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#ifndef stock_h
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#define stock_h
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#include "areatime.h" |
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#include "agebandmatrix.h" |
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#include "agebandmatrixratioptrvector.h" |
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#include "base.h" |
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#include "conversionindex.h" |
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#include "stockptrvector.h" |
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#include "tagptrvector.h" |
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#include "commentstream.h" |
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class Stock;
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class Keeper;
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class NaturalMortality;
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class Grower;
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class InitialCond;
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class Migration;
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class Transition;
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class PopPredator;
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class StockPrey;
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class Maturity;
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class RenewalData;
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class SpawnData;
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class StrayData;
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/**
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* \class Stock
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* \brief This is the class used to model a stock within the Gadget model
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*
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* This class is used to model the population of a stock during a model simulation.
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*/
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class Stock : public BaseClass {
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public:
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/**
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* \brief This is the Stock constructor
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* \param infile is the CommentStream to read the stock parameters from
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* \param givenname is the name of the stock
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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 keeper is the Keeper for the current model
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*/
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Stock(CommentStream& infile, const char* givenname, const AreaClass* const Area,
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const TimeClass* const TimeInfo, Keeper* const keeper);
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/**
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* \brief This is the default Stock constructor
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* \param givenname is the name of the stock
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*/
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Stock(const char* givenname);
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/**
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* \brief This is the default Stock destructor
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*/
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virtual ~Stock();
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/**
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* \brief This function will update the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void calcNumbers(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will reduce the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void reducePop(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will calculate the growth of the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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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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*/
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virtual void Grow(int area, const AreaClass* const Area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will calculate any transition of the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void updateAgePart1(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will calculate the age increase of the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void updateAgePart2(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will implement the transiton of the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void updateAgePart3(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will calculate the spawning of the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void updatePopulationPart1(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will calculate add the newly matured stock into the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void updatePopulationPart2(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will calculate add the new recruits into the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void updatePopulationPart3(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will calculate calculate the straying of the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void updatePopulationPart4(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will calculate add the strayed stock into the model population for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void updatePopulationPart5(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will calculate the modelled consumption for an area in the model
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* \param area is an integer to denote the internal area of interest
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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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*/
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virtual void calcEat(int area, const AreaClass* const Area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will check the modelled consumption for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void checkEat(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will adjust the modelled consumption for an area in the model
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* \param area is an integer to denote the internal area of interest
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void adjustEat(int area, const TimeClass* const TimeInfo);
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/**
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* \brief This function will reset the model population
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void Reset(const TimeClass* const TimeInfo);
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/**
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* \brief This function will print the model population
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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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void Print(ofstream& outfile) const;
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/**
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* \brief This function will implement the migration of the model population for the model
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* \param TimeInfo is the TimeClass for the current model
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*/
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virtual void Migrate(const TimeClass* const TimeInfo);
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/**
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* \brief This function will add a AgeBandMatrix to the current stock population
