Annotation of /trunk/gadget/stockmemberfunctions.cc

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1 :	agomez	1	#include "stock.h"
2 :			#include "keeper.h"
3 :			#include "areatime.h"
4 :			#include "naturalm.h"
5 :			#include "grower.h"
6 :			#include "stockprey.h"
7 :			#include "stockpredator.h"
8 :			#include "migration.h"
9 :			#include "maturity.h"
10 :			#include "renewal.h"
11 :			#include "transition.h"
12 :			#include "spawner.h"
13 :			#include "stray.h"
14 :			#include "errorhandler.h"
15 :			#include "gadget.h"
16 :			#include "global.h"
17 :
18 :			void Stock::Migrate(const TimeClass* const TimeInfo) {
19 :			if (doesmigrate && migration->isMigrationStep(TimeInfo)) {
20 :			Alkeys.Migrate(migration->getMigrationMatrix(TimeInfo), tmpMigrate);
21 :			if (istagged && tagAlkeys.numTagExperiments() > 0)
22 :			tagAlkeys.Migrate(migration->getMigrationMatrix(TimeInfo), Alkeys);
23 :			}
24 :			}
25 :
26 :			//-------------------------------------------------------------------
27 :			//Sum up into Growth+Predator and Prey Lengthgroups. Storage is a
28 :			//vector of PopInfo that stores the sum over each lengthgroup.
29 :			void Stock::calcNumbers(int area, const TimeClass* const TimeInfo) {
30 :			int inarea = this->areaNum(area);
31 :			Alkeys[inarea].sumColumns(tmpPopulation[inarea]);
32 :			if (doesgrow)
33 :			grower->Sum(tmpPopulation[inarea], area);
34 :			if (iseaten) {
35 :			prey->Sum(Alkeys[inarea], area);
36 :			if (istagged) {
37 :			int i;
38 :			for (i = 0; i < allTags.Size(); i++)
39 :			allTags[i]->storeConsumptionALK(area, this->getName());
40 :			}
41 :			}
42 :			if (doeseat)
43 :			((StockPredator*)predator)->Sum(Alkeys[inarea], area);
44 :			}
45 :
46 :			//-------------------------------------------------------------------
47 :			void Stock::calcEat(int area, const AreaClass* const Area, const TimeClass* const TimeInfo) {
48 :			if (doeseat)
49 :			predator->Eat(area, Area, TimeInfo);
50 :			}
51 :
52 :			void Stock::checkEat(int area, const TimeClass* const TimeInfo) {
53 :			if (iseaten)
54 :			prey->checkConsumption(area, TimeInfo);
55 :			}
56 :
57 :			void Stock::adjustEat(int area, const TimeClass* const TimeInfo) {
58 :			if (doeseat)
59 :			predator->adjustConsumption(area, TimeInfo);
60 :			}
61 :
62 :			//-------------------------------------------------------------------
63 :			void Stock::reducePop(int area, const TimeClass* const TimeInfo) {
64 :			int inarea = this->areaNum(area);
65 :
66 :			//Predation
67 :			if (iseaten)
68 :			prey->Subtract(Alkeys[inarea], area);
69 :
70 :			//Natural mortality
71 :			if (TimeInfo->numSubSteps() == 1) {
72 :			Alkeys[inarea].Multiply(naturalm->getProportion(area));
73 :			} else {
74 :			//changed to include the possibility of substeps
75 :			DoubleVector* PropSurviving;
76 :			PropSurviving = new DoubleVector(naturalm->getProportion(area));
77 :			double timeratio = 1.0 / TimeInfo->numSubSteps();
78 :
79 :			int i;
80 :			for (i = 0; i < PropSurviving->Size(); i++)
81 :			(*PropSurviving)[i] = pow((*PropSurviving)[i], timeratio);
82 :
83 :			Alkeys[inarea].Multiply(*PropSurviving);
84 :			delete PropSurviving;
85 :			}
86 :
87 :			if (istagged && tagAlkeys.numTagExperiments() > 0)
88 :			tagAlkeys[inarea].updateAndTagLoss(Alkeys[inarea], tagAlkeys.getTagLoss());
89 :			}
90 :
91 :			//-----------------------------------------------------------------------
92 :			//Function that updates the length distributions and makes part of the stock Mature.
