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Mon Feb 10 17:09:07 2014 UTC
(10 years, 6 months ago)
by agomez File size: 6421 byte(s)
Initial version based on Gadget 2.2.00
#ifndef catchinkilos_h
#define catchinkilos_h
#include "likelihood.h"
#include "actionattimes.h"
#include "commentstream.h"
#include "charptrvector.h"
#include "predatorptrvector.h"
#include "doublematrix.h"
#include "intmatrix.h"
/**
* \class CatchInKilos
* \brief This is the class used to calculate a likelihood score based on the biomass of stocks caught by fleets
*
* 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.
*/
class CatchInKilos : public Likelihood {
public:
/**
* \brief This is the CatchInKilos constructor
* \param infile is the CommentStream to read the CatchInKilos data from
* \param Area is the AreaClass for the current model
* \param TimeInfo is the TimeClass for the current model
* \param weight is the weight for the likelihood component
* \param name is the name for the likelihood component
*/
CatchInKilos(CommentStream& infile, const AreaClass* const Area,
const TimeClass* const TimeInfo, double weight, const char* name);
/**
* \brief This is the default CatchInKilos destructor
*/
~CatchInKilos();
/**
* \brief This function will reset the CatchInKilos likelihood information
* \param keeper is the Keeper for the current model
*/
virtual void Reset(const Keeper* const keeper);
/**
* \brief This function will print the summary CatchInKilos likelihood information
* \param outfile is the ofstream that all the model information gets sent to
*/
virtual void Print(ofstream& outfile) const;
/**
* \brief This function will print summary information from each CatchInKilos likelihood calculation
* \param outfile is the ofstream that all the model likelihood information gets sent to
*/
virtual void printSummary(ofstream& outfile);
/**
* \brief This function will print information from each CatchInKilos calculation
* \param outfile is the ofstream that all the model likelihood information gets sent to
* \param TimeInfo is the TimeClass for the current model
*/
virtual void printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo);
/**
* \brief This function will calculate the likelihood score for the CatchInKilos component
* \param TimeInfo is the TimeClass for the current model
*/
virtual void addLikelihood(const TimeClass* const TimeInfo);
/**
* \brief This will select the fleets and stocks required to calculate the CatchInKilos likelihood score
* \param Fleets is the FleetPtrVector of all the available fleets
* \param Stocks is the StockPtrVector of all the available stocks
*/
void setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks);
private:
/**
* \brief This function will read the CatchInKilos data from the input file
* \param infile is the CommentStream to read the CatchInKilos data from
* \param TimeInfo is the TimeClass for the current model
* \param numarea is the number of areas that the likelihood data covers
*/
void readCatchInKilosData(CommentStream& infile, const TimeClass* TimeInfo, int numarea);
/**
* \brief This function will calculate the likelihood score for the current timestep based on a sum of squares function
* \param TimeInfo is the TimeClass for the current model
* \return likelihood score
*/
double calcLikSumSquares(const TimeClass* const TimeInfo);
/**
* \brief This is the CharPtrVector of the names of the fleets that will be used to calculate the likelihood score
*/
CharPtrVector fleetnames;
/**
* \brief This is the CharPtrVector of the names of the stocks that will be used to calculate the likelihood score
*/
CharPtrVector stocknames;
/**
* \brief This is the CharPtrVector of the names of the areas
*/
CharPtrVector areaindex;
/**
* \brief This is the IntMatrix used to denote which fleets catch which stocks
*/
IntMatrix preyindex;
/**
* \brief This is the PredatorPtrVector of the predators that will be used to calculate the likelihood score
*/
PredatorPtrVector predators;
/**
* \brief This is the IntMatrix used to store area information
*/
IntMatrix areas;
/**
* \brief This is the DoubleMatrix used to store catch information specified in the input file
* \note The indices for this object are [time][area]
*/
DoubleMatrix obsDistribution;
/**
* \brief This is the DoubleMatrix used to store catch information calculated in the model
* \note The indices for this object are [time][area]
*/
DoubleMatrix modelDistribution;
/**
* \brief This is the DoubleMatrix used to store the calculated likelihood information
* \note The indices for this object are [time][area]
*/
DoubleMatrix likelihoodValues;
/**
* \brief This is the flag to denote whether the likelihood calculation should aggregate data over a whole year.
* \note The default value is 0, which calculates the likelihood score on each timestep
*/
int yearly;
/**
* \brief This is the value of epsilon used when calculating the likelihood score
*/
double epsilon;
/**
* \brief This ActionAtTimes stores information about when the likelihood score should be calculated
*/
ActionAtTimes AAT;
/**
* \brief This is the IntVector used to store information about the years when the likelihood score should be calculated
*/
IntVector Years;
/**
* \brief This is the IntVector used to store information about the steps when the likelihood score should be calculated
*/
IntVector Steps;
/**
* \brief This is the index of the timesteps for the likelihood component data
*/
int timeindex;
/**
* \brief This is the identifier of the function to be used to calculate the likelihood component
*/
int functionnumber;
/**
* \brief This is the name of the function to be used to calculate the likelihood component
*/
char* functionname;
};
#endif