Annotation of /trunk/gadget/catchinkilos.h

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1 :	agomez	1	#ifndef catchinkilos_h
2 :			#define catchinkilos_h
3 :
4 :			#include "likelihood.h"
5 :			#include "actionattimes.h"
6 :			#include "commentstream.h"
7 :			#include "charptrvector.h"
8 :			#include "predatorptrvector.h"
9 :			#include "doublematrix.h"
10 :			#include "intmatrix.h"
11 :
12 :			/**
13 :			* \class CatchInKilos
14 :			* \brief This is the class used to calculate a likelihood score based on the biomass of stocks caught by fleets
15 :			*
16 :			* 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.
17 :			*/
18 :			class CatchInKilos : public Likelihood {
19 :			public:
20 :			/**
21 :			* \brief This is the CatchInKilos constructor
22 :			* \param infile is the CommentStream to read the CatchInKilos data from
23 :			* \param Area is the AreaClass for the current model
24 :			* \param TimeInfo is the TimeClass for the current model
25 :			* \param weight is the weight for the likelihood component
26 :			* \param name is the name for the likelihood component
27 :			*/
28 :			CatchInKilos(CommentStream& infile, const AreaClass* const Area,
29 :			const TimeClass* const TimeInfo, double weight, const char* name);
30 :			/**
31 :			* \brief This is the default CatchInKilos destructor
32 :			*/
33 :			~CatchInKilos();
34 :			/**
35 :			* \brief This function will reset the CatchInKilos likelihood information
36 :			* \param keeper is the Keeper for the current model
37 :			*/
38 :			virtual void Reset(const Keeper* const keeper);
39 :			/**
40 :			* \brief This function will print the summary CatchInKilos likelihood information
41 :			* \param outfile is the ofstream that all the model information gets sent to
42 :			*/
43 :			virtual void Print(ofstream& outfile) const;
44 :			/**
45 :			* \brief This function will print summary information from each CatchInKilos likelihood calculation
46 :			* \param outfile is the ofstream that all the model likelihood information gets sent to
47 :			*/
48 :			virtual void printSummary(ofstream& outfile);
49 :			/**
50 :			* \brief This function will print information from each CatchInKilos calculation
51 :			* \param outfile is the ofstream that all the model likelihood information gets sent to
52 :			* \param TimeInfo is the TimeClass for the current model
53 :			*/
54 :			virtual void printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo);
55 :			/**
56 :			* \brief This function will calculate the likelihood score for the CatchInKilos component
57 :			* \param TimeInfo is the TimeClass for the current model
58 :			*/
59 :			virtual void addLikelihood(const TimeClass* const TimeInfo);
60 :			/**
61 :			* \brief This will select the fleets and stocks required to calculate the CatchInKilos likelihood score
62 :			* \param Fleets is the FleetPtrVector of all the available fleets
63 :			* \param Stocks is the StockPtrVector of all the available stocks
64 :			*/
65 :			void setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks);
66 :			private:
67 :			/**
68 :			* \brief This function will read the CatchInKilos data from the input file
69 :			* \param infile is the CommentStream to read the CatchInKilos data from
70 :			* \param TimeInfo is the TimeClass for the current model
71 :			* \param numarea is the number of areas that the likelihood data covers
72 :			*/
73 :			void readCatchInKilosData(CommentStream& infile, const TimeClass* TimeInfo, int numarea);
74 :			/**
75 :			* \brief This function will calculate the likelihood score for the current timestep based on a sum of squares function
76 :			* \param TimeInfo is the TimeClass for the current model
77 :			* \return likelihood score
78 :			*/
79 :			double calcLikSumSquares(const TimeClass* const TimeInfo);
80 :			/**
81 :			* \brief This is the CharPtrVector of the names of the fleets that will be used to calculate the likelihood score
82 :			*/
83 :			CharPtrVector fleetnames;
84 :			/**
85 :			* \brief This is the CharPtrVector of the names of the stocks that will be used to calculate the likelihood score
86 :			*/
87 :			CharPtrVector stocknames;
88 :			/**
89 :			* \brief This is the CharPtrVector of the names of the areas
90 :			*/
91 :			CharPtrVector areaindex;
92 :			/**
93 :			* \brief This is the IntMatrix used to denote which fleets catch which stocks
94 :			*/
95 :			IntMatrix preyindex;
96 :			/**
97 :			* \brief This is the PredatorPtrVector of the predators that will be used to calculate the likelihood score
98 :			*/
99 :			PredatorPtrVector predators;
100 :			/**
101 :			* \brief This is the IntMatrix used to store area information
102 :			*/
103 :			IntMatrix areas;
104 :			/**
105 :			* \brief This is the DoubleMatrix used to store catch information specified in the input file
106 :			* \note The indices for this object are [time][area]
107 :			*/
108 :			DoubleMatrix obsDistribution;
109 :			/**
110 :			* \brief This is the DoubleMatrix used to store catch information calculated in the model
111 :			* \note The indices for this object are [time][area]
112 :			*/
113 :			DoubleMatrix modelDistribution;
114 :			/**
115 :			* \brief This is the DoubleMatrix used to store the calculated likelihood information
116 :			* \note The indices for this object are [time][area]
117 :			*/
118 :			DoubleMatrix likelihoodValues;
119 :			/**
120 :			* \brief This is the flag to denote whether the likelihood calculation should aggregate data over a whole year.
121 :			* \note The default value is 0, which calculates the likelihood score on each timestep
122 :			*/
123 :			int yearly;
124 :			/**
125 :			* \brief This is the value of epsilon used when calculating the likelihood score
126 :			*/
127 :			double epsilon;
128 :			/**
129 :			* \brief This ActionAtTimes stores information about when the likelihood score should be calculated
130 :			*/
131 :			ActionAtTimes AAT;
132 :			/**
133 :			* \brief This is the IntVector used to store information about the years when the likelihood score should be calculated
134 :			*/
135 :			IntVector Years;
136 :			/**
137 :			* \brief This is the IntVector used to store information about the steps when the likelihood score should be calculated
138 :			*/
139 :			IntVector Steps;
140 :			/**
141 :			* \brief This is the index of the timesteps for the likelihood component data
142 :			*/
143 :			int timeindex;
144 :			/**
145 :			* \brief This is the identifier of the function to be used to calculate the likelihood component
146 :			*/
147 :			int functionnumber;
148 :			/**
149 :			* \brief This is the name of the function to be used to calculate the likelihood component
150 :			*/
151 :			char* functionname;
152 :			};
153 :
154 :			#endif

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