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agomez |
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#ifndef migrationproportion_h
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#define migrationproportion_h
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#include "likelihood.h" |
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#include "intmatrix.h" |
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#include "doublematrix.h" |
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#include "actionattimes.h" |
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#include "charptrvector.h" |
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#include "stockptrvector.h" |
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/**
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* \class MigrationProportion
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* \brief This is the class used to calculate a likelihood score based on the biomass of stocks caught by fleets
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*
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* This class calculates a likelihood score based on the difference between the biomass caught according to the model and the biomass caught by fleets, according to the landings data. This should lead to a zero likelihood score for a fleet that has been declared as a TotalPredator, since catch for that fleet should exactly match the landings data. However, for a fleet that has been declared as a LinearPredator, or a NumberPredator, the model will be calculating the catch based on model parameters and so will probably lead to a difference between the modelled landings biomass and actual landed catch.
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*/
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class MigrationProportion : public Likelihood {
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public:
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/**
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* \brief This is the MigrationProportion constructor
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* \param infile is the CommentStream to read the CatchDistribution data from
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* \param Area is the AreaClass for the current model
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* \param TimeInfo is the TimeClass for the current model
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* \param weight is the weight for the likelihood component
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* \param name is the name for the likelihood component
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*/
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MigrationProportion(CommentStream& infile, const AreaClass* const Area,
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const TimeClass* const TimeInfo, double weight, const char* name);
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/**
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* \brief This is the default MigrationProportion destructor
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*/
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virtual ~MigrationProportion();
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/**
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* \brief This function will calculate the likelihood score for the MigrationProportion component
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void addLikelihood(const TimeClass* const TimeInfo);
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/**
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* \brief This function will reset the MigrationProportion likelihood information
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* \param keeper is the Keeper for the current model
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*/
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virtual void Reset(const Keeper* const keeper);
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/**
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* \brief This function will print the summary MigrationProportion likelihood information
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* \param outfile is the ofstream that all the model information gets sent to
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*/
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virtual void Print(ofstream& outfile) const;
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/**
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* \brief This will select the fleets and stocks required to calculate the MigrationProportion likelihood score
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* \param Fleets is the FleetPtrVector of all the available fleets
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* \param Stocks is the StockPtrVector of all the available stocks
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*/
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void setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks);
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/**
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* \brief This function will print information from each MigrationProportion calculation
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* \param outfile is the ofstream that all the model likelihood information gets sent to
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo);
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/**
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* \brief This function will print summary information from each MigrationProportion likelihood calculation
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* \param outfile is the ofstream that all the model likelihood information gets sent to
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*/
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virtual void printSummary(ofstream& outfile);
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private:
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/**
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* \brief This function will read the MigrationProportion data from the input file
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* \param infile is the CommentStream to read the CatchDistribution data from
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* \param TimeInfo is the TimeClass for the current model
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* \param numarea is the number of areas that the likelihood data covers
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*/
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void readProportionData(CommentStream& infile, const TimeClass* TimeInfo, int numarea);
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/**
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* \brief This function will calculate the likelihood score for the current timestep based on a sum of squares function
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* \param TimeInfo is the TimeClass for the current model
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* \return likelihood score
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*/
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double calcLikSumSquares(const TimeClass* const TimeInfo);
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/**
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* \brief This is the DoubleMatrix used to store area distribution information specified in the input file
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* \note The indices for this object are [time][area]
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*/
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DoubleMatrix obsDistribution;
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/**
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* \brief This is the DoubleMatrix used to store area distribution information calculated in the model
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* \note The indices for this object are [time][area]
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*/
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DoubleMatrix modelDistribution;
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/**
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* \brief This is the DoubleVector used to store the calculated likelihood information
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* \note The indices for this object are [time]
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*/
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DoubleVector likelihoodValues;
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/**
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* \brief This is the CharPtrVector of the names of the stocks that will be used to calculate the likelihood score
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*/
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CharPtrVector stocknames;
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/**
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* \brief This is the IntMatrix used to store area information
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*/
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IntMatrix areas;
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/**
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* \brief This is the CharPtrVector of the names of the areas
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*/
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CharPtrVector areaindex;
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/**
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* \brief This is the identifier of the function to be used to calculate the likelihood component
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*/
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int functionnumber;
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/**
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* \brief This is the name of the function to be used to calculate the likelihood component
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*/
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char* functionname;
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/**
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* \brief This is the flag used to denote whether the biomass consumed or the numbers consumed is used to calculate the likelihood score (default is to print biomass)
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*/
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int biomass;
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/**
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* \brief This is the index of the timesteps for the likelihood component data
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*/
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int timeindex;
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/**
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* \brief This ActionAtTimes stores information about when the likelihood score should be calculated
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*/
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ActionAtTimes AAT;
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/**
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* \brief This is the IntVector used to store information about the years when the likelihood score should be calculated
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*/
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IntVector Years;
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/**
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* \brief This is the IntVector used to store information about the steps when the likelihood score should be calculated
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*/
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IntVector Steps;
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/**
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* \brief This is the StockPtrVector of the stocks that will be used to calculate the likelihood score
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*/
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StockPtrVector stocks;
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};
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#endif
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