| 1 : |
agomez |
1 |
#include "stockpredator.h" |
| 2 : |
|
|
#include "keeper.h" |
| 3 : |
|
|
#include "errorhandler.h" |
| 4 : |
|
|
#include "readfunc.h" |
| 5 : |
|
|
#include "prey.h" |
| 6 : |
|
|
#include "areatime.h" |
| 7 : |
|
|
#include "suits.h" |
| 8 : |
|
|
#include "readword.h" |
| 9 : |
|
|
#include "gadget.h" |
| 10 : |
|
|
#include "global.h" |
| 11 : |
|
|
|
| 12 : |
|
|
StockPredator::StockPredator(CommentStream& infile, const char* givenname, const IntVector& Areas,
|
| 13 : |
|
|
const LengthGroupDivision* const OtherLgrpDiv, const LengthGroupDivision* const GivenLgrpDiv,
|
| 14 : |
|
|
int minage, int numage, const TimeClass* const TimeInfo, Keeper* const keeper)
|
| 15 : |
|
|
: PopPredator(givenname, Areas, OtherLgrpDiv, GivenLgrpDiv) {
|
| 16 : |
|
|
|
| 17 : |
|
|
type = STOCKPREDATOR;
|
| 18 : |
|
|
functionnumber = 0;
|
| 19 : |
|
|
keeper->addString("predator");
|
| 20 : |
|
|
keeper->addString(givenname);
|
| 21 : |
|
|
|
| 22 : |
|
|
//first read in the suitability parameters
|
| 23 : |
|
|
this->readSuitability(infile, TimeInfo, keeper);
|
| 24 : |
|
|
|
| 25 : |
|
|
//now we read in the prey preference parameters - should be one for each prey
|
| 26 : |
|
|
int i, check, count = 0;
|
| 27 : |
|
|
char text[MaxStrLength];
|
| 28 : |
|
|
strncpy(text, "", MaxStrLength);
|
| 29 : |
|
|
|
| 30 : |
|
|
keeper->addString("preypreference");
|
| 31 : |
|
|
infile >> text >> ws;
|
| 32 : |
|
|
while (!infile.eof() && (((strcasecmp(text, "maxconsumption") != 0)) && (strcasecmp(text, "whaleconsumption") != 0))) {
|
| 33 : |
|
|
check = 0;
|
| 34 : |
|
|
for (i = 0; i < preference.Size(); i++) {
|
| 35 : |
|
|
if (strcasecmp(text, this->getPreyName(i)) == 0) {
|
| 36 : |
|
|
infile >> preference[i] >> ws;
|
| 37 : |
|
|
count++;
|
| 38 : |
|
|
check = 1;
|
| 39 : |
|
|
}
|
| 40 : |
|
|
}
|
| 41 : |
|
|
if (!check)
|
| 42 : |
|
|
handle.logMessage(LOGWARN, "Warning in stockpredator - failed to match prey", text);
|
| 43 : |
|
|
infile >> text >> ws;
|
| 44 : |
|
|
}
|
| 45 : |
|
|
if (count != preference.Size())
|
| 46 : |
|
|
handle.logMessage(LOGFAIL, "Error in stockpredator - missing prey preference data");
|
| 47 : |
|
|
preference.Inform(keeper);
|
| 48 : |
|
|
keeper->clearLast();
|
| 49 : |
|
|
|
| 50 : |
|
|
//then read in the maximum consumption parameters
|
| 51 : |
|
|
keeper->addString("consumption");
|
| 52 : |
|
|
if (strcasecmp(text, "maxconsumption") == 0) {
|
| 53 : |
|
|
functionnumber = 1;
|
| 54 : |
|
|
consParam.resize(5, keeper);
|
| 55 : |
|
|
for (i = 0; i < 4; i++)
|
| 56 : |
|
|
if (!(infile >> consParam[i]))
|
| 57 : |
|
|