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* \param Addition is the AgeBandMatrix that will be added to the population
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* \param CI is the ConversionIndex that will convert between the length groups
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* \param area is an integer to denote the internal area of interest
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* \param ratio is a multiplicative constant applied
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*/
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void Add(const AgeBandMatrix& Addition, const ConversionIndex* const CI, int area, double ratio);
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/**
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* \brief This function will add a AgeBandMatrixRatioPtrVector to the current tagged stock population
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* \param Addition is the AgeBandMatrixRatioPtrVector that will be added to the tagged population
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* \param CI is the ConversionIndex that will convert between the length groups
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* \param area is an integer to denote the internal area of interest
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* \param ratio is a multiplicative constant applied
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*/
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void Add(const AgeBandMatrixRatioPtrVector& Addition, const ConversionIndex* const CI, int area, double ratio);
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/**
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* \brief This will return the prey information for the stock
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* \return prey
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*/
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StockPrey* getPrey() const;
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/**
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* \brief This will return the migration information for the stock
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* \return migration
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*/
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Migration* getMigration() const;
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/**
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* \brief This will return the predation information for the stock
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* \return predator
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*/
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PopPredator* getPredator() const;
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/**
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* \brief This will return the current population of the stock on a given area
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* \param area is the area identifier
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* \return alkeys, a AgeBandMatrix containing the population of the stock
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*/
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AgeBandMatrix& getCurrentALK(int area) { return Alkeys[this->areaNum(area)]; };
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/**
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* \brief This will return the population of the stock on a given area at the start of the current timestep
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* \param area is the area identifier
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* \return alkeys, a AgeBandMatrix containing the population of the stock
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*/
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AgeBandMatrix& getConsumptionALK(int area);
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/**
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* \brief This will return the length group information for the stock
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* \return LgrpDiv
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*/
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const LengthGroupDivision* getLengthGroupDiv() const { return LgrpDiv; };
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/**
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* \brief This function will initialise the stock and set-up links to any related stocks
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* \param stockvec is the StockPtrVector of all the available stocks
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*/
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void setStock(StockPtrVector& stockvec);
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/**
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* \brief This function will check to see if the age of the stock should be increased on the current timestep or not
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* \param TimeInfo is the TimeClass for the current model
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* \return 1 if the age of the stock should be increased, 0 otherwise
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*/
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int isBirthday(const TimeClass* const TimeInfo) const;
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/**
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* \brief This function will return the flag used to denote whether the stock is eaten or not
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* \return flag
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*/
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int isEaten() const { return iseaten; };
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/**
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* \brief This function will return the flag used to denote whether the stock will spawn or not
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* \return flag
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*/
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int doesSpawn() const { return doesspawn; };
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/**
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* \brief This function will return the flag used to denote whether the stock will stray or not
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* \return flag
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*/
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int doesStray() const { return doesstray; };
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/**
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* \brief This function will return the flag used to denote whether the stock will move or not
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* \return flag
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*/
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int doesMove() const { return doesmove; };
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/**
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* \brief This function will return the flag used to denote whether the stock will eat or not
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* \return flag
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*/
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int doesEat() const { return doeseat; };
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/**
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* \brief This function will return the flag used to denote whether the stock will mature or not
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* \return flag
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*/
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int doesMature() const { return doesmature; };
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/**
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* \brief This function will return the flag used to denote whether the stock will renew or not
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* \return flag
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*/