93 :			void Stock::Grow(int area, const AreaClass* const Area, const TimeClass* const TimeInfo) {
94 :
95 :			if (!doesgrow)
96 :			return;
97 :
98 :			if (doeseat)
99 :			grower->calcGrowth(area, Area, TimeInfo, ((StockPredator*)predator)->getFPhi(area),
100 :			((StockPredator*)predator)->getMaxConsumption(area));
101 :			else
102 :			grower->calcGrowth(area, Area, TimeInfo);
103 :
104 :			int inarea = this->areaNum(area);
105 :			if (grower->getFixedWeights()) {
106 :			//Weights at length are fixed to the value in the input file
107 :			grower->implementGrowth(area, LgrpDiv);
108 :			if (doesmature && maturity->isMaturationStep(TimeInfo))
109 :			Alkeys[inarea].Grow(grower->getLengthIncrease(area), grower->getWeight(area), maturity, area);
110 :			else
111 :			Alkeys[inarea].Grow(grower->getLengthIncrease(area), grower->getWeight(area));
112 :
113 :			} else {
114 :			//New weights at length are calculated
115 :			grower->implementGrowth(area, tmpPopulation[inarea], LgrpDiv);
116 :			if (doesmature && maturity->isMaturationStep(TimeInfo))
117 :			Alkeys[inarea].Grow(grower->getLengthIncrease(area), grower->getWeightIncrease(area), maturity, area);
118 :			else
119 :			Alkeys[inarea].Grow(grower->getLengthIncrease(area), grower->getWeightIncrease(area));
120 :			}
121 :
122 :			if (istagged && tagAlkeys.numTagExperiments() > 0) {
123 :			if (doesmature && maturity->isMaturationStep(TimeInfo))
124 :			tagAlkeys[inarea].Grow(grower->getLengthIncrease(area), Alkeys[inarea], maturity, area);
125 :			else
126 :			tagAlkeys[inarea].Grow(grower->getLengthIncrease(area), Alkeys[inarea]);
127 :			}
128 :			}
129 :
130 :			//-----------------------------------------------------------------------
131 :			//A number of Special functions, Spawning, Renewal, Maturation and
132 :			//Transition to other Stocks, Maturity due to age and increased age.
133 :			void Stock::updateAgePart1(int area, const TimeClass* const TimeInfo) {
134 :			if (doesmove && transition->isTransitionStep(TimeInfo)) {
135 :			if (istagged && tagAlkeys.numTagExperiments() > 0)
136 :			transition->storeTransitionStock(area, Alkeys[this->areaNum(area)], tagAlkeys[this->areaNum(area)], TimeInfo);
137 :			else
138 :			transition->storeTransitionStock(area, Alkeys[this->areaNum(area)], TimeInfo);
139 :			}
140 :			}
141 :
142 :			void Stock::updateAgePart2(int area, const TimeClass* const TimeInfo) {
143 :			if (this->isBirthday(TimeInfo)) {
144 :			Alkeys[this->areaNum(area)].IncrementAge();
145 :			if (istagged && tagAlkeys.numTagExperiments() > 0)
146 :			tagAlkeys[this->areaNum(area)].IncrementAge(Alkeys[this->areaNum(area)]);
147 :			}
148 :			}
149 :
150 :			void Stock::updateAgePart3(int area, const TimeClass* const TimeInfo) {
151 :			if (doesmove && transition->isTransitionStep(TimeInfo)) {
152 :			if (istagged && transitionTags.Size() > 0) {
153 :			int i;
154 :			for (i = 0; i < transitionTags.Size(); i++)
155 :			transitionTags[i]->updateTransitionStock(TimeInfo);
156 :			transitionTags.deleteAll();
157 :			}
158 :			transition->Move(area, TimeInfo);
159 :			}
160 :
161 :			//JMB - only update the ratio for the tagged stock after all other age updates
162 :			if (istagged && tagAlkeys.numTagExperiments() > 0)
163 :			tagAlkeys[this->areaNum(area)].updateRatio(Alkeys[this->areaNum(area)]);
164 :			}
165 :
166 :			void Stock::updatePopulationPart1(int area, const TimeClass* const TimeInfo) {
167 :			if (doesspawn && spawner->isSpawnStepArea(area, TimeInfo)) {
168 :			spawner->Spawn(Alkeys[this->areaNum(area)], area, TimeInfo);
169 :			if (istagged && tagAlkeys.numTagExperiments() > 0)
170 :			tagAlkeys[this->areaNum(area)].updateNumbers(Alkeys[this->areaNum(area)]);
171 :			}
172 :			}
173 :
174 :			void Stock::updatePopulationPart2(int area, const TimeClass* const TimeInfo) {
175 :			if (doesmature && maturity->isMaturationStep(TimeInfo)) {
176 :			if (istagged && matureTags.Size() > 0) {
177 :			int i;
178 :			for (i = 0; i < matureTags.Size(); i++)
179 :			matureTags[i]->updateMatureStock(TimeInfo);
180 :			matureTags.deleteAll();
181 :			}
182 :			maturity->Move(area, TimeInfo);
183 :			}
184 :			}
185 :
186 :			void Stock::updatePopulationPart3(int area, const TimeClass* const TimeInfo) {
187 :			if (doesrenew && renewal->isRenewalStepArea(area, TimeInfo))
188 :			renewal->addRenewal(Alkeys[this->areaNum(area)], area, TimeInfo);
189 :
190 :			if (doesspawn && spawner->isSpawnStepArea(area, TimeInfo))