handle.logFileMessage(LOGFAIL, "invalid format for maxconsumption vector");
|
| 58 : |
|
|
|
| 59 : |
|
|
readWordAndVariable(infile, "halffeedingvalue", consParam[4]);
|
| 60 : |
|
|
|
| 61 : |
|
|
} else if (strcasecmp(text, "whaleconsumption") == 0) {
|
| 62 : |
|
|
functionnumber = 2;
|
| 63 : |
|
|
consParam.resize(16, keeper);
|
| 64 : |
|
|
for (i = 0; i < 15; i++)
|
| 65 : |
|
|
if (!(infile >> consParam[i]))
|
| 66 : |
|
|
handle.logFileMessage(LOGFAIL, "invalid format for whaleconsumption vector");
|
| 67 : |
|
|
|
| 68 : |
|
|
readWordAndVariable(infile, "halffeedingvalue", consParam[15]);
|
| 69 : |
|
|
|
| 70 : |
|
|
} else
|
| 71 : |
|
|
handle.logFileUnexpected(LOGFAIL, "maxconsumption", text);
|
| 72 : |
|
|
|
| 73 : |
|
|
consParam.Inform(keeper);
|
| 74 : |
|
|
keeper->clearLast();
|
| 75 : |
|
|
|
| 76 : |
|
|
//everything has been read from infile ... resize objects
|
| 77 : |
|
|
int numlength = LgrpDiv->numLengthGroups();
|
| 78 : |
|
|
int numarea = areas.Size();
|
| 79 : |
|
|
IntVector lower(numage, 0);
|
| 80 : |
|
|
IntVector agesize(numage, numlength);
|
| 81 : |
|
|
predAlkeys.resize(numarea, minage, lower, agesize);
|
| 82 : |
|
|
for (i = 0; i < predAlkeys.Size(); i++)
|
| 83 : |
|
|
predAlkeys[i].setToZero();
|
| 84 : |
|
|
maxcons.AddRows(numarea, numlength, 0.0);
|
| 85 : |
|
|
Phi.AddRows(numarea, numlength, 0.0);
|
| 86 : |
|
|
fphi.AddRows(numarea, numlength, 0.0);
|
| 87 : |
|
|
subfphi.AddRows(numarea, numlength, 0.0);
|
| 88 : |
|
|
|
| 89 : |
|
|
keeper->clearLast();
|
| 90 : |
|
|
keeper->clearLast();
|
| 91 : |
|
|
}
|
| 92 : |
|
|
|
| 93 : |
|
|
void StockPredator::Print(ofstream& outfile) const {
|
| 94 : |
|
|
int i, area;
|
| 95 : |
|
|
outfile << "\nStock predator\n";
|
| 96 : |
|
|
PopPredator::Print(outfile);
|
| 97 : |
|
|
outfile << "\n\tPredator age length keys\n";
|
| 98 : |
|
|
for (area = 0; area < areas.Size(); area++) {
|
| 99 : |
|
|
outfile << "\tInternal area " << areas[area] << "\n\tNumbers\n";
|
| 100 : |
|
|
predAlkeys[area].printNumbers(outfile);
|
| 101 : |
|
|
outfile << "\tMean weights\n";
|
| 102 : |
|
|
predAlkeys[area].printWeights(outfile);
|
| 103 : |
|
|
}
|
| 104 : |
|
|
outfile << "\n\tConsumption information\n";
|
| 105 : |
|
|
for (area = 0; area < areas.Size(); area++) {
|
| 106 : |
|
|
outfile << "\tPhi by length on internal area " << areas[area] << ":\n\t";
|
| 107 : |
|
|
for (i = 0; i < fphi.Ncol(area); i++)
|
| 108 : |
|
|
outfile << setw(smallwidth) << setprecision(smallprecision) << fphi[area][i] << sep;
|
| 109 : |
|
|
outfile << "\n\tMaximum consumption by length on internal area " << areas[area] << ":\n\t";
|