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int doesRenew() const { return doesrenew; };
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/**
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* \brief This function will return the flag used to denote whether the stock will grow or not
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* \return flag
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*/
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int doesGrow() const { return doesgrow; };
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/**
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* \brief This function will return the flag used to denote whether the stock will migrate or not
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* \return flag
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*/
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int doesMigrate() const { return doesmigrate; };
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/**
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* \brief This function will return the flag used to denote whether the stock has been tagged or not
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* \return flag
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*/
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int isTagged() const { return istagged; };
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/**
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* \brief This function will set the flag to denote that the stock has been tagged
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*/
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void setTaggedStock() { istagged = 1; };
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/**
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* \brief This function will initialise the tagging experiments for the stock and any related stocks
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*/
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void setTagged();
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/**
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* \brief This will return the minimum age of the stock
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* \return minimum age
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*/
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int minAge() const { return Alkeys[0].minAge(); };
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/**
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* \brief This will return the maximum age of the stock
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* \return maximum age
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*/
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int maxAge() const { return Alkeys[0].maxAge(); };
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/**
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* \brief This will return the total population size (in numbers) of the stock on a given area
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* \param area is the area identifier
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* \return population size
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*/
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double getTotalStockNumber(int area) const;
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/**
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* \brief This will return the total population size (in numbers) of the stock across all areas
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* \return population size
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*/
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double getTotalStockNumberAllAreas() const;
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/**
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* \brief This will return the total population biomass of the stock on a given area
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* \param area is the area identifier
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* \return population biomass
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*/
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double getTotalStockBiomass(int area) const;
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/**
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* \brief This will return the total population biomass of the stock across all areas
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* \return population biomass
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*/
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double getTotalStockBiomassAllAreas() const;
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/**
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* \brief This will return the stocks that this stock will mature in to
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* \return maturestocks, a StockPtrVector of the stocks that this stock will mature into
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*/
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const StockPtrVector& getMatureStocks();
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/**
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* \brief This will return the stocks that this stock will move in to
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* \return transitionstocks, a StockPtrVector of the stocks that this stock will move into
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*/
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const StockPtrVector& getTransitionStocks();
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/**
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* \brief This will return the stocks that this stock will stray in to
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* \return straystocks, a StockPtrVector of the stocks that this stock will stray into
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*/
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const StockPtrVector& getStrayStocks();
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| 319 : |
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/**
|
| 320 : |
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* \brief This function will add details for a new tagging experiment on the current stock
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| 321 : |
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* \param tagbyagelength is the AgeBandMatrixPtrVector of the new tagged population
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| 322 : |
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* \param newtag is the Tags for the new tagging experiment
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| 323 : |
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* \param tagloss is the proportion of tags that are lost for the new tagging experiment
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| 324 : |
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*/
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| 325 : |
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void addTags(AgeBandMatrixPtrVector* tagbyagelength, Tags* newtag, double tagloss);
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| 326 : |
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/**
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| 327 : |
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* \brief This function will remove a tagging experiment from the current tagged stock population
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| 328 : |
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* \param tagname is the name of the tagging experiment to be removed
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| 329 : |
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*/
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| 330 : |
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void deleteTags(const char* tagname);
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| 331 : |
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protected:
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| 332 : |