191 :			spawner->addSpawnStock(area, TimeInfo);
192 :			}
193 :
194 :			void Stock::updatePopulationPart4(int area, const TimeClass* const TimeInfo) {
195 :			if (doesstray && stray->isStrayStepArea(area, TimeInfo)) {
196 :			if (istagged && tagAlkeys.numTagExperiments() > 0)
197 :			stray->storeStrayingStock(area, Alkeys[this->areaNum(area)], tagAlkeys[this->areaNum(area)], TimeInfo);
198 :			else
199 :			stray->storeStrayingStock(area, Alkeys[this->areaNum(area)], TimeInfo);
200 :			}
201 :			}
202 :
203 :			void Stock::updatePopulationPart5(int area, const TimeClass* const TimeInfo) {
204 :			if (doesstray && stray->isStrayStepArea(area, TimeInfo)) {
205 :			if (istagged && strayTags.Size() > 0) {
206 :			int i;
207 :			for (i = 0; i < strayTags.Size(); i++)
208 :			strayTags[i]->updateStrayStock(TimeInfo);
209 :			strayTags.deleteAll();
210 :			}
211 :			stray->addStrayStock(area, TimeInfo);
212 :			}
213 :
214 :			//JMB - only update the ratio for the tagged stock after all other population updates
215 :			if (istagged && tagAlkeys.numTagExperiments() > 0)
216 :			tagAlkeys[this->areaNum(area)].updateRatio(Alkeys[this->areaNum(area)]);
217 :			}
218 :
219 :			void Stock::Add(const AgeBandMatrix& Addition,
220 :			const ConversionIndex* const CI, int area, double ratio) {
221 :
222 :			Alkeys[this->areaNum(area)].Add(Addition, *CI, ratio);
223 :			}
224 :
225 :			void Stock::Add(const AgeBandMatrixRatioPtrVector& Addition,
226 :			const ConversionIndex* const CI, int area, double ratio) {
227 :
228 :			if (!istagged)
229 :			return;
230 :
231 :			if ((Addition.numTagExperiments() > 0) && (Addition.numTagExperiments() <= tagAlkeys.numTagExperiments())) {
232 :			tagAlkeys.Add(Addition, this->areaNum(area), *CI, ratio);
233 :			tagAlkeys[this->areaNum(area)].updateRatio(Alkeys[this->areaNum(area)]);
234 :			}
235 :			}
236 :
237 :			void Stock::addTags(AgeBandMatrixPtrVector* tagbyagelength, Tags* newtag, double tagloss) {
238 :
239 :			if (!istagged)
240 :			return;
241 :
242 :			tagAlkeys.addTag(tagbyagelength, Alkeys, newtag->getName(), tagloss);
243 :			allTags.resize(newtag);
244 :			if (doesmature) {
245 :			maturity->addMaturityTag(newtag->getName());
246 :			matureTags.resize(newtag);
247 :			}
248 :			if (doesmove) {
249 :			transition->addTransitionTag(newtag->getName());
250 :			transitionTags.resize(newtag);
251 :			}
252 :			if (doesstray) {
253 :			stray->addStrayTag(newtag->getName());
254 :			strayTags.resize(newtag);
255 :			}
256 :			}
257 :
258 :			void Stock::deleteTags(const char* tagname) {
259 :
260 :			if (!istagged)
261 :			return;
262 :
263 :			allTags.Delete(tagAlkeys.getTagID(tagname));
264 :			tagAlkeys.deleteTag(tagname);
265 :			if (doesmature)
266 :			maturity->deleteMaturityTag(tagname);
267 :			if (doesmove)
268 :			transition->deleteTransitionTag(tagname);
269 :			if (doesstray)
270 :			stray->deleteStrayTag(tagname);
271 :			}
272 :
273 :			double Stock::getTotalStockNumber(int area) const {
274 :			int inarea = this->areaNum(area);
275 :			if (inarea == -1)
276 :			return 0.0;
277 :
278 :			int age, len;
279 :			double num = 0.0;
280 :			for (age = Alkeys[inarea].minAge(); age <= Alkeys[inarea].maxAge(); age++)
281 :			for (len = Alkeys[inarea].minLength(age); len < Alkeys[inarea].maxLength(age); len++)
282 :			num += (Alkeys[inarea])[age][len].N;
283 :
284 :			return num;
285 :			}
286 :
287 :			double Stock::getTotalStockNumberAllAreas() const {
288 :			int a;
289 :			double sum = 0.0;
290 :			for (a = 0; a <= Alkeys.Size(); a++)
291 :			sum += this->getTotalStockNumber(a);
292 :
293 :			return sum;
294 :			}
295 :
296 :			double Stock::getTotalStockBiomass(int area) const {
297 :			int inarea = this->areaNum(area);
298 :			if (inarea == -1)
299 :			return 0.0;
300 :
301 :			int age, len;
302 :			double kilos = 0.0;
303 :			for (age = Alkeys[inarea].minAge(); age <= Alkeys[inarea].maxAge(); age++)
304 :			for (len = Alkeys[inarea].minLength(age); len < Alkeys[inarea].maxLength(age); len++)
305 :			kilos += ((Alkeys[inarea])[age][len].N * (Alkeys[inarea])[age][len].W);
306 :
307 :			return kilos;
308 :			}
309 :
310 :			double Stock::getTotalStockBiomassAllAreas() const {
311 :			int a;
312 :			double sum = 0.0;
313 :			for (a = 0; a <= Alkeys.Size(); a++)
314 :			sum += this->getTotalStockBiomass(a);
315 :
316 :			return sum;
317 :			}

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