Annotation of /trunk/gadget/sionstep.h

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1 :	agomez	1	#ifndef sionstep_h
2 :			#define sionstep_h
3 :
4 :			#include "areatime.h"
5 :			#include "doublematrixptrvector.h"
6 :			#include "intmatrix.h"
7 :			#include "charptrvector.h"
8 :			#include "conversionindex.h"
9 :			#include "commentstream.h"
10 :			#include "actionattimes.h"
11 :			#include "agebandmatrix.h"
12 :			#include "stockaggregator.h"
13 :			#include "regressionline.h"
14 :			#include "hasname.h"
15 :			#include "gadget.h"
16 :
17 :			enum FitType { LINEARFIT = 1, LOGLINEARFIT, WEIGHTLINEARFIT, LOGWEIGHTLINEARFIT,
18 :			FIXEDSLOPELINEARFIT, FIXEDSLOPELOGLINEARFIT, FIXEDSLOPEWEIGHTLINEARFIT,
19 :			FIXEDSLOPELOGWEIGHTLINEARFIT, FIXEDINTERCEPTLINEARFIT, FIXEDINTERCEPTLOGLINEARFIT,
20 :			FIXEDINTERCEPTWEIGHTLINEARFIT, FIXEDINTERCEPTLOGWEIGHTLINEARFIT,
21 :			FIXEDLINEARFIT, FIXEDLOGLINEARFIT, FIXEDWEIGHTLINEARFIT, FIXEDLOGWEIGHTLINEARFIT };
22 :			enum SIType { SILENGTH = 1, SIAGE, SIFLEET, SIEFFORT, SIACOUSTIC };
23 :
24 :			/**
25 :			* \class SIOnStep
26 :			* \brief This is the base class used to calculate a likelihood score by fitting a regression line to the model population and survey index data
27 :			* \note This will always be overridden by the derived classes that actually calculate the survey indices and the likelihood score from the regression line
28 :			*/
29 :			class SIOnStep : public HasName {
30 :			public:
31 :			/**
32 :			* \brief This is the default SIOnStep constructor
33 :			* \param infile is the CommentStream to read the SIOnStep data from
34 :			* \param datafilename is the name of the file to read the index data from
35 :			* \param aindex is the CharPtrVector of the names of the areas for the survey indices
36 :			* \param TimeInfo is the TimeClass for the current model
37 :			* \param areas is the IntMatrix of the areas that the survey indices are calculated on
38 :			* \param charindex is the CharPtrVector of the names of the column index for the survey indices
39 :			* \param givenname is the name for the SIOnStep component
40 :			* \param bio is the flag to denote whether the index should be based on the biomass or not
41 :			* \param type is the SIType of the SIOnStep
42 :			*/
43 :			SIOnStep(CommentStream& infile, const char* datafilename, const CharPtrVector& aindex,
44 :			const TimeClass* const TimeInfo, const IntMatrix& areas, const CharPtrVector& charindex,
45 :			const char* givenname, int bio, SIType type);
46 :			/**
47 :			* \brief This is the default SIOnStep destructor
48 :			*/
49 :			virtual ~SIOnStep();
50 :			/**
51 :			* \brief This function will sum the survey index data
52 :			* \param TimeInfo is the TimeClass for the current model
53 :			*/
54 :			virtual void Sum(const TimeClass* const TimeInfo) = 0;
55 :			/**
56 :			* \brief This will select the fleets and stocks required to calculate the regression line
57 :			* \param Fleets is the FleetPtrVector of all the available fleets
58 :			* \param Stocks is the StockPtrVector of all the available stocks
59 :			*/
60 :			virtual void setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks) = 0;
61 :			/**
62 :			* \brief This function will reset the SIOnStep information
63 :			*/
64 :			virtual void Reset();
65 :			/**
66 :			* \brief This function will print the SIOnStep information
67 :			* \param outfile is the ofstream that all the model information gets sent to
68 :			*/
69 :			virtual void Print(ofstream& outfile) const = 0;
70 :			/**
71 :			* \brief This function will print information from each SIOnStep regression calculation
72 :			* \param outfile is the ofstream that all the model likelihood information gets sent to
73 :			* \param TimeInfo is the TimeClass for the current model
74 :			*/
75 :			virtual void printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo);
76 :			/**
77 :			* \brief This function will print summary information from each SIOnStep regression calculation
78 :			* \param outfile is the ofstream that all the model likelihood information gets sent to
79 :			* \param weight is the weight of the likelihood component
80 :			*/
81 :			virtual void printSummary(ofstream& outfile, const double weight);
82 :			/**
83 :			* \brief This function will calculate the SSE from the regression line
84 :			* \return SSE from the regession line
85 :			*/
86 :			virtual double calcSSE();
87 :			/**
88 :			* \brief This will return the fit type for the regression line
89 :			* \return fittype
90 :			*/
91 :			FitType getType() const { return fittype; };
92 :			/**
93 :			* \brief This will return the type of survey index data to be used
94 :			* \return sitype
95 :			*/
96 :			SIType getSIType() const { return sitype; };
97 :			protected:
98 :			/**
99 :			* \brief This is the IntMatrix used to store information about the areas that the survey index should be calculated on
100 :			*/
101 :			IntMatrix Areas;
102 :			/**
103 :			* \brief This is the IntVector used to store information about the years when the survey index should be calculated
104 :			*/
105 :			IntVector Years;
106 :			/**
107 :			* \brief This is the IntVector used to store information about the steps when the survey index should be calculated
108 :			*/
109 :			IntVector Steps;
110 :			/**
111 :			* \brief This is the IntMatrix used to store information about the ages that the survey index should be calculated on
112 :			*/
113 :			IntMatrix Ages;
114 :			/**
115 :			* \brief This is the LengthGroupDivision used to store information about the lengths that the survey index should be calculated on
116 :			*/
117 :			LengthGroupDivision* LgrpDiv;
118 :			/**
119 :			* \brief This is the DoubleVector used to store the calculated likelihood information
120 :			*/
121 :			DoubleVector likelihoodValues;
122 :			/**
123 :			* \brief This ActionAtTimes stores information about when the survey index should be calculated
124 :			*/
125 :			ActionAtTimes AAT;
126 :			/**
127 :			* \brief This is the DoubleMatrixPtrVector used to store the survey indices specified in the input file
128 :			* \note The indices for this object are [time][area][index]
129 :			*/
130 :			DoubleMatrixPtrVector obsIndex;
131 :			/**
132 :			* \brief This is the DoubleMatrixPtrVector used to store the survey indices calculated in the model
133 :			* \note The indices for this object are [time][area][index]
134 :			*/
135 :			DoubleMatrixPtrVector modelIndex;
136 :			/**
137 :			* \brief This is the DoubleMatrixPtrVector used to store the weights specified for the regression line
138 :			* \note The indices for this object are [time][area][weight]
139 :			*/
140 :			DoubleMatrixPtrVector weightIndex;
141 :			/**
142 :			* \brief This is the AgeBandMatrixPtrVector used to temporarily store the information returned from the aggregatation function
143 :			*/
144 :			const AgeBandMatrixPtrVector* alptr;
145 :			/**
146 :			* \brief This denotes what type of survey index data is to be used
147 :			*/
148 :			SIType sitype;
149 :			/**
150 :			* \brief This is the index of the timesteps for the survey index data
151 :			*/
152 :			int timeindex;
153 :			/**
154 :			* \brief This is the flag to denote whether the index should be based on the biomass or not
155 :			* \note The default value for this is 0, which means that the index is based on the number of the population
156 :			*/
157 :			int biomass;
158 :			/**
159 :			* \brief This is the flag to denote whether weighted regression line should be used when calculating the fit to the data or not
160 :			* \note The default value for this is 0, which means that the regression line doesnt use weights
161 :			*/
162 :			int useweight;
163 :			private:
164 :			/**
165 :			* \brief This function will read the SIOnStep data from the input file
166 :			* \param infile is the CommentStream to read the SIOnStep data from
167 :			* \param TimeInfo is the TimeClass for the current model
168 :			*/
169 :			void readSIData(CommentStream& infile, const TimeClass* const TimeInfo);
170 :			/**
171 :			* \brief This function will read the regression data data from the input file
172 :			* \param infile is the CommentStream to read the regression data from
173 :			*/
174 :			void readSIRegressionData(CommentStream& infile);
175 :			/**
176 :			* \brief This is used to fix the slope of the regression lines if specified by the user
177 :			*/
178 :			double slope;
179 :			/**
180 :			* \brief This is used to fix the intercept of the regression lines if specified by the user
181 :			*/
182 :			double intercept;
183 :			/**
184 :			* \brief This is the DoubleMatrix used to store information about the slope of the regression lines
185 :			*/
186 :			DoubleMatrix slopes;
187 :			/**
188 :			* \brief This is the DoubleMatrix used to store information about the intercept of the regression lines
189 :			*/
190 :			DoubleMatrix intercepts;
191 :			/**
192 :			* \brief This is the DoubleMatrix used to store information about the sse of the regression lines
193 :			*/
194 :			DoubleMatrix sse;
195 :			/**
196 :			* \brief This is the DoubleVector used to temporarily store the model indices when calculating the fit to the regression line
197 :			*/
198 :			DoubleVector tmpModel;
199 :			/**
200 :			* \brief This is the DoubleVector used to temporarily store the observed data indices when calculating the fit to the regression line
201 :			*/
202 :			DoubleVector tmpData;
203 :			/**
204 :			* \brief This is the DoubleVector used to temporarily store the weights when calculating the fit to the regression line
205 :			*/
206 :			DoubleVector tmpWeight;
207 :			/**
208 :			* \brief This is the CharPtrVector of the names of the areas
209 :			*/
210 :			CharPtrVector areaindex;
211 :			/**
212 :			* \brief This is the CharPtrVector of the names of the indices
213 :			*/
214 :			CharPtrVector colindex;
215 :			/**
216 :			* \brief This denotes what type of fit is to be used for the linear regression line
217 :			*/
218 :			FitType fittype;
219 :			/**
220 :			* \brief This is a Regression that stores the regression line used when calculating the likelihood score
221 :			*/
222 :			Regression* LR;
223 :			};
224 :
225 :			#endif

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