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/**
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| 333 : |
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* \brief This is the AgeBandMatrixPtrVector used to store information about the stock population
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| 334 : |
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*/
|
| 335 : |
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AgeBandMatrixPtrVector Alkeys;
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| 336 : |
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/**
|
| 337 : |
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* \brief This is the AgeBandMatrixRatioPtrVector used to store information about the tagged population from any tagging experiments performed on the stock
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| 338 : |
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*/
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| 339 : |
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AgeBandMatrixRatioPtrVector tagAlkeys;
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| 340 : |
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/**
|
| 341 : |
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* \brief This is the TagPtrVector used to store information about the tagging experiments
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| 342 : |
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*/
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| 343 : |
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TagPtrVector allTags;
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| 344 : |
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/**
|
| 345 : |
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* \brief This is the TagPtrVector used to store information about how the tagging experiments affect the population that mature
|
| 346 : |
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*/
|
| 347 : |
|
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TagPtrVector matureTags;
|
| 348 : |
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/**
|
| 349 : |
|
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* \brief This is the TagPtrVector used to store information about how the tagging experiments affect the population that move
|
| 350 : |
|
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*/
|
| 351 : |
|
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TagPtrVector transitionTags;
|
| 352 : |
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/**
|
| 353 : |
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* \brief This is the TagPtrVector used to store information about how the tagging experiments affect the population that stray
|
| 354 : |
|
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*/
|
| 355 : |
|
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TagPtrVector strayTags;
|
| 356 : |
|
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/**
|
| 357 : |
|
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* \brief This is the StrayData used to calculate information about the straying of the stock
|
| 358 : |
|
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*/
|
| 359 : |
|
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StrayData* stray;
|
| 360 : |
|
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/**
|
| 361 : |
|
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* \brief This is the SpawnData used to calculate information about the spawning of the stock
|
| 362 : |
|
|
*/
|
| 363 : |
|
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SpawnData* spawner;
|
| 364 : |
|
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/**
|
| 365 : |
|
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* \brief This is the RenewalData used to calculate information about the renewal of the stock
|
| 366 : |
|
|
*/
|
| 367 : |
|
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RenewalData* renewal;
|
| 368 : |
|
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/**
|
| 369 : |
|
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* \brief This is the Maturity used to calculate information about the maturation of the stock
|
| 370 : |
|
|
*/
|
| 371 : |
|
|
Maturity* maturity;
|
| 372 : |
|
|
/**
|
| 373 : |
|
|
* \brief This is the Transition used to calculate information about the movement of the stock
|
| 374 : |
|
|
*/
|
| 375 : |
|
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Transition* transition;
|
| 376 : |
|
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/**
|
| 377 : |
|
|
* \brief This is the Migration used to calculate information about the migration of the stock
|
| 378 : |
|
|
*/
|
| 379 : |
|
|
Migration* migration;
|
| 380 : |
|
|
/**
|
| 381 : |
|
|
* \brief This is the Prey used to calculate information about the consumption of the stock
|
| 382 : |
|
|
*/
|
| 383 : |
|
|
StockPrey* prey;
|
| 384 : |
|
|
/**
|
| 385 : |
|
|
* \brief This is the PopPredator used to calculate information about the consumption by the stock
|
| 386 : |
|
|
*/
|
| 387 : |
|
|
PopPredator* predator;
|
| 388 : |
|
|
/**
|
| 389 : |
|
|
* \brief This is the InitialCond used to calculate information about the initial conditions of the stock
|
| 390 : |
|
|
*/
|
| 391 : |
|
|
InitialCond* initial;
|
| 392 : |
|
|
/**
|
| 393 : |
|
|
* \brief This is the LengthGroupDivision used to store length information
|
| 394 : |
|
|
*/
|
| 395 : |
|
|
LengthGroupDivision* LgrpDiv;
|
| 396 : |
|
|
/**
|
| 397 : |
|
|
* \brief This is the Grower used to calculate information about the growth of the stock
|
| 398 : |
|
|
*/
|
| 399 : |
|
|
Grower* grower;
|
| 400 : |
|
|
/**
|
| 401 : |
|
|
* \brief This is the NaturalMortality used to calculate information about the natural mortality of the stock
|
| 402 : |
|
|
*/
|
| 403 : |
|
|
NaturalMortality* naturalm;
|
| 404 : |
|
|
/**
|
| 405 : |
|
|
* \brief This is the flag used to denote whether the stock will eat (ie. is a Predator) or not
|
| 406 : |
|
|
*/
|
| 407 : |
|
|
int doeseat;
|
| 408 : |
|
|
/**
|
| 409 : |
|
|
* \brief This is the flag used to denote whether the stock will move or not
|
| 410 : |
|
|
*/
|
| 411 : |
|
|
int doesmove;
|
| 412 : |
|
|
/**
|
| 413 : |
|
|
* \brief This is the flag used to denote whether the stock is eaten (ie. is a Prey) or not
|
| 414 : |
|
|
*/
|
| 415 : |
|
|
int iseaten;
|
| 416 : |
|
|
/**
|
| 417 : |
|
|
* \brief This is the flag used to denote whether the stock will spawn or not
|
| 418 : |
|
|
*/
|
| 419 : |
|
|
int doesspawn;
|
| 420 : |
|
|
/**
|
| 421 : |
|
|
* \brief This is the flag used to denote whether the stock will mature or not
|
| 422 : |
|
|
*/
|
| 423 : |
|
|
int doesmature;
|
| 424 : |
|
|
/**
|
| 425 : |
|
|
* \brief This is the flag used to denote whether the stock will renew or not
|
| 426 : |
|
|
*/
|
| 427 : |
|
|
int doesrenew;
|
| 428 : |
|
|
/**
|
| 429 : |
|
|
* \brief This is the flag used to denote whether the stock will grow or not
|
| 430 : |
|
|
*/
|
| 431 : |
|
|
int doesgrow;
|
| 432 : |
|
|
/**
|
| 433 : |
|
|
* \brief This is the flag used to denote whether the stock will migrate or not
|
| 434 : |
|
|
*/
|
| 435 : |
|
|
int doesmigrate;
|
| 436 : |
|
|
/**
|
| 437 : |
|
|
* \brief This is the flag used to denote whether the stock will stray or not
|
| 438 : |
|
|
*/
|
| 439 : |
|
|
int doesstray;
|
| 440 : |
|
|
/**
|
| 441 : |
|
|
* \brief This is the timestep that the population will increase in age in the simulation
|
| 442 : |
|
|
* \note This is currently set to the last timestep in the year
|
| 443 : |
|
|
*/
|
| 444 : |
|
|
int birthdate;
|
| 445 : |
|
|
/**
|
| 446 : |
|
|
* \brief This is the flag used to denote whether the stock has been included in a tagging experiment or not
|
| 447 : |
|
|
*/
|
| 448 : |
|
|
int istagged;
|
| 449 : |
|
|
/**
|
| 450 : |
|
|
* \brief This is the PopInfoMatrix used to temporarily store the population during the growth calculation
|
| 451 : |
|
|
*/
|
| 452 : |
|
|
PopInfoMatrix tmpPopulation;
|
| 453 : |
|
|
/**
|
| 454 : |
|
|
* \brief This is the PopInfoVector used to temporarily store the population during the migration calculation
|
| 455 : |
|
|
*/
|
| 456 : |
|
|
PopInfoVector tmpMigrate;
|
| 457 : |
|
|
};
|
| 458 : |
|
|
|
| 459 : |
|
|
#endif
|
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