/// <summary>
/// Output the mortality profile of a cohort becoming extinct
/// </summary>
/// <param name="cohortID">The ID of the cohort becoming extinct</param>
public void OutputMortalityProfile(uint cohortID)
{
string CohortIDString = Convert.ToString(cohortID);
if (MortalityList.ContainsKey(CohortIDString))
{
if (RandomNumberGenerator.GetUniform() > 0.95)
{
var Lines = ((IEnumerable)MortalityList[CohortIDString]).Cast <object>().ToList();
foreach (var Line in Lines)
{
SyncMortalityWriter.WriteLine(Line);
}
}
MortalityList.Remove(CohortIDString);
}
/*
* if (MortalityList.ContainsKey(StringCID))
* {
* lock (MortalityList.SyncRoot)
* {
* var Lines = ((IEnumerable)MortalityList[StringCID]).Cast<object>().ToList();
* // Loop over mortality events for the specified cohort and write these to the output file
* foreach (var Line in Lines)
* {
* SyncMortalityWriter.WriteLine(Line);
* }
*
* // Remove the cohort from the list of mortality profiles
* MortalityList.Remove(Convert.ToString(cohortID));
* }
* }
*/
}
/// <summary>
/// Generate a random value to see if a cohort disperses
/// </summary>
/// <param name="dispersalProbability">The probability of dispersal</param>
/// <returns>Returns either the random value, if it less than dispersal probability, or -1</returns>
protected double CheckForDispersal(double dispersalProbability)
{
// Randomly check to see if dispersal occurs
double RandomValue = RandomNumberGenerator.GetUniform();
if (dispersalProbability >= RandomValue)
{
return(RandomValue);
}
else
{
return(-1.0);
}
}
/// <summary>
/// Apply the changes from predation to prey cohorts, and update deltas for the predator cohort
/// </summary>
/// <param name="gridCellCohorts">The cohorts in the current grid cell</param>
/// <param name="gridCellStocks">The stocks in the current grid cell</param>
/// <param name="actingCohort">The acting cohort</param>
/// <param name="cellEnvironment">The environment in the current grid cell</param>
/// <param name="deltas">The sorted list to track changes in biomass and abundance of the acting cohort in this grid cell</param>
/// <param name="madingleyCohortDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="madingleyStockDefinitions">The functional group definitions for stocks in the model</param>
/// <param name="trackProcesses">An instance of ProcessTracker to hold diagnostics for predation</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
/// <param name="outputDetail">The level of output detail used in this model run</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void RunEating(GridCellCohortHandler gridCellCohorts, GridCellStockHandler gridCellStocks, int[] actingCohort, SortedList <string, double[]>
cellEnvironment, Dictionary <string, Dictionary <string, double> > deltas, FunctionalGroupDefinitions madingleyCohortDefinitions,
FunctionalGroupDefinitions madingleyStockDefinitions, ProcessTracker trackProcesses, uint currentTimestep, Boolean specificLocations,
string outputDetail, MadingleyModelInitialisation initialisation)
{
if (trackProcesses.TrackProcesses)
{
Track = (RandomNumberGenerator.GetUniform() > 0.975) ? true : false;
}
TempDouble = 0.0;
// Temporary variable to hold the total time spent eating + 1. Saves an extra calculation in CalculateAbundanceEaten
double TotalTimeUnitsToHandlePlusOne = TimeUnitsToHandlePotentialFoodItems + 1;
// Loop over potential prey functional groups
foreach (int FunctionalGroup in _FunctionalGroupIndicesToEat)
{
// Loop over cohorts within the functional group
for (int i = 0; i < NumberCohortsPerFunctionalGroupNoNewCohorts[FunctionalGroup]; i++)
{
// Get the individual body mass of this cohort
_BodyMassPrey = gridCellCohorts[FunctionalGroup][i].IndividualBodyMass;
// Calculate the actual abundance of prey eaten from this cohort
if (gridCellCohorts[FunctionalGroup][i].CohortAbundance > 0)
{
// Calculate the actual abundance of prey eaten from this cohort
_AbundancesEaten[FunctionalGroup][i] = CalculateAbundanceEaten(_PotentialAbundanceEaten[FunctionalGroup][i], _PredatorAbundanceMultipliedByTimeEating,
TotalTimeUnitsToHandlePlusOne, gridCellCohorts[FunctionalGroup][i].CohortAbundance);
}
else
{
_AbundancesEaten[FunctionalGroup][i] = 0;
}
// Remove number of prey eaten from the prey cohort
gridCellCohorts[FunctionalGroup][i].CohortAbundance -= _AbundancesEaten[FunctionalGroup][i];
gridCellCohorts[actingCohort].TrophicIndex += (_BodyMassPrey + gridCellCohorts[FunctionalGroup][i].IndividualReproductivePotentialMass) * _AbundancesEaten[FunctionalGroup][i] * gridCellCohorts[FunctionalGroup][i].TrophicIndex;
// If the process tracker is set and output detail is set to high and the prey cohort has never been merged,
// then track its mortality owing to predation
if (trackProcesses.TrackProcesses)
{
if ((outputDetail == "high") && (gridCellCohorts[FunctionalGroup][i].CohortID.Count == 1) &&
AbundancesEaten[FunctionalGroup][i] > 0)
{
trackProcesses.RecordMortality((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0], gridCellCohorts
[FunctionalGroup][i].BirthTimeStep, currentTimestep, gridCellCohorts[FunctionalGroup][i].IndividualBodyMass,
gridCellCohorts[FunctionalGroup][i].AdultMass, gridCellCohorts[FunctionalGroup][i].FunctionalGroupIndex,
gridCellCohorts[FunctionalGroup][i].CohortID[0], AbundancesEaten[FunctionalGroup][i], "predation");
}
// If the model is being run for specific locations and if track processes has been specified, then track the mass flow between
// prey and predator
if (specificLocations)
{
trackProcesses.RecordPredationMassFlow(currentTimestep, _BodyMassPrey, _BodyMassPredator, _BodyMassPrey *
_AbundancesEaten[FunctionalGroup][i]);
if (outputDetail == "high")
{
trackProcesses.TrackPredationTrophicFlow((uint)cellEnvironment["LatIndex"][0], (uint)cellEnvironment["LonIndex"][0],
gridCellCohorts[FunctionalGroup][i].FunctionalGroupIndex, gridCellCohorts[actingCohort].FunctionalGroupIndex,
madingleyCohortDefinitions, (_AbundancesEaten[FunctionalGroup][i] * _BodyMassPrey), _BodyMassPredator, _BodyMassPrey,
initialisation, cellEnvironment["Realm"][0] == 2.0);
}
}
}
// Check that the abundance eaten from this cohort is not negative
// Commented out for the purposes of speed
//Debug.Assert( _AbundancesEaten[FunctionalGroup][i].CompareTo(0.0) >= 0,
// "Predation negative for this prey cohort" + actingCohort);
// Create a temporary value to speed up the predation function
// This is equivalent to the body mass of the prey cohort including reproductive potential mass, times the abundance eaten of the prey cohort,
// divided by the abundance of the predator
TempDouble += (_BodyMassPrey + gridCellCohorts[FunctionalGroup][i].IndividualReproductivePotentialMass) * _AbundancesEaten[FunctionalGroup][i] / _AbundancePredator;
}
}
// Add the biomass eaten and assimilated by an individual to the delta biomass for the acting (predator) cohort
deltas["biomass"]["predation"] = TempDouble * _PredatorAssimilationEfficiency;
// Move the biomass eaten but not assimilated by an individual into the organic matter pool
deltas["organicpool"]["predation"] = TempDouble * _PredatorNonAssimilation * _AbundancePredator;
// Check that the delta biomass from eating for the acting cohort is not negative
//Debug.Assert(deltas["biomass"]["predation"] >= 0, "Predation yields negative biomass");
// Calculate the total biomass eaten by the acting (predator) cohort
_TotalBiomassEatenByCohort = deltas["biomass"]["predation"] * _AbundancePredator;
}
/// <summary>
/// Merge cohorts until below a specified threshold number of cohorts in each grid cell
/// </summary>
/// <param name="gridCellCohorts">The cohorts within this grid cell</param>
/// <param name="TotalNumberOfCohorts">The total number of cohorts in this grid cell</param>
/// <param name="TargetCohortThreshold">The target threshold to reduce the number of cohorts to</param>
/// <returns>The number of cohorts that have been merged</returns>
public int MergeToReachThreshold(GridCellCohortHandler gridCellCohorts, int TotalNumberOfCohorts, int TargetCohortThreshold)
{
// A list of shortest distances between pairs of cohorts
List <Tuple <double, int, int[]> > ShortestDistances = new List <Tuple <double, int, int[]> >();
// A holding list
// List<Tuple<double, int, int[]>> HoldingList = new List<Tuple<double, int, int[]>>();
// Vector of lists of shortest distances in each functional group
// List<Tuple<double, int, int[]>>[] ShortestDistancesPerFunctionalGroup = new List<Tuple<double, int, int[]>>[gridCellCohorts.Count];
// Temporary
List <Tuple <double, int, int[]> >[] ShortestDistancesPerFunctionalGroup2 = new List <Tuple <double, int, int[]> > [gridCellCohorts.Count];
// How many cohorts to remove to hit the threshold
int NumberToRemove = TotalNumberOfCohorts - TargetCohortThreshold;
// Holds the pairwise distances between two cohorts; the functional group of the cohorts; the cohort IDs of each cohort
Tuple <double, int, int[]> PairwiseDistance;
// Loop through functional groups
for (int ff = 0; ff < gridCellCohorts.Count; ff++)
{
// Temporary
ShortestDistancesPerFunctionalGroup2[ff] = new List <Tuple <double, int, int[]> >();
// Loop through cohorts within functional groups
for (int cc = 0; cc < gridCellCohorts[ff].Count - 1; cc++)
{
// Loop through comparison cohorts
for (int dd = cc + 1; dd < gridCellCohorts[ff].Count; dd++)
{
// Randomly select which cohort is to be merge to & calculate distance between cohort pair
if (RandomNumberGenerator.GetUniform() < 0.5)
{
PairwiseDistance = new Tuple <double, int, int[]>(CalculateDistance(gridCellCohorts[ff][cc], gridCellCohorts[ff][dd]), ff, new int[] { cc, dd });
}
else
{
PairwiseDistance = new Tuple <double, int, int[]>(CalculateDistance(gridCellCohorts[ff][cc], gridCellCohorts[ff][dd]), ff, new int[] { dd, cc });
}
// Temporary
ShortestDistancesPerFunctionalGroup2[ff].Add(PairwiseDistance);
}
}
// Temporary
ShortestDistancesPerFunctionalGroup2[ff] = ShortestDistancesPerFunctionalGroup2[ff].OrderBy(x => x.Item1).ToList();
}
// Hold the current position in the shortest distance list
int CurrentListPosition = 0;
List <int> IndicesToRemove;
// Now that the shortest distances have been calculated, do the merging execution
int FunctionalGroup;
int CohortToMergeFrom;
int CohortToMergeTo;
// Temporary
for (int gg = 0; gg < gridCellCohorts.Count; gg++)
{
IndicesToRemove = new List <int>();
CurrentListPosition = 0;
while (CurrentListPosition < ShortestDistancesPerFunctionalGroup2[gg].Count)
{
CohortToMergeFrom = ShortestDistancesPerFunctionalGroup2[gg][CurrentListPosition].Item3[1];
CohortToMergeTo = ShortestDistancesPerFunctionalGroup2[gg][CurrentListPosition].Item3[0];
for (int cc = ShortestDistancesPerFunctionalGroup2[gg].Count - 1; cc > CurrentListPosition; cc--)
{
if (ShortestDistancesPerFunctionalGroup2[gg][cc].Item3[0] == CohortToMergeFrom ||
ShortestDistancesPerFunctionalGroup2[gg][cc].Item3[1] == CohortToMergeFrom)
{
ShortestDistancesPerFunctionalGroup2[gg].RemoveAt(cc);
}
}
CurrentListPosition++;
}
}
// Compile all shortest distances into a single list for merging purposes - note that we only need to do a limited number of merges
for (int gg = 0; gg < gridCellCohorts.Count; gg++)
{
foreach (var distance in ShortestDistancesPerFunctionalGroup2[gg])
{
ShortestDistances.Add(distance);
}
}
ShortestDistances = ShortestDistances.OrderBy(x => x.Item1).ToList();
// Counts the number of merges that have happened
int MergeCounter = 0;
CurrentListPosition = 0;
// While merging does not reach threshold, and while there are still elements in the list
while ((MergeCounter < NumberToRemove) && (CurrentListPosition < ShortestDistances.Count))
{
// Get pairwise traits
FunctionalGroup = ShortestDistances[CurrentListPosition].Item2;
CohortToMergeFrom = ShortestDistances[CurrentListPosition].Item3[1];
CohortToMergeTo = ShortestDistances[CurrentListPosition].Item3[0];
// Check whether either cohort has already merged to something else this timestep merge
// execution, and hence is empty
// if ((gridCellCohorts[FunctionalGroup][CohortToMergeFrom].CohortAbundance.CompareTo(0.0) > 0) ||
// (gridCellCohorts[FunctionalGroup][CohortToMergeTo].CohortAbundance.CompareTo(0.0) > 0))
// {
// Add the abundance of the second cohort to that of the first
gridCellCohorts[FunctionalGroup][CohortToMergeTo].CohortAbundance += (gridCellCohorts[FunctionalGroup][CohortToMergeFrom].CohortAbundance * gridCellCohorts[FunctionalGroup][CohortToMergeFrom].IndividualBodyMass) / gridCellCohorts[FunctionalGroup][CohortToMergeTo].IndividualBodyMass;
// Add the reproductive potential mass of the second cohort to that of the first
gridCellCohorts[FunctionalGroup][CohortToMergeTo].IndividualReproductivePotentialMass += (gridCellCohorts[FunctionalGroup][CohortToMergeFrom].IndividualReproductivePotentialMass * gridCellCohorts[FunctionalGroup][CohortToMergeFrom].CohortAbundance) / gridCellCohorts[FunctionalGroup][CohortToMergeTo].CohortAbundance;
// Set the abundance of the second cohort to zero
gridCellCohorts[FunctionalGroup][CohortToMergeFrom].CohortAbundance = 0.0;
// Designate both cohorts as having merged
gridCellCohorts[FunctionalGroup][CohortToMergeTo].Merged = true;
gridCellCohorts[FunctionalGroup][CohortToMergeFrom].Merged = true;
MergeCounter++;
CurrentListPosition++;
// }
// else
// {
// CurrentListPosition++;
// }
}
return(MergeCounter);
}
public uint[] WeightedMassOrderedIndices(GridCellCohortHandler gridCellCohorts, uint[][] cohortIndices, uint numberIndices)
{
NonStaticSimpleRNG random = new NonStaticSimpleRNG();
random.SetSeedFromSystemTime();
// A vector to hold indices of cohorts in order
int[] MassOrderedIndices;
double AboveMinMass = 0;
double OverallMinMass = 1E9;
double MaxMass = 0;
int MaxFG = 0;
int MaxC = 0;
double MinMass = 1E9;
int MinFG = 0;
int MinC = 0;
for (int ll = 0; ll < gridCellCohorts.Count; ll++)
{
// Loop over gridCellCohorts in the functional group
for (int kk = 0; kk < gridCellCohorts[ll].Count(); kk++)
{
//Check if this cohort is the smallest
if (gridCellCohorts[ll][kk].IndividualBodyMass.CompareTo(MaxMass) > 0)
{
MaxFG = ll;
MaxC = kk;
MaxMass = gridCellCohorts[ll][kk].IndividualBodyMass;
}
//Check if this cohort is the smallest
if (gridCellCohorts[ll][kk].IndividualBodyMass.CompareTo(OverallMinMass) < 0)
{
MinFG = ll;
MinC = kk;
OverallMinMass = gridCellCohorts[ll][kk].IndividualBodyMass;
}
}
}
double MassRange = MaxMass - OverallMinMass;
double logMassRange = Math.Log(MaxMass) - Math.Log(OverallMinMass);
MassOrderedIndices = (int[])(object)this.RandomlyOrderedIndices(numberIndices);//this.MassOrderedIndices(gridCellCohorts,cohortIndices,numberIndices);
uint[] OrderedIndices = new uint[numberIndices];
int[] Acted = new int[numberIndices];
int[] UseIndices;
int[] UnActedIndices;
uint UnActedCounter;
double p = 0;
int OrderIndex = 0;
int[] Cinds;
do
{
//UseIndices = MassOrderedIndices.Where((x,idx) => Acted[idx] == 0).ToArray();
UseIndices = new int[numberIndices - Acted.Sum()];
UnActedIndices = new int[numberIndices - Acted.Sum()];
UnActedCounter = 0;
for (int i = 0; i < Acted.Length; i++)
{
if (Acted[i] == 0)
{
UnActedIndices[UnActedCounter] = i;
UnActedCounter++;
}
}
for (int i = 0; i < UnActedIndices.Length; i++)
{
UseIndices[i] = MassOrderedIndices[UnActedIndices[i]];
}
foreach (uint i in UseIndices)
{
Cinds = FindJaggedArrayIndex(i, cohortIndices, numberIndices);
p = (Math.Log(gridCellCohorts[Cinds[0]][Cinds[1]].IndividualBodyMass) - Math.Log(OverallMinMass)) / logMassRange;
if (random.GetUniform() > p)
{
OrderedIndices[OrderIndex] = cohortIndices[Cinds[0]][Cinds[1]];
OrderIndex++;
Acted[Array.FindIndex(MassOrderedIndices, row => row == i)] = 1;
}
}
} while (Acted.Sum() < (int)(numberIndices * 0.8));
UseIndices = new int[numberIndices - Acted.Sum()];
UnActedIndices = new int[numberIndices - Acted.Sum()];
UnActedCounter = 0;
for (int i = 0; i < Acted.Length; i++)
{
if (Acted[i] == 0)
{
UnActedIndices[UnActedCounter] = i;
UnActedCounter++;
}
}
for (int i = 0; i < UnActedIndices.Length; i++)
{
UseIndices[i] = MassOrderedIndices[UnActedIndices[i]];
}
foreach (uint i in UseIndices)
{
Cinds = FindJaggedArrayIndex(i, cohortIndices, numberIndices);
OrderedIndices[OrderIndex] = cohortIndices[Cinds[0]][Cinds[1]];
OrderIndex++;
Acted[Array.FindIndex(MassOrderedIndices, row => row == i)] = 1;
}
//OrderedIndices[OrderIndex] = cohortIndices[MaxFG][MaxC];
return(OrderedIndices);
}