| 110 : |
|
|
for (i = 0; i < maxcons.Ncol(area); i++)
|
| 111 : |
|
|
outfile << setw(smallwidth) << setprecision(smallprecision) << maxcons[area][i] << sep;
|
| 112 : |
|
|
outfile << endl;
|
| 113 : |
|
|
}
|
| 114 : |
|
|
outfile << endl;
|
| 115 : |
|
|
}
|
| 116 : |
|
|
|
| 117 : |
|
|
void StockPredator::Sum(const AgeBandMatrix& stockAlkeys, int area) {
|
| 118 : |
|
|
int inarea = this->areaNum(area);
|
| 119 : |
|
|
predAlkeys[inarea].setToZero();
|
| 120 : |
|
|
predAlkeys[inarea].Add(stockAlkeys, *CI);
|
| 121 : |
|
|
predAlkeys[inarea].sumColumns(prednumber[inarea]);
|
| 122 : |
|
|
}
|
| 123 : |
|
|
|
| 124 : |
|
|
void StockPredator::Reset(const TimeClass* const TimeInfo) {
|
| 125 : |
|
|
PopPredator::Reset(TimeInfo);
|
| 126 : |
|
|
|
| 127 : |
|
|
//check that the various parameters that can be estimated are sensible
|
| 128 : |
|
|
if ((handle.getLogLevel() >= LOGWARN) && (TimeInfo->getTime() == 1)) {
|
| 129 : |
|
|
int i, check;
|
| 130 : |
|
|
if (functionnumber == 1)
|
| 131 : |
|
|
for (i = 0; i < consParam.Size(); i++)
|
| 132 : |
|
|
if (consParam[i] < 0.0)
|
| 133 : |
|
|
handle.logMessage(LOGWARN, "Warning in stockpredator - negative consumption parameter", consParam[i]);
|
| 134 : |
|
|
check = 0;
|
| 135 : |
|
|
if (preference.Size() > 1)
|
| 136 : |
|
|
for (i = 1; i < preference.Size(); i++)
|
| 137 : |
|
|
if (!(isEqual(preference[0], preference[i])))
|
| 138 : |
|
|
check++;
|
| 139 : |
|
|
if (check != 0)
|
| 140 : |
|
|
handle.logMessage(LOGWARN, "Warning in stockpredator - preference parameters differ for", this->getName());
|
| 141 : |
|
|
}
|
| 142 : |
|
|
}
|
| 143 : |
|
|
|
| 144 : |
|
|
void StockPredator::Eat(int area, const AreaClass* const Area, const TimeClass* const TimeInfo) {
|
| 145 : |
|
|
|
| 146 : |
|
|
int prey, predl, preyl, check;
|
| 147 : |
|
|
int inarea = this->areaNum(area);
|
| 148 : |
|
|
double tmp;
|
| 149 : |
|
|
|
| 150 : |
|
|
if (TimeInfo->getSubStep() == 1) {
|
| 151 : |
|
|
//this is the first substep of the timestep so need to reset things
|
| 152 : |
|
|
for (predl = 0; predl < LgrpDiv->numLengthGroups(); predl++) {
|
| 153 : |
|
|
Phi[inarea][predl] = 0.0;
|
| 154 : |
|
|
fphi[inarea][predl] = 0.0;
|
| 155 : |
|
|
}
|
| 156 : |
|
|
|
| 157 : |
|
|
if (functionnumber == 1) {
|
| 158 : |
|
|
double temperature = Area->getTemperature(area, TimeInfo->getTime());
|
| 159 : |
|
|
tmp = exp(temperature * (consParam[1] - temperature * temperature * consParam[2]))
|
| 160 : |
|
|
* consParam[0] * TimeInfo->getTimeStepLength() / TimeInfo->numSubSteps();
|
| 161 : |
|
|
for (predl = 0; predl < LgrpDiv->numLengthGroups(); predl