C# FunctionalGroupDefinitions.GetAllTraitNames方法代码示例

        /// <summary>
        /// Calculates functional diversity of cohorts in a grid cell as functional richness and functional diveregence (using the Rao Index)
        /// </summary>
        /// <param name="ecosystemModelGrid">The model grid</param>
        /// <param name="cohortDefinitions">The functional group definitions for cohorts in the model</param>
        /// <param name="cellIndices">The list of cell indices in the current model simulation</param>
        /// <param name="cellIndex">The index of the current cell within the list of cells to run</param>
        /// <returns>A pair of values representing the functional richness and functional divergence (functional richness currently disabled!)</returns>
        public double[] CalculateFunctionalDiversity(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortDefinitions, 
            List<uint[]> cellIndices, int cellIndex)
        {
            //Get the cohorts for the specified cell
            GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);

            //Variable to hold the functional richness value for the current cohorts
            double FunctionalRichness;
            //Variable to hold the functional divergence value for the current cohorts
            double RaoFunctionalDivergence = 0.0;
            double[,] Distances= new double[CellCohorts.GetNumberOfCohorts(), CellCohorts.GetNumberOfCohorts()];

            List<string> AllTraitNames = cohortDefinitions.GetAllTraitNames().ToList();

            AllTraitNames.Remove("realm");
            AllTraitNames.Remove("heterotroph/autotroph");
            AllTraitNames.Remove("diet");
            string[] TraitNames = AllTraitNames.ToArray();

            //Define upper and lower limits for body mass
            double MinMass = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("minimum mass").Min();
            double MaxMass = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("maximum mass").Max();
            //Define upp and lower limits for trophic index
            double MaxTI = 40.0;
            double MinTI = 1.0;

            // Construct an array of functional trait values for each cohort
            // Rows are specific cohorts
            // Columns are the functional traits (these include different types:
            //      quantative: current mass, trophic index
            //      nominal: diet, reproductive strategy, mobility, metabolism
            Tuple<double[], string[]>[] CohortFunctionalTraits = new Tuple<double[], string[]>[CellCohorts.GetNumberOfCohorts()];
            double[] IndividualBodyMasses = new double[CellCohorts.GetNumberOfCohorts()];
            double[] TrophicIndex = new double[CellCohorts.GetNumberOfCohorts()];
            string[][] CohortNominalTraitValues= new string[TraitNames.Length][];

            for (int i = 0; i < TraitNames.Length; i++)
            {
                CohortNominalTraitValues[i] = new string[CellCohorts.GetNumberOfCohorts()];
            }

            // Construct a vector of cohort biomass (in case we want to weight by them)
            double[] CohortTotalBiomasses = new double[CellCohorts.GetNumberOfCohorts()];

            string[] TraitValues = new string[TraitNames.Length];
            double[] QuantitativeTraitValues= new double[2];
            int CohortNumberCounter = 0;
            for (int fg = 0; fg < CellCohorts.Count; fg++)
            {
                foreach (Cohort c in CellCohorts[fg])
                {
                    TraitValues = cohortDefinitions.GetTraitValues(TraitNames, fg);
                    for (int ii = 0; ii < TraitValues.Length; ii++)
                    {
                        CohortNominalTraitValues[ii][CohortNumberCounter] = TraitValues[ii];
                    }

                    IndividualBodyMasses[CohortNumberCounter] = c.IndividualBodyMass;
                    TrophicIndex[CohortNumberCounter] = c.TrophicIndex;

                    QuantitativeTraitValues[0] = c.IndividualBodyMass;
                    QuantitativeTraitValues[1] = c.TrophicIndex;

                    CohortFunctionalTraits[CohortNumberCounter] = new Tuple<double[], string[]>(QuantitativeTraitValues, TraitValues);

                    CohortTotalBiomasses[CohortNumberCounter] = (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;

                    CohortNumberCounter++;
                }
            }

            List<double[,]> DistanceList = new List<double[,]>();

            DistanceList.Add(CalculateDistanceMatrix(IndividualBodyMasses, MaxMass, MinMass));
            DistanceList.Add(CalculateDistanceMatrix(TrophicIndex, MaxTI, MinTI));
            foreach (string[] t in CohortNominalTraitValues)
            {
                DistanceList.Add(CalculateDistanceMatrix(t));
            }

            Distances = CalculateAggregateDistance(DistanceList);

            RaoFunctionalDivergence = RaoEntropy(Distances, CohortTotalBiomasses);

            return new double[] {0.0,RaoFunctionalDivergence};
        }