes(female, attribute, maleAttribute);
}
}
/// <summary>
/// Calculate conception rate for a female
/// </summary>
/// <param name="female">Female to calculate conception rate for</param>
/// <param name="status">Returns conception status</param>
/// <returns></returns>
private double ConceptionRate(RuminantFemale female, out Reporting.ConceptionStatus status)
{
bool isConceptionReady = false;
status = Reporting.ConceptionStatus.NotAvailable;
if (!female.IsPregnant)
{
status = Reporting.ConceptionStatus.NotReady;
if (female.Age >= female.BreedParams.MinimumAge1stMating && female.NumberOfBirths == 0)
{
isConceptionReady = true;
}
else
{
// add one to age to ensure that conception is due this timestep
if ((female.Age + 1 - female.AgeAtLastBirth) * 30.4 > female.BreedParams.MinimumDaysBirthToConception)
{
// only based upon period since birth
isConceptionReady = true;
// DEVELOPMENT NOTE:
// The following IPI calculation and check present in NABSA has been removed for testing
// It is assumed that the individual based model with weight influences will handle the old IPI calculation
// These parameters can now be removed form the RuminantType list
//double currentIPI = female.BreedParams.InterParturitionIntervalIntercept * Math.Pow(female.ProportionOfNormalisedWeight, female.BreedParams.InterParturitionIntervalCoefficient) * 30.4;
//double ageNextConception = female.AgeAtLastConception + (currentIPI / 30.4);
//isConceptionReady = (female.Age+1 >= ageNextConception);
}
}
}
// if first mating and of age or sufficient time since last birth
if (isConceptionReady)
{
status = Reporting.ConceptionStatus.Unsuccessful;
// Get conception rate from conception model associated with the Ruminant Type parameters
if (female.BreedParams.ConceptionModel == null)
{
throw new ApsimXException(this, String.Format("No conception details were found for [r={0}]\r\nPlease add a conception component below the [r=RuminantType]", female.BreedParams.Name));
}
return(female.BreedParams.ConceptionModel.ConceptionRate(female));
}
return(0);
}
private void SetFemaleMateAttributes(RuminantFemale female, KeyValuePair <string, IIndividualAttribute> femaleAttribute, IIndividualAttribute maleAttribute)
{
if (maleAttribute != null)
{
if (femaleAttribute.Value != null && femaleAttribute.Value.InheritanceStyle != maleAttribute.InheritanceStyle)
{
string errorMsg;
if (useControlledMating)
{
errorMsg = $"provided from [a={controlledMating.NameWithParent}]";
}
else
{
errorMsg = $"from the herd in [a={NameWithParent}]";
}
throw new ApsimXException(this, $"The inheritance style for attribute [{femaleAttribute.Key}] differs between the breeder [{femaleAttribute.Value.InheritanceStyle}] and breeding male [{maleAttribute.InheritanceStyle}] {errorMsg}");
}
if (femaleAttribute.Value != null)
{
femaleAttribute.Value.StoredMateValue = maleAttribute.StoredValue;
}
}
else
{
if (femaleAttribute.Value != null)
{
femaleAttribute.Value.StoredMateValue = null;
}
if (female.BreedParams.IsMandatoryAttribute(femaleAttribute.Key))
{
string errorMsg;
if (useControlledMating)
{
errorMsg = $"Cannot locate the madatory attribute [{femaleAttribute.Key}] in [a={controlledMating.NameWithParent}]{Environment.NewLine}Add a [SetAttribute] component below the [a=RuminantnActivityControlledMating]";
}
else
{
errorMsg = $"Cannot locate the madatory attribute [{femaleAttribute.Key}] in from the breeding male selected from the herd in [a={NameWithParent}]{Environment.NewLine}Ensure all sires in initial herd or purchased provide the appropriate [SetAttribute] component";
}
throw new ApsimXException(this, errorMsg);
}
}
}
/// <summary>
/// Set the milk production of the selected female given diet drymatter digesibility
/// </summary>
/// <param name="ind">Female individual</param>
/// <returns>energy of milk</returns>
private double CalculateMilkProduction(RuminantFemale ind)
{
ind.MilkMilkedThisTimeStep = 0;
ind.MilkSuckledThisTimeStep = 0;
double energyMetabolic = EnergyGross * (((ind.DietDryMatterDigestibility == 0)?50:ind.DietDryMatterDigestibility) / 100.0) * 0.81;
// Reference: SCA p.
double kl = ind.BreedParams.ELactationEfficiencyCoefficient * energyMetabolic / EnergyGross + ind.BreedParams.ELactationEfficiencyIntercept;
double milkTime = ind.DaysLactating;
double milkCurve;
// determine milk production curve to use
// if milking is taking place use the non-suckling curve for duration of lactation
// otherwise use the suckling curve where there is a larger drop off in milk production
if (ind.MilkingPerformed)
{
milkCurve = ind.BreedParams.MilkCurveNonSuckling;
}
else // no milking
{
milkCurve = ind.BreedParams.MilkCurveSuckling;
}
ind.MilkProductionPotential = 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));
ind.MilkProductionPotential = Math.Max(ind.MilkProductionPotential, 0.0);
// Reference: Potential milk prodn, 3.2 MJ/kg milk - Jouven et al 2008
double energyMilk = ind.MilkProductionPotential * 3.2 / kl;
// adjust last time step's energy balance
double adjustedEnergyBalance = ind.EnergyBalance;
if (adjustedEnergyBalance < (-0.5936 / 0.322 * energyMilk))
{
adjustedEnergyBalance = (-0.5936 / 0.322 * energyMilk);
}
// set milk production in lactating females for consumption.
ind.MilkProduction = Math.Max(0.0, ind.MilkProductionPotential * (0.5936 + 0.322 * adjustedEnergyBalance / energyMilk));
ind.MilkCurrentlyAvailable = ind.MilkProduction * 30.4;
// returns the energy required for milk production
return(ind.MilkProduction * 3.2 / kl);
}
/// <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);
}
/// <summary>
/// A method to add the available male attributes to the female store at mating using attributes supplied by controlled mating
/// </summary>
/// <param name="female">The female breeder successfully mated</param>
/// <param name="maleAttributes">a list of available male attributes setters</param>
private void AddMalesAttributeDetails(RuminantFemale female, List <SetAttributeWithValue> maleAttributes)
{
foreach (var attribute in female.Attributes)
{
var maleAttribute = maleAttributes.Where(a => a.AttributeName == attribute.Key).FirstOrDefault();
if (maleAttribute != null)
{
var calculatedAttribute = maleAttribute.GetRandomSetAttribute();
if (attribute.Value.InheritanceStyle != calculatedAttribute.InheritanceStyle)
{
throw new ApsimXException(this, $"The inheritance style for attribute [{attribute.Key}] differs between the breeder and attributes supplied by controlled mating in [a={this.Name}]");
}
attribute.Value.storedMateValue = calculatedAttribute.storedValue;
}
else
{
attribute.Value.storedMateValue = null;
if (female.BreedParams.IsMandatoryAttribute(attribute.Key))
{
throw new ApsimXException(this, $"The sire attributes provided for [a={this.Name}] do not include the madatory attribute [{attribute.Key}]");
}
}
}
}
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;
bool isConceptionReady = false;
if (female.Age >= female.BreedParams.MinimumAge1stMating && female.NumberOfBirths == 0)
{
isConceptionReady = true;
}
else
{
double IPIcurrent = female.BreedParams.InterParturitionIntervalIntercept * Math.Pow((female.Weight / female.StandardReferenceWeight), female.BreedParams.InterParturitionIntervalCoefficient) * 30.64;
// calculate inter-parturition interval
IPIcurrent = Math.Max(IPIcurrent, female.BreedParams.GestationLength * 30.4 + female.BreedParams.MinimumDaysBirthToConception); // 2nd param was 61
double ageNextConception = female.AgeAtLastConception + (IPIcurrent / 30.4);
isConceptionReady = (female.Age >= ageNextConception);
}
// if first mating and of age or suffcient time since last birth/conception
if (isConceptionReady)
{
// get advanced conception rate if available otherwise use defaults.
if (female.BreedParams.AdvancedConceptionParameters != null)
{
// generalised curve
switch (female.NumberOfBirths)
{
case 0:
// first mating
if (female.BreedParams.MinimumAge1stMating >= 24)
{
// 1st mated at 24 months or older
rate = female.BreedParams.AdvancedConceptionParameters.ConceptionRateAsymptote[1] / (1 + Math.Exp(female.BreedParams.AdvancedConceptionParameters.ConceptionRateCoefficent[1] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.AdvancedConceptionParameters.ConceptionRateIntercept[1]));
}
else if (female.BreedParams.MinimumAge1stMating >= 12)
{
// 1st mated between 12 and 24 months
double rate24 = female.BreedParams.AdvancedConceptionParameters.ConceptionRateAsymptote[1] / (1 + Math.Exp(female.BreedParams.AdvancedConceptionParameters.ConceptionRateCoefficent[1] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.AdvancedConceptionParameters.ConceptionRateIntercept[1]));
double rate12 = female.BreedParams.AdvancedConceptionParameters.ConceptionRateAsymptote[0] / (1 + Math.Exp(female.BreedParams.AdvancedConceptionParameters.ConceptionRateCoefficent[0] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.AdvancedConceptionParameters.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
}
else
{
// first mating < 12 months old
rate = female.BreedParams.AdvancedConceptionParameters.ConceptionRateAsymptote[0] / (1 + Math.Exp(female.BreedParams.AdvancedConceptionParameters.ConceptionRateCoefficent[0] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.AdvancedConceptionParameters.ConceptionRateIntercept[0]));
}
break;
case 1:
// second offspring mother
rate = female.BreedParams.AdvancedConceptionParameters.ConceptionRateAsymptote[2] / (1 + Math.Exp(female.BreedParams.AdvancedConceptionParameters.ConceptionRateCoefficent[2] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.AdvancedConceptionParameters.ConceptionRateIntercept[2]));
break;
default:
// females who have had more than two births (twins should count as one birth)
if (female.WeightAtConception > female.BreedParams.CriticalCowWeight * female.StandardReferenceWeight)
{
rate = female.BreedParams.AdvancedConceptionParameters.ConceptionRateAsymptote[3] / (1 + Math.Exp(female.BreedParams.AdvancedConceptionParameters.ConceptionRateCoefficent[3] * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.AdvancedConceptionParameters.ConceptionRateIntercept[3]));
}
break;
}
}
else
{
// use default values
rate = female.BreedParams.ConceptionRateAsymptote / (1 + Math.Exp(female.BreedParams.ConceptionRateCoefficent * female.WeightAtConception / female.StandardReferenceWeight + female.BreedParams.ConceptionRateIntercept));
}
}
return(rate / 100);
}
/// <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)
{
double intakeDaily = ind.Intake / 30.4;
double potentialIntakeDaily = ind.PotentialIntake / 30.4;
// 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 * intakeDaily;
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)
{
// calculate engergy and growth from milk intake
// old code
// dum = potential milk intake daily
// dumshort = potential intake. check that it isnt monthly
// Below now uses actual intake received rather than assume all potential intake is eaten
double kml = 1;
double kgl = 1;
if ((ind.Intake + ind.MilkIntake) > 0)
{
// average energy efficiency for maintenance
kml = ((ind.MilkIntake * 0.7) + (intakeDaily * km)) / (ind.MilkIntake + intakeDaily);
// average energy efficiency for growth
kgl = ((ind.MilkIntake * 0.7) + (intakeDaily * kg)) / (ind.MilkIntake + intakeDaily);
}
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.AgeZeroCorrected);
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
{
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 * intakeDaily * ((13 + 7.52 * energyMetabolic) + energyMetablicFromIntake / energyMaintenance * (23.7 - 3.36 * energyMetabolic)); // MJ per day
methaneProduced /= 55.28 * 1000; // grams per day
}
private void OnCLEMAnimalManage(object sender, EventArgs e)
{
// purchase details only on timer
if (TimingOK)
{
this.Status = ActivityStatus.NotNeeded;
// remove any old potential sales from list as these will be updated here
Resources.RuminantHerd().PurchaseIndividuals.RemoveAll(a => a.Breed == this.PredictedHerdBreed && a.SaleFlag == HerdChangeReason.TradePurchase);
foreach (RuminantTypeCohort purchasetype in this.Children.Where(a => a.GetType() == typeof(RuminantTypeCohort)).Cast <RuminantTypeCohort>())
{
double number = purchasetype.Number;
if (numberToStock != null && foodStore != null)
{
//NOTE: ensure calculation method in relationship is fixed values
number = Convert.ToInt32(numberToStock.SolveY(foodStore.TonnesPerHectare), CultureInfo.InvariantCulture);
}
for (int i = 0; i < number; i++)
{
object ruminantBase = null;
double u1 = RandomNumberGenerator.Generator.NextDouble();
double u2 = RandomNumberGenerator.Generator.NextDouble();
double randStdNormal = Math.Sqrt(-2.0 * Math.Log(u1)) *
Math.Sin(2.0 * Math.PI * u2);
double weight = purchasetype.Weight + purchasetype.WeightSD * randStdNormal;
if (purchasetype.Gender == Sex.Male)
{
ruminantBase = new RuminantMale(purchasetype.Age, purchasetype.Gender, weight, herdToUse);
}
else
{
ruminantBase = new RuminantFemale(purchasetype.Age, purchasetype.Gender, weight, herdToUse);
}
Ruminant ruminant = ruminantBase as Ruminant;
ruminant.ID = 0;
ruminant.Breed = this.PredictedHerdBreed;
ruminant.HerdName = this.PredictedHerdName;
ruminant.PurchaseAge = purchasetype.Age;
ruminant.SaleFlag = HerdChangeReason.TradePurchase;
ruminant.Location = grazeStore;
ruminant.PreviousWeight = ruminant.Weight;
switch (purchasetype.Gender)
{
case Sex.Male:
RuminantMale ruminantMale = ruminantBase as RuminantMale;
ruminantMale.BreedingSire = false;
break;
case Sex.Female:
RuminantFemale ruminantFemale = ruminantBase as RuminantFemale;
ruminantFemale.DryBreeder = true;
ruminantFemale.WeightAtConception = ruminant.Weight;
ruminantFemale.NumberOfBirths = 0;
break;
default:
break;
}
Resources.RuminantHerd().PurchaseIndividuals.Add(ruminantBase as Ruminant);
this.Status = ActivityStatus.Success;
}
}
}
// sale details any timestep when conditions are met.
foreach (Ruminant ind in this.CurrentHerd(true))
{
if (ind.Age - ind.PurchaseAge >= MinMonthsKept)
{
ind.SaleFlag = HerdChangeReason.TradeSale;
this.Status = ActivityStatus.Success;
}
if (TradeWeight > 0 && ind.Weight >= TradeWeight)
{
ind.SaleFlag = HerdChangeReason.TradeSale;
this.Status = ActivityStatus.Success;
}
}
}
private void OnCLEMAnimalManage(object sender, EventArgs e)
{
RuminantHerd ruminantHerd = Resources.RuminantHerd();
// remove only the individuals that are affected by this activity.
// these are old purchases that were not made. This list will be regenerated in this method.
ruminantHerd.PurchaseIndividuals.RemoveAll(a => a.Breed == this.PredictedHerdBreed);
List <Ruminant> herd = this.CurrentHerd(true);
// 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.
// SellFemalesLikeMales will grow out excess heifers until age/weight rather than sell immediately.
if (this.TimingOK || ContinuousMaleSales)
{
foreach (var ind in herd.Where(a => a.Weaned && (SellFemalesLikeMales ? true : (a.Gender == Sex.Male)) && (a.Age >= MaleSellingAge || a.Weight >= MaleSellingWeight)))
{
bool sell = true;
if (ind.GetType() == typeof(RuminantMale))
{
// don't sell breeding sires.
sell = !((ind as RuminantMale).BreedingSire);
}
else
{
// only sell females that were marked as excess
sell = ind.Tags.Contains("GrowHeifer");
}
if (sell)
{
ind.SaleFlag = HerdChangeReason.AgeWeightSale;
}
}
}
// if management month
if (this.TimingOK)
{
// ensure pasture limits are ok before purchases
bool sufficientFood = true;
if (foodStore != null)
{
sufficientFood = (foodStore.TonnesPerHectare * 1000) >= MinimumPastureBeforeRestock;
}
// 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 = HerdChangeReason.MaxAgeSale;
// ensure females are not pregnant and add warning if pregnant old females found.
if (ind.Gender == Sex.Female && (ind as RuminantFemale).IsPregnant)
{
string warning = "Some females sold at maximum age in [a=" + this.Name + "] were pregnant.\nConsider changing the MaximumBreederAge in [a=RuminantActivityManage] or ensure [r=RuminantType.MaxAgeMating] is less than or equal to the MaximumBreederAge to avoid selling pregnant individuals.";
if (!Warnings.Exists(warning))
{
Warnings.Add(warning);
Summary.WriteWarning(this, warning);
}
}
}
// MALES
// check for breeder bulls after sale of old individuals and buy/sell
int numberMaleSiresInHerd = herd.Where(a => a.Gender == Sex.Male && a.SaleFlag == HerdChangeReason.None).Cast <RuminantMale>().Where(a => a.BreedingSire).Count();
// Number of females
int numberFemaleBreedingInHerd = herd.Where(a => a.Gender == Sex.Female && a.Age >= a.BreedParams.MinimumAge1stMating && a.SaleFlag == HerdChangeReason.None).Count();
int numberFemaleTotalInHerd = herd.Where(a => a.Gender == Sex.Female && a.SaleFlag == HerdChangeReason.None).Count();
// these are females that will exceed max age and be sold in next 12 months
int numberFemaleOldInHerd = herd.Where(a => a.Gender == Sex.Female && (a.Age + 12 >= MaximumBreederAge) && a.SaleFlag == HerdChangeReason.None).Count();
// defined heifers here as weaned and will be a breeder in the next year
int numberFemaleHeifersInHerd = herd.Where(a => a.Gender == Sex.Female && a.Weaned && ((a.Age - a.BreedParams.MinimumAge1stMating < 0) && (a.Age - a.BreedParams.MinimumAge1stMating > -12)) && a.SaleFlag == HerdChangeReason.None).Count();
if (numberMaleSiresInHerd > SiresKept)
{
// sell bulls
// What rule? oldest first as they may be lost soonest?
int numberToRemove = numberMaleSiresInHerd - SiresKept;
if (numberToRemove > 0)
{
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 = HerdChangeReason.ExcessBullSale;
numberToRemove--;
if (numberToRemove == 0)
{
break;
}
}
}
}
else if (numberMaleSiresInHerd < SiresKept)
{
if ((foodStore == null) || (sufficientFood))
{
if (AllowSireReplacement)
{
// 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 == HerdChangeReason.AgeWeightSale).OrderByDescending(a => a.Weight))
{
male.SaleFlag = HerdChangeReason.None;
male.BreedingSire = true;
numberMaleSiresInHerd++;
if (numberMaleSiresInHerd >= SiresKept)
{
break;
}
}
// if still insufficent, look into current herd for replacement
// remaining males assumed to be too small, so await next time-step
}
// if still insufficient buy bulls.
if (numberMaleSiresInHerd < SiresKept && (MaximumSiresPerPurchase > 0))
{
// limit by breeders as proportion of max breeders so we don't spend alot on sires when building the herd and females more valuable
double propOfBreeders = (double)numberFemaleBreedingInHerd / (double)MaximumBreedersKept;
propOfBreeders = 1;
int sires = Convert.ToInt32(Math.Ceiling(Math.Ceiling(SiresKept * propOfBreeders)));
int numberToBuy = Math.Min(MaximumSiresPerPurchase, Math.Max(0, sires - numberMaleSiresInHerd));
for (int i = 0; i < numberToBuy; i++)
{
if (i < MaximumSiresPerPurchase)
{
RuminantMale newbull = new RuminantMale(48, Sex.Male, 450, breedParams)
{
Location = grazeStore,
Breed = this.PredictedHerdBreed,
HerdName = this.PredictedHerdName,
BreedingSire = true,
Gender = Sex.Male,
ID = 0, // Next unique ide will be assigned when added
PreviousWeight = 450,
SaleFlag = HerdChangeReason.SirePurchase
};
// add to purchase request list and await purchase in Buy/Sell
ruminantHerd.PurchaseIndividuals.Add(newbull);
}
}
}
}
}
// FEMALES
// Breeding herd sold as heifers only, purchased as breeders (>= minAge1stMating)
int excessBreeders = 0;
// get the mortality rate for the herd if available or assume zero
double mortalityRate = breedParams.MortalityBase;
// shortfall between actual and desired numbers of breeders (-ve for shortfall)
excessBreeders = numberFemaleBreedingInHerd - MaximumBreedersKept;
// IAT-NABSA removes adjusts to account for the old animals that will be sold in the next year
// This is not required in CLEM as they have been sold in this method, and it wont be until this method is called again that the next lot are sold.
// Like IAT-NABSA we will account for mortality losses in the next year in our breeder purchases
// Account for whole individuals only.
int numberDyingInNextYear = Convert.ToInt32(Math.Floor(numberFemaleBreedingInHerd * mortalityRate), CultureInfo.InvariantCulture);
// adjust for future mortality
excessBreeders -= numberDyingInNextYear;
// account for heifers already in the herd
// These are the next cohort that will become breeders in the next 12 months (before this method is called again)
excessBreeders += numberFemaleHeifersInHerd;
if (excessBreeders > 0) // surplus heifers to sell
{
foreach (var female in herd.Where(a => a.Gender == Sex.Female && (a as RuminantFemale).IsHeifer).Take(excessBreeders))
{
// if sell like males tag for grow out otherwise mark for sale
if (SellFemalesLikeMales)
{
if (!female.Tags.Contains("GrowHeifer"))
{
female.Tags.Add("GrowHeifer");
}
}
else
{
// tag for sale.
female.SaleFlag = HerdChangeReason.ExcessHeiferSale;
}
excessBreeders--;
if (excessBreeders == 0)
{
break;
}
}
}
else if (excessBreeders < 0) // shortfall heifers to buy
{
double minBreedAge = breedParams.MinimumAge1stMating;
excessBreeders *= -1;
if ((foodStore == null) || (sufficientFood))
{
// remove grow out heifers from grow out herd to replace breeders
if (SellFemalesLikeMales)
{
foreach (Ruminant female in herd.Where(a => a.Tags.Contains("GrowHeifer")).OrderByDescending(a => a.Age))
{
female.Tags.Remove("GrowHeifer");
excessBreeders--;
if (excessBreeders == 0)
{
break;
}
}
}
// 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 == HerdChangeReason.AgeWeightSale || a.SaleFlag == HerdChangeReason.ExcessHeiferSale)).OrderByDescending(a => a.Age))
{
female.SaleFlag = HerdChangeReason.None;
excessBreeders--;
if (excessBreeders == 0)
{
break;
}
}
// if still insufficient buy breeders.
if (excessBreeders > 0 && (MaximumProportionBreedersPerPurchase > 0))
{
int ageOfBreeder = 0;
// IAT-NABSA had buy mortality base% more to account for deaths before these individuals grow to breeding age
// These individuals are already of breeding age so we will ignore this in CLEM
// minimum of (max kept x prop in single purchase) and (the number needed + annual mortality)
int numberToBuy = Math.Min(excessBreeders, Convert.ToInt32(Math.Ceiling(MaximumProportionBreedersPerPurchase * MaximumBreedersKept), CultureInfo.InvariantCulture));
int numberPerPurchaseCohort = Convert.ToInt32(Math.Ceiling(numberToBuy / Convert.ToDouble(NumberOfBreederPurchaseAgeClasses, CultureInfo.InvariantCulture)), CultureInfo.InvariantCulture);
int numberBought = 0;
while (numberBought < numberToBuy)
{
int breederClass = Convert.ToInt32(numberBought / numberPerPurchaseCohort, CultureInfo.InvariantCulture);
ageOfBreeder = Convert.ToInt32(minBreedAge + (breederClass * 12), CultureInfo.InvariantCulture);
RuminantFemale newBreeder = new RuminantFemale(ageOfBreeder, Sex.Female, 0, breedParams)
{
Location = grazeStore,
Breed = this.PredictedHerdBreed,
HerdName = this.PredictedHerdName,
BreedParams = breedParams,
Gender = Sex.Female,
ID = 0,
SaleFlag = HerdChangeReason.BreederPurchase
};
// weight will be set to normalised weight as it was assigned 0 at initialisation
newBreeder.PreviousWeight = newBreeder.Weight;
// this individual must be weaned to be permitted to start breeding.
newBreeder.Wean(false, "Initial");
// add to purchase request list and await purchase in Buy/Sell
ruminantHerd.PurchaseIndividuals.Add(newBreeder);
numberBought++;
}
}
}
}
// Breeders themselves don't get sold. Trading is with Heifers
// Breeders can be sold in seasonal and ENSO destocking.
// 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
}
}
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;
}
private void OnCLEMAnimalBreeding(object sender, EventArgs e)
{
List <Ruminant> herd = CurrentHerd(true);
int aDay = Clock.Today.Year;
// get list of all individuals of breeding age and condition
// grouped by location
var breeders = from ind in herd
where ind.IsBreedingCondition
group ind by ind.Location into grp
select grp;
// calculate labour and finance limitations if needed when doing AI
int breedersCount = breeders.Count();
int numberPossible = breedersCount;
int numberServiced = 1;
double limiter = 1;
if (UseAI && TimingOK)
{
// attempt to get required resources
List <ResourceRequest> resourcesneeded = GetResourcesNeededForActivityLocal();
CheckResources(resourcesneeded, Guid.NewGuid());
bool tookRequestedResources = TakeResources(resourcesneeded, true);
// get all shortfalls
if (tookRequestedResources && (ResourceRequestList != null))
{
//TODO: fix this to account for perHead payments and labour and not fixed expenses
double amountCashNeeded = resourcesneeded.Where(a => a.ResourceType == typeof(Finance)).Sum(a => a.Required);
double amountCashProvided = resourcesneeded.Where(a => a.ResourceType == typeof(Finance)).Sum(a => a.Provided);
double amountLabourNeeded = resourcesneeded.Where(a => a.ResourceType == typeof(Labour)).Sum(a => a.Required);
double amountLabourProvided = resourcesneeded.Where(a => a.ResourceType == typeof(Labour)).Sum(a => a.Provided);
double cashlimit = 1;
if (amountCashNeeded > 0)
{
cashlimit = amountCashProvided == 0 ? 0 : amountCashNeeded / amountCashProvided;
}
double labourlimit = 1;
if (amountLabourNeeded > 0)
{
labourlimit = amountLabourProvided == 0 ? 0 : amountLabourNeeded / amountLabourProvided;
}
limiter = Math.Min(cashlimit, labourlimit);
// TODO: determine if fixed payments were not possible
// TODO: determine limits by insufficient labour or cash for per head payments
}
// report that this activity was performed as it does not use base GetResourcesRequired
this.TriggerOnActivityPerformed();
}
if (!UseAI)
{
// report that this activity was performed as it does not use base GetResourcesRequired
this.TriggerOnActivityPerformed();
this.Status = ActivityStatus.NotNeeded;
}
// for each location where parts of this herd are located
foreach (var location in breeders)
{
// determine all fetus and newborn mortality of all pregnant females.
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().Where(a => a.IsPregnant).ToList())
{
// calculate fetus and newborn mortality
// total mortality / (gestation months + 1) to get monthly mortality
// done here before births to account for post birth motality as well..
// IsPregnant status does not change until births occur in next section so will include mortality in month of birth
// needs to be caclulated for each offspring carried.
for (int i = 0; i < female.CarryingCount; i++)
{
if (RandomNumberGenerator.Generator.NextDouble() < (female.BreedParams.PrenatalMortality / (female.BreedParams.GestationLength + 1)))
{
female.OneOffspringDies();
if (female.NumberOfOffspring == 0)
{
// report conception status changed when last multiple birth dies.
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(Reporting.ConceptionStatus.Failed, female, Clock.Today));
}
}
}
}
// check for births of all pregnant females.
int month = Clock.Today.Month;
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().ToList())
{
if (female.BirthDue)
{
int numberOfNewborn = female.CarryingCount;
for (int i = 0; i < numberOfNewborn; i++)
{
// Foetal mortality is now performed each timestep at base of this method
object newCalf = null;
bool isMale = (RandomNumberGenerator.Generator.NextDouble() <= female.BreedParams.ProportionOffspringMale);
double weight = female.BreedParams.SRWBirth * female.StandardReferenceWeight * (1 - 0.33 * (1 - female.Weight / female.StandardReferenceWeight));
if (isMale)
{
newCalf = new RuminantMale(0, Sex.Male, weight, female.BreedParams);
}
else
{
newCalf = new RuminantFemale(0, Sex.Female, weight, female.BreedParams);
}
Ruminant newCalfRuminant = newCalf as Ruminant;
newCalfRuminant.HerdName = female.HerdName;
newCalfRuminant.Breed = female.BreedParams.Breed;
newCalfRuminant.ID = Resources.RuminantHerd().NextUniqueID;
newCalfRuminant.Location = female.Location;
newCalfRuminant.Mother = female;
newCalfRuminant.Number = 1;
newCalfRuminant.SetUnweaned();
// calf weight from Freer
newCalfRuminant.PreviousWeight = newCalfRuminant.Weight;
newCalfRuminant.SaleFlag = HerdChangeReason.Born;
Resources.RuminantHerd().AddRuminant(newCalfRuminant, this);
// add to sucklings
female.SucklingOffspringList.Add(newCalfRuminant);
// this now reports for each individual born not a birth event as individual wean events are reported
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(Reporting.ConceptionStatus.Birth, female, Clock.Today));
}
female.UpdateBirthDetails();
this.Status = ActivityStatus.Success;
}
}
numberPossible = -1;
if (!UseAI)
{
numberPossible = 0;
// uncontrolled conception
if (location.GroupBy(a => a.Gender).Count() == 2)
{
int maleCount = location.Where(a => a.Gender == Sex.Male).Count();
int femaleCount = location.Where(a => a.Gender == Sex.Female).Count();
numberPossible = Convert.ToInt32(Math.Ceiling(maleCount * location.FirstOrDefault().BreedParams.MaximumMaleMatingsPerDay * 30), CultureInfo.InvariantCulture);
}
}
else
{
// controlled mating (AI)
if (this.TimingOK)
{
numberPossible = Convert.ToInt32(limiter * location.Where(a => a.Gender == Sex.Female).Count(), CultureInfo.InvariantCulture);
}
}
numberServiced = 1;
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().Where(a => !a.IsPregnant & a.Age <= a.BreedParams.MaximumAgeMating).ToList())
{
Reporting.ConceptionStatus status = Reporting.ConceptionStatus.NotMated;
if (numberServiced <= numberPossible)
{
// calculate conception
double conceptionRate = ConceptionRate(female, out status);
if (conceptionRate > 0)
{
if (RandomNumberGenerator.Generator.NextDouble() <= conceptionRate)
{
female.UpdateConceptionDetails(female.CalulateNumberOfOffspringThisPregnancy(), conceptionRate, 0);
status = Reporting.ConceptionStatus.Conceived;
}
}
numberServiced++;
this.Status = ActivityStatus.Success;
}
// report change in breeding status
// do not report for -1 (controlled mating outside timing)
if (numberPossible >= 0 && status != Reporting.ConceptionStatus.NotAvailable)
{
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(status, female, Clock.Today));
}
}
// report a natural mating locations for transparency via a message
if (this.Status == ActivityStatus.Success && !UseAI)
{
string warning = "Natural (uncontrolled) mating ocurred in [r=" + location.Key + "]";
if (!Warnings.Exists(warning))
{
Warnings.Add(warning);
Summary.WriteMessage(this, warning);
}
}
}
}
private void OnCLEMAnimalBreeding(object sender, EventArgs e)
{
this.Status = ActivityStatus.NotNeeded;
NumberConceived = 0;
// get list of all pregnant females
List <RuminantFemale> pregnantherd = CurrentHerd(true).Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().Where(a => a.IsPregnant).ToList();
// determine all fetus and newborn mortality of all pregnant females.
foreach (RuminantFemale female in pregnantherd)
{
// calculate fetus and newborn mortality
// total mortality / (gestation months + 1) to get monthly mortality
// done here before births to account for post birth motality as well..
// IsPregnant status does not change until births occur in next section so will include mortality in month of birth
// needs to be calculated for each offspring carried.
for (int i = 0; i < female.CarryingCount; i++)
{
if (RandomNumberGenerator.Generator.NextDouble() < (female.BreedParams.PrenatalMortality / (female.BreedParams.GestationLength + 1)))
{
female.OneOffspringDies();
if (female.NumberOfOffspring == 0)
{
// report conception status changed when last multiple birth dies.
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(Reporting.ConceptionStatus.Failed, female, Clock.Today));
}
}
}
if (female.BirthDue)
{
int numberOfNewborn = female.CarryingCount;
for (int i = 0; i < numberOfNewborn; i++)
{
object newCalf = null;
bool isMale = (RandomNumberGenerator.Generator.NextDouble() <= female.BreedParams.ProportionOffspringMale);
double weight = female.BreedParams.SRWBirth * female.StandardReferenceWeight * (1 - 0.33 * (1 - female.Weight / female.StandardReferenceWeight));
if (isMale)
{
newCalf = new RuminantMale(0, Sex.Male, weight, female.BreedParams);
}
else
{
newCalf = new RuminantFemale(0, Sex.Female, weight, female.BreedParams);
}
Ruminant newCalfRuminant = newCalf as Ruminant;
newCalfRuminant.HerdName = female.HerdName;
newCalfRuminant.Breed = female.BreedParams.Breed;
newCalfRuminant.ID = Resources.RuminantHerd().NextUniqueID;
newCalfRuminant.Location = female.Location;
newCalfRuminant.Mother = female;
newCalfRuminant.Number = 1;
newCalfRuminant.SetUnweaned();
// calf weight from Freer
newCalfRuminant.PreviousWeight = newCalfRuminant.Weight;
newCalfRuminant.SaleFlag = HerdChangeReason.Born;
// add attributes inherited from mother
foreach (var attribute in female.Attributes)
{
newCalfRuminant.AddAttribute(attribute.Key, attribute.Value.GetInheritedAttribute() as ICLEMAttribute);
}
Resources.RuminantHerd().AddRuminant(newCalfRuminant, this);
// add to sucklings
female.SucklingOffspringList.Add(newCalfRuminant);
// this now reports for each individual born not a birth event as individual wean events are reported
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(Reporting.ConceptionStatus.Birth, female, Clock.Today));
}
female.UpdateBirthDetails();
this.Status = ActivityStatus.Success;
}
}
// Perform breeding
IEnumerable <Ruminant> herd = null;
if (useControlledMating && controlledMating.TimingOK)
{
// determined by controlled mating and subsequent timer (e.g. smart milking)
herd = controlledMating.BreedersToMate();
this.TriggerOnActivityPerformed();
}
else if (!useControlledMating && TimingOK)
{
// whole herd for activity
herd = CurrentHerd(true);
// report that this activity was performed as it does not use base GetResourcesRequired
this.TriggerOnActivityPerformed();
}
if (herd != null && herd.Count() > 0)
{
// group by location
var breeders = from ind in herd
where ind.IsAbleToBreed
group ind by ind.Location into grp
select grp;
int breedersCount = breeders.Count();
int numberPossible = breedersCount;
int numberServiced = 1;
List <Ruminant> maleBreeders = new List <Ruminant>();
// for each location where parts of this herd are located
foreach (var location in breeders)
{
numberPossible = -1;
if (useControlledMating)
{
numberPossible = Convert.ToInt32(location.Where(a => a.Gender == Sex.Female).Count(), CultureInfo.InvariantCulture);
}
else
{
numberPossible = 0;
// uncontrolled conception
if (location.GroupBy(a => a.Gender).Count() == 2)
{
int maleCount = location.Where(a => a.Gender == Sex.Male).Count();
// get a list of males to provide attributes when incontrolled mating.
if (maleCount > 0 && location.FirstOrDefault().BreedParams.IncludedAttributeInheritanceWhenMating)
{
maleBreeders = location.Where(a => a.Gender == Sex.Male).ToList();
}
int femaleCount = location.Where(a => a.Gender == Sex.Female).Count();
numberPossible = Convert.ToInt32(Math.Ceiling(maleCount * location.FirstOrDefault().BreedParams.MaximumMaleMatingsPerDay * 30), CultureInfo.InvariantCulture);
}
}
numberServiced = 1;
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().Where(a => !a.IsPregnant & a.Age <= a.BreedParams.MaximumAgeMating).ToList())
{
Reporting.ConceptionStatus status = Reporting.ConceptionStatus.NotMated;
if (numberServiced <= numberPossible)
{
// calculate conception
double conceptionRate = ConceptionRate(female, out status);
if (conceptionRate > 0)
{
if (RandomNumberGenerator.Generator.NextDouble() <= conceptionRate)
{
female.UpdateConceptionDetails(female.CalulateNumberOfOffspringThisPregnancy(), conceptionRate, 0);
// if mandatory attributes are present in the herd, save male value with female details.
if (female.BreedParams.IncludedAttributeInheritanceWhenMating)
{
if (useControlledMating)
{
// save all male attributes
AddMalesAttributeDetails(female, controlledMating.SireAttributes);
}
else
{
// randomly select male
AddMalesAttributeDetails(female, maleBreeders[RandomNumberGenerator.Generator.Next(0, maleBreeders.Count() - 1)]);
}
}
status = Reporting.ConceptionStatus.Conceived;
NumberConceived++;
}
}
numberServiced++;
this.Status = ActivityStatus.Success;
}
// report change in breeding status
// do not report for -1 (controlled mating outside timing)
if (numberPossible >= 0 && status != Reporting.ConceptionStatus.NotAvailable)
{
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(status, female, Clock.Today));
}
}
// report a natural mating locations for transparency via a message
if (numberServiced > 0 & !useControlledMating)
{
string warning = "Natural (uncontrolled) mating ocurred in [r=" + location.Key + "]";
if (!Warnings.Exists(warning))
{
Warnings.Add(warning);
Summary.WriteMessage(this, warning);
}
}
}
}
}
private void OnCLEMAnimalManage(object sender, EventArgs e)
{
// purchase details only on timer
if (TimingOK)
{
// remove any old potential sales from list as these will be updated here
Resources.RuminantHerd().PurchaseIndividuals.RemoveAll(a => a.Breed == this.PredictedHerdBreed & a.SaleFlag == HerdChangeReason.TradePurchase);
foreach (RuminantTypeCohort purchasetype in this.Children.Where(a => a.GetType() == typeof(RuminantTypeCohort)).Cast <RuminantTypeCohort>())
{
for (int i = 0; i < purchasetype.Number; i++)
{
object ruminantBase = null;
if (purchasetype.Gender == Sex.Male)
{
ruminantBase = new RuminantMale();
}
else
{
ruminantBase = new RuminantFemale();
}
Ruminant ruminant = ruminantBase as Ruminant;
ruminant.ID = 0;
ruminant.BreedParams = herdToUse;
ruminant.Breed = this.PredictedHerdBreed;
ruminant.HerdName = this.PredictedHerdName;
ruminant.Gender = purchasetype.Gender;
ruminant.Age = purchasetype.Age;
ruminant.PurchaseAge = purchasetype.Age;
ruminant.SaleFlag = HerdChangeReason.TradePurchase;
ruminant.Location = "";
double u1 = ZoneCLEM.RandomGenerator.NextDouble();
double u2 = ZoneCLEM.RandomGenerator.NextDouble();
double randStdNormal = Math.Sqrt(-2.0 * Math.Log(u1)) *
Math.Sin(2.0 * Math.PI * u2);
ruminant.Weight = purchasetype.Weight + purchasetype.WeightSD * randStdNormal;
ruminant.PreviousWeight = ruminant.Weight;
switch (purchasetype.Gender)
{
case Sex.Male:
RuminantMale ruminantMale = ruminantBase as RuminantMale;
ruminantMale.BreedingSire = false;
break;
case Sex.Female:
RuminantFemale ruminantFemale = ruminantBase as RuminantFemale;
ruminantFemale.DryBreeder = true;
ruminantFemale.WeightAtConception = ruminant.Weight;
ruminantFemale.NumberOfBirths = 0;
break;
default:
break;
}
Resources.RuminantHerd().PurchaseIndividuals.Add(ruminantBase as Ruminant);
}
}
//this.TriggerOnActivityPerformed();
}
// sale details any timestep when conditions are met.
foreach (Ruminant ind in this.CurrentHerd(true))
{
if (ind.Age - ind.PurchaseAge >= MinMonthsKept & ind.Weight >= TradeWeight)
{
ind.SaleFlag = HerdChangeReason.TradeSale;
}
}
}
/// <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)
{
double intakeDaily = ind.MetabilicIntake / 30.4;
// 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 * intakeDaily;
double km = ind.BreedParams.EMaintEfficiencyCoefficient * energyMetabolic / EnergyGross + ind.BreedParams.EMaintEfficiencyIntercept;
// Reference: SCA p.49
double kg = ind.BreedParams.EGrowthEfficiencyCoefficient * energyMetabolic / EnergyGross + ind.BreedParams.EGrowthEfficiencyIntercept;
double energyPredictedBodyMassChange;
double energyMaintenance;
if (!ind.Weaned)
{
// calculate engergy and growth from milk intake
// recalculate milk intake based on mothers updated milk production for the time step
double potentialMilkIntake = ind.BreedParams.MilkIntakeIntercept + ind.BreedParams.MilkIntakeCoefficient * ind.Weight;
ind.MilkIntake = Math.Min(potentialMilkIntake, ind.MothersMilkProductionAvailable);
if (ind.Mother != null)
{
ind.Mother.TakeMilk(ind.MilkIntake * 30.4, MilkUseReason.Suckling);
}
// Below now uses actual intake received rather than assume all potential intake is eaten
double kml = 1;
double kgl = 1;
if ((ind.MetabilicIntake + ind.MilkIntake) > 0)
{
// average energy efficiency for maintenance
kml = ((ind.MilkIntake * 0.7) + (intakeDaily * km)) / (ind.MilkIntake + intakeDaily);
// average energy efficiency for growth
kgl = ((ind.MilkIntake * 0.7) + (intakeDaily * kg)) / (ind.MilkIntake + intakeDaily);
}
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.AgeZeroCorrected);
ind.EnergyBalance = energyMilkConsumed - energyMaintenance + energyMetablicFromIntake;
double feedingValue;
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
{
double energyMilk = 0;
double energyFoetus = 0;
if (ind.Gender == Sex.Female)
{
RuminantFemale femaleind = ind as RuminantFemale;
// calculate energy for lactation
if (femaleind.IsLactating)
{
// recalculate milk production based on DMD of food provided
energyMilk = CalculateMilkProduction(femaleind);
}
else
{
femaleind.MilkProductionPotential = 0;
}
// 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) * 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 individual energy requirement
// set maintenance age to maximum of 6 years (2190 days). Now uses EnergeyMaintenanceMaximumAge
double maintenanceAge = Math.Min(ind.Age * 30.4, ind.BreedParams.EnergyMaintenanceMaximumAge * 365);
// Reference: SCA p.24
// Reference 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 * (ind.BreedParams.EMaintCoefficient * Math.Pow(ind.Weight, 0.75) / km) * Math.Exp(-ind.BreedParams.EMaintExponent * maintenanceAge) + (ind.BreedParams.EMaintIntercept * energyMetablicFromIntake);
ind.EnergyBalance = energyMetablicFromIntake - energyMaintenance - energyMilk - energyFoetus; // milk will be zero for non lactating individuals.
double feedingValue;
// Reference: Feeding_value = Ajustment for rate of loss or gain (SCA p.43, ? different from Hirata model)
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
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;
if (ind.Gender == Sex.Female && (ind as RuminantFemale).BirthDue)
{
ind.Weight -= (ind as RuminantFemale).WeightLossDueToCalf;
}
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
// methane is 0.02 * intakeDaily * ((13 + 7.52 * energyMetabolic) + energyMetablicFromIntake / energyMaintenance * (23.7 - 3.36 * energyMetabolic)); // MJ per day
// methane is methaneProduced / 55.28 * 1000; // grams per day
// Charmely et al 2016 can be substituted by intercept = 0 and coefficient = 20.7
methaneProduced = ind.BreedParams.MethaneProductionCoefficient * intakeDaily;
}
private void CalculatePotentialIntake(Ruminant ind)
{
// calculate daily potential intake for the selected individual/cohort
double standardReferenceWeight = ind.StandardReferenceWeight;
// now calculated in Ruminant
// 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;
// now performed at allocation of weight in Ruminant
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;
ind.MilkIntakePotential = 0;
// calculate milk intake shortfall for sucklings
if (!ind.Weaned)
{
// potential milk intake/animal/day
ind.MilkIntakePotential = ind.BreedParams.MilkIntakeIntercept + ind.BreedParams.MilkIntakeCoefficient * ind.Weight;
// get estimated milk available
// this will be updated to the corrected milk available in the calculate energy section.
ind.MilkIntake = Math.Min(ind.MilkIntakePotential, ind.MothersMilkProductionAvailable);
// 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);
}
}
else
{
if (ind.Weaner)
{
// Reference: SCA Metabolic LWTs
// restored in v112 of NABSA for weaner animals
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)));
// older individual check. previous method before adding calulation for weaners after discussions with Cam McD
//double prevint = ind.BreedParams.IntakeCoefficient * liveWeightForIntake * (ind.BreedParams.IntakeIntercept - liveWeightForIntake / standardReferenceWeight);
}
else // 12month+ individuals
{
// 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)
{
// move to half way through timestep
double dayOfLactation = femaleind.DaysLactating;
// Reference: Intake multiplier for lactating cow (M.Freer)
// 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))) * (1 - 0.5 + 0.5 * (ind.Weight / ind.NormalisedAnimalWeight));
// 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
// replaces (A), (B) and (C)
potentialIntake *= intakeMilkMultiplier;
// calculate estimated milk production for time step here
// assuming average feed quality if no previous diet values
// This need to happen before suckling potential intake can be determined.
CalculateMilkProduction(femaleind);
femaleind.MilkProducedThisTimeStep = femaleind.MilkProduction * 30.4;
}
else
{
femaleind.MilkProduction = 0;
}
}
//TODO: option to restrict potential further due to stress (e.g. heat, cold, rain)
}
// get monthly intake
potentialIntake *= 30.4;
ind.PotentialIntake = potentialIntake;
}
private void OnCLEMAnimalBreeding(object sender, EventArgs e)
{
// RuminantHerd ruminantHerd = Resources.RuminantHerd();
List <Ruminant> herd = CurrentHerd(true); //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;
// calculate labour and finance limitations if needed when doing AI
int breedersCount = breeders.Count();
int numberPossible = breedersCount;
int numberServiced = 1;
if (UseAI & TimingOK)
{
// attempt to get required resources
List <ResourceRequest> resourcesneeded = GetResourcesNeededForActivityLocal();
bool tookRequestedResources = TakeResources(resourcesneeded, true);
// get all shortfalls
if (tookRequestedResources & (ResourceRequestList != null))
{
//TODO: fix this to account for perHead payments and labour and not fixed expenses
double amountCashNeeded = resourcesneeded.Where(a => a.ResourceType == typeof(Finance)).Sum(a => a.Required);
double amountCashProvided = resourcesneeded.Where(a => a.ResourceType == typeof(Finance)).Sum(a => a.Provided);
double amountLabourNeeded = resourcesneeded.Where(a => a.ResourceType == typeof(Labour)).Sum(a => a.Required);
double amountLabourProvided = resourcesneeded.Where(a => a.ResourceType == typeof(Labour)).Sum(a => a.Provided);
double cashlimit = 1;
if (amountCashNeeded > 0)
{
if (amountCashProvided == 0)
{
cashlimit = 0;
}
else
{
cashlimit = amountCashNeeded / amountCashProvided;
}
}
double labourlimit = 1;
if (amountLabourNeeded > 0)
{
if (amountLabourProvided == 0)
{
labourlimit = 0;
}
else
{
labourlimit = amountLabourNeeded / amountLabourProvided;
}
}
double limiter = Math.Min(cashlimit, labourlimit);
numberPossible = Convert.ToInt32(limiter * breedersCount);
// TODO: determine if fixed payments were not possible
// TODO: determine limits by insufficient labour or cash for per head payments
}
// report that this activity was performed as it does not use base GetResourcesRequired
this.TriggerOnActivityPerformed();
}
if (!UseAI)
{
// report that this activity was performed as it does not use base GetResourcesRequired
this.TriggerOnActivityPerformed();
}
// for each location where parts of this herd are located
foreach (var location in breeders)
{
// 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 + 1) to get monthly mortality
// done here before births to account for post birth motality as well..
double rnd = ZoneCLEM.RandomGenerator.NextDouble();
if (rnd < (female.BreedParams.PrenatalMortality / (female.BreedParams.GestationLength + 1)))
{
female.OneOffspringDies();
}
}
}
// check for births of all pregnant females.
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().ToList())
{
if (female.BirthDue)
{
female.WeightLossDueToCalf = 0;
int numberOfNewborn = (female.CarryingTwins) ? 2 : 1;
for (int i = 0; i < numberOfNewborn; i++)
{
// Foetal mortality is now performed each timestep at base of this method
object newCalf = null;
bool isMale = (ZoneCLEM.RandomGenerator.NextDouble() > 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.Breed = female.BreedParams.Breed;
newCalfRuminant.Gender = (isMale) ? Sex.Male : Sex.Female;
newCalfRuminant.ID = Resources.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 = HerdChangeReason.Born;
Resources.RuminantHerd().AddRuminant(newCalfRuminant);
// add to sucklings
female.SucklingOffspring.Add(newCalfRuminant);
// remove calf weight from female
female.WeightLossDueToCalf += newCalfRuminant.Weight;
}
female.UpdateBirthDetails();
}
}
// uncontrolled conception
if (!UseAI)
{
// 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.Min(1.0, matingsPossible / femaleCount);
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().ToList())
{
if (!female.IsPregnant && !female.IsLactating && (female.Age - female.AgeAtLastBirth) * 30.4 >= female.BreedParams.MinimumDaysBirthToConception)
{
// calculate conception
double conceptionRate = ConceptionRate(female) * maleLimiter;
conceptionRate = Math.Min(conceptionRate, MaximumConceptionRateUncontrolled);
if (ZoneCLEM.RandomGenerator.NextDouble() <= conceptionRate)
{
female.UpdateConceptionDetails(ZoneCLEM.RandomGenerator.NextDouble() < female.BreedParams.TwinRate, conceptionRate);
}
}
}
}
}
// controlled conception
else
{
if (this.TimingOK)
{
foreach (RuminantFemale female in location.Where(a => a.Gender == Sex.Female).Cast <RuminantFemale>().ToList())
{
if (!female.IsPregnant && !female.IsLactating && (female.Age - female.AgeAtLastBirth) * 30.4 >= female.BreedParams.MinimumDaysBirthToConception)
{
// calculate conception
double conceptionRate = ConceptionRate(female);
if (numberServiced <= numberPossible) // labour/finance limited number
{
if (ZoneCLEM.RandomGenerator.NextDouble() <= conceptionRate)
{
female.UpdateConceptionDetails(ZoneCLEM.RandomGenerator.NextDouble() < female.BreedParams.TwinRate, conceptionRate);
}
numberServiced++;
}
}
}
}
}
}
}
private void OnCLEMAnimalManage(object sender, EventArgs e)
{
//List<Ruminant> localHerd = this.CurrentHerd();
RuminantHerd ruminantHerd = Resources.RuminantHerd();
// clear store of individuals to try and purchase
// ruminantHerd.PurchaseIndividuals.Clear();
// remove only the individuals that are affected by this activity.
ruminantHerd.PurchaseIndividuals.RemoveAll(a => a.Breed == this.PredictedHerdBreed);
List <Ruminant> herd = this.CurrentHerd(true);
// List<Ruminant> herd = ruminantHerd.Herd.Where(a => a.HerdName == HerdName).ToList();
// 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.
if (this.TimingOK || ContinuousMaleSales)
{
foreach (var ind in herd.Where(a => a.Weaned & (SellFemalesLikeMales ? true : (a.Gender == Sex.Male)) & (a.Age >= MaleSellingAge || a.Weight >= MaleSellingWeight)))
{
bool sell = true;
if (ind.GetType() == typeof(RuminantMale))
{
// don't sell breeding sires.
sell = !((ind as RuminantMale).BreedingSire);
}
if (sell)
{
ind.SaleFlag = HerdChangeReason.AgeWeightSale;
}
}
}
// if management month
if (this.TimingOK)
{
bool sufficientFood = true;
if (foodStore != null)
{
sufficientFood = (foodStore.TonnesPerHectare * 1000) > MinimumPastureBeforeRestock;
}
// 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 = HerdChangeReason.MaxAgeSale;
}
// MALES
// check for breeder bulls after sale of old individuals and buy/sell
int numberMaleSiresInHerd = herd.Where(a => a.Gender == Sex.Male & a.SaleFlag == HerdChangeReason.None).Cast <RuminantMale>().Where(a => a.BreedingSire).Count();
// Number of females
int numberFemaleBreedingInHerd = herd.Where(a => a.Gender == Sex.Female & a.Age >= a.BreedParams.MinimumAge1stMating & a.SaleFlag == HerdChangeReason.None).Count();
int numberFemaleTotalInHerd = herd.Where(a => a.Gender == Sex.Female & a.SaleFlag == HerdChangeReason.None).Count();
int numberFemaleOldInHerd = herd.Where(a => a.Gender == Sex.Female & MaximumBreederAge - a.Age <= 12 & a.SaleFlag == HerdChangeReason.None).Count();
if (numberMaleSiresInHerd > MaximumSiresKept)
{
// sell bulls
// What rule? oldest first as they may be lost soonest
int numberToRemove = MaximumSiresKept - numberMaleSiresInHerd;
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 = HerdChangeReason.ExcessBullSale;
numberToRemove--;
if (numberToRemove == 0)
{
break;
}
}
}
else if (numberMaleSiresInHerd < MaximumSiresKept)
{
if ((foodStore == null) || (sufficientFood))
{
if (AllowSireReplacement)
{
// 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 == HerdChangeReason.AgeWeightSale).OrderByDescending(a => a.Weight))
{
male.SaleFlag = HerdChangeReason.None;
male.BreedingSire = true;
numberMaleSiresInHerd++;
if (numberMaleSiresInHerd >= MaximumSiresKept)
{
break;
}
}
// if still insufficent, look into current herd for replacement
// remaining males assumed to be too small, so await next time-step
}
// if still insufficient buy bulls.
if (numberMaleSiresInHerd < MaximumSiresKept && (MaximumSiresPerPurchase > 0))
{
// limit by breeders as proportion of max breeders so we don't spend alot on sires when building the herd and females more valuable
double propOfBreeders = (double)numberFemaleBreedingInHerd / (double)MaximumBreedersKept;
int sires = Convert.ToInt32(Math.Ceiling(Math.Ceiling(MaximumSiresKept * propOfBreeders)));
int numberToBuy = Math.Min(MaximumSiresPerPurchase, Math.Max(0, sires - numberMaleSiresInHerd));
for (int i = 0; i < numberToBuy; i++)
{
RuminantMale newbull = new RuminantMale
{
Location = GrazeFoodStoreName,
Age = 48,
Breed = this.PredictedHerdBreed,// breedParams.Breed;
HerdName = this.PredictedHerdName,
BreedingSire = true,
BreedParams = breedParams,
Gender = Sex.Male,
ID = 0, // ruminantHerd.NextUniqueID;
Weight = 450,
HighWeight = 450,
SaleFlag = HerdChangeReason.SirePurchase
};
// add to purchase request list and await purchase in Buy/Sell
ruminantHerd.PurchaseIndividuals.Add(newbull);
}
}
}
}
// FEMALES
// Breeding herd traded as heifers only
int excessHeifers = 0;
// check for maximum number of breeders remaining after sale and buy/sell
if (numberFemaleBreedingInHerd > MaximumBreedersKept)
{
// herd mortality of 5% plus those that will be culled in next 12 months
excessHeifers = Convert.ToInt32((numberFemaleTotalInHerd - numberFemaleOldInHerd) * 0.05) + numberFemaleOldInHerd;
// shortfall + (number of young - replacement heifers)
excessHeifers = (numberFemaleTotalInHerd - MaximumBreedersKept) + ((numberFemaleTotalInHerd - numberFemaleBreedingInHerd) - excessHeifers);
}
else
{
// shortfall between actual and desired numbers
excessHeifers = MaximumBreedersKept - numberFemaleBreedingInHerd;
// add future cull for age + 5%
excessHeifers += Convert.ToInt32((numberFemaleTotalInHerd - numberFemaleOldInHerd) * 0.05) + numberFemaleOldInHerd;
excessHeifers = (numberFemaleTotalInHerd - numberFemaleBreedingInHerd) - excessHeifers;
}
// surplus heifers to sell
if (excessHeifers > 0)
{
foreach (var female in herd.Where(a => a.Gender == Sex.Female & a.Age < a.BreedParams.MinimumAge1stMating & a.Weaned).OrderByDescending(a => a.Age).Take(excessHeifers))
{
// tag fo sale.
female.SaleFlag = HerdChangeReason.ExcessHeiferSale;
excessHeifers--;
if (excessHeifers == 0)
{
break;
}
}
}
else if (excessHeifers < 0)
{
excessHeifers *= -1;
if ((foodStore == null) || (sufficientFood))
{
// 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 == HerdChangeReason.AgeWeightSale).OrderByDescending(a => a.Age))
{
female.SaleFlag = HerdChangeReason.None;
excessHeifers--;
if (excessHeifers == 0)
{
break;
}
}
// if still insufficient buy heifers.
if (excessHeifers > 0 & (MaximumBreedersPerPurchase > 0))
{
int ageOfHeifer = 12;
double weightOfHeifer = 260;
// buy 5% more to account for deaths before these individuals grow to breeding age
int numberToBuy = Math.Min(MaximumBreedersPerPurchase, Math.Max(0, Convert.ToInt32(excessHeifers * 1.05)));
for (int i = 0; i < numberToBuy; i++)
{
RuminantFemale newheifer = new RuminantFemale
{
Location = GrazeFoodStoreName,
Age = ageOfHeifer,
Breed = this.PredictedHerdBreed,
HerdName = this.PredictedHerdName,
BreedParams = breedParams,
Gender = Sex.Female,
ID = 0,
Weight = weightOfHeifer,
HighWeight = weightOfHeifer,
SaleFlag = HerdChangeReason.HeiferPurchase
};
// add to purchase request list and await purchase in Buy/Sell
ruminantHerd.PurchaseIndividuals.Add(newheifer);
}
}
}
}
// report that this activity was performed as it does not use base GetResourcesRequired
//this.TriggerOnActivityPerformed();
// Breeders themselves don't get sold. Trading is with Heifers
// Breeders can be sold in seasonal and ENSO destocking.
// 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 = Convert.ToInt32((numberFemaleInHerd-MaximumBreedersKept));
// foreach (var female in herd.Where(a => a.Gender == Sex.Female & a.Age >= a.BreedParams.MinimumAge1stMating).OrderByDescending(a => a.Age).Take(numberToRemove))
// {
// female.SaleFlag = HerdChangeReason.ExcessBreederSale;
// numberToRemove--;
// if (numberToRemove == 0) break;
// }
// }
//else
//{
//}
}
}
private void OnCLEMAnimalBreeding(object sender, EventArgs e)
{
this.Status = ActivityStatus.NotNeeded;
NumberConceived = 0;
// get list of all pregnant females
List <RuminantFemale> pregnantherd = CurrentHerd(true).OfType <RuminantFemale>().Where(a => a.IsPregnant).ToList();
// determine all fetus and newborn mortality of all pregnant females.
foreach (RuminantFemale female in pregnantherd)
{
// calculate fetus and newborn mortality
// total mortality / (gestation months + 1) to get monthly mortality
// done here before births to account for post birth motality as well..
// IsPregnant status does not change until births occur in next section so will include mortality in month of birth
// needs to be calculated for each offspring carried.
for (int i = 0; i < female.CarryingCount; i++)
{
var rnd = RandomNumberGenerator.Generator.NextDouble();
if (rnd < (female.BreedParams.PrenatalMortality / (female.BreedParams.GestationLength + 1)))
{
female.OneOffspringDies();
if (female.NumberOfOffspring == 0)
{
// report conception status changed when last multiple birth dies.
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(Reporting.ConceptionStatus.Failed, female, clock.Today));
}
}
}
if (female.BirthDue)
{
int numberOfNewborn = female.CarryingCount;
for (int i = 0; i < numberOfNewborn; i++)
{
bool isMale = RandomNumberGenerator.Generator.NextDouble() <= female.BreedParams.ProportionOffspringMale;
Sex sex = isMale ? Sex.Male : Sex.Female;
double weight = female.BreedParams.SRWBirth * female.StandardReferenceWeight * (1 - 0.33 * (1 - female.Weight / female.StandardReferenceWeight));
Ruminant newSucklingRuminant = Ruminant.Create(sex, female.BreedParams, 0, weight);
newSucklingRuminant.HerdName = female.HerdName;
newSucklingRuminant.Breed = female.BreedParams.Breed;
newSucklingRuminant.ID = HerdResource.NextUniqueID;
newSucklingRuminant.Location = female.Location;
newSucklingRuminant.Mother = female;
newSucklingRuminant.Number = 1;
newSucklingRuminant.SetUnweaned();
// suckling/calf weight from Freer
newSucklingRuminant.PreviousWeight = newSucklingRuminant.Weight;
newSucklingRuminant.SaleFlag = HerdChangeReason.Born;
// add attributes inherited from mother
foreach (var attribute in female.Attributes.Items)
{
if (attribute.Value != null)
{
newSucklingRuminant.Attributes.Add(attribute.Key, attribute.Value.GetInheritedAttribute() as IIndividualAttribute);
}
}
HerdResource.AddRuminant(newSucklingRuminant, this);
// add to sucklings
female.SucklingOffspringList.Add(newSucklingRuminant);
// this now reports for each individual born not a birth event as individual wean events are reported
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(Reporting.ConceptionStatus.Birth, female, clock.Today));
}
female.UpdateBirthDetails();
this.Status = ActivityStatus.Success;
}
}
// Perform breeding
IEnumerable <Ruminant> herd = null;
if (useControlledMating && controlledMating.TimingOK)
{
// determined by controlled mating and subsequent timer (e.g. smart milking)
herd = controlledMating.BreedersToMate();
}
else if (!useControlledMating && TimingOK)
{
// whole herd for activity including males
herd = CurrentHerd(true);
}
if (herd != null && herd.Any())
{
// group by location
var breeders = from ind in herd
where ind.IsAbleToBreed
group ind by ind.Location into grp
select grp;
// identify not ready for reporting and tracking
var notReadyBreeders = herd.Where(a => a.Sex == Sex.Female).Cast <RuminantFemale>().Where(a => a.IsBreeder && !a.IsAbleToBreed && !a.IsPregnant);
foreach (RuminantFemale female in notReadyBreeders)
{
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(Reporting.ConceptionStatus.NotReady, female, clock.Today));
}
int numberPossible = breeders.Sum(a => a.Count());
int numberServiced = 1;
List <Ruminant> maleBreeders = new List <Ruminant>();
// for each location where parts of this herd are located
foreach (var location in breeders)
{
numberPossible = -1;
if (useControlledMating)
{
numberPossible = Convert.ToInt32(location.OfType <RuminantFemale>().Count(), CultureInfo.InvariantCulture);
}
else
{
numberPossible = 0;
// uncontrolled conception
if (location.GroupBy(a => a.Sex).Count() == 2)
{
int maleCount = location.OfType <RuminantMale>().Count();
// get a list of males to provide attributes when incontrolled mating.
if (maleCount > 0 && location.FirstOrDefault().BreedParams.IncludedAttributeInheritanceWhenMating)
{
maleBreeders = location.Where(a => a.Sex == Sex.Male).ToList();
}
int femaleCount = location.Where(a => a.Sex == Sex.Female).Count();
numberPossible = Convert.ToInt32(Math.Ceiling(maleCount * location.FirstOrDefault().BreedParams.MaximumMaleMatingsPerDay * 30), CultureInfo.InvariantCulture);
}
}
numberServiced = 0;
lastJoinIndex = -1;
int cnt = 0;
// shuffle the not pregnant females when obtained to avoid any inherant order by creation of individuals affecting which individuals are available first
var notPregnantFemales = location.OfType <RuminantFemale>().Where(a => !a.IsPregnant).OrderBy(a => RandomNumberGenerator.Generator.Next()).ToList();
int totalToBreed = notPregnantFemales.Count;
while (cnt < totalToBreed)
{
RuminantFemale female = notPregnantFemales.ElementAt(cnt);
Reporting.ConceptionStatus status = Reporting.ConceptionStatus.NotMated;
if (numberServiced < numberPossible)
{
// calculate conception
double conceptionRate = ConceptionRate(female, out status);
// if mandatory attributes are present in the herd, save male value with female details.
// update male for both successful and failed matings (next if statement
if (female.BreedParams.IncludedAttributeInheritanceWhenMating)
{
object male = null;
if (useControlledMating)
{
bool newJoining = needsNewJoiningMale(controlledMating.JoiningsPerMale, numberServiced);
// save all male attributes
AddMalesAttributeDetails(female, controlledMating.SireAttributes, newJoining);
}
else
{
male = maleBreeders[RandomNumberGenerator.Generator.Next(0, maleBreeders.Count() - 1)];
female.LastMatingStyle = ((male as RuminantMale).IsWildBreeder ? MatingStyle.WildBreeder : MatingStyle.Natural);
// randomly select male
AddMalesAttributeDetails(female, male as Ruminant);
}
}
if (conceptionRate > 0)
{
if (RandomNumberGenerator.Generator.NextDouble() <= conceptionRate)
{
female.UpdateConceptionDetails(female.CalulateNumberOfOffspringThisPregnancy(), conceptionRate, 0);
if (useControlledMating)
{
female.LastMatingStyle = MatingStyle.Controlled;
}
status = Reporting.ConceptionStatus.Conceived;
NumberConceived++;
}
else
{
status = Reporting.ConceptionStatus.Unsuccessful;
}
}
numberServiced++;
this.Status = ActivityStatus.Success;
}
// report change in breeding status
// do not report for -1 (controlled mating outside timing)
if (numberPossible >= 0 && status != Reporting.ConceptionStatus.NotAvailable)
{
female.BreedParams.OnConceptionStatusChanged(new Reporting.ConceptionStatusChangedEventArgs(status, female, clock.Today));
}
cnt++;
}
// report a natural mating locations for transparency via a message
if (numberServiced > 0 & !useControlledMating)
{
string warning = $"Natural (uncontrolled) mating ocurred in [r={(location.Key ?? "Not specified - general yards")}]";
Warnings.CheckAndWrite(warning, Summary, this, MessageType.Information);
}
}
}
// report that this activity was performed as it does not use base GetResourcesRequired
this.TriggerOnActivityPerformed();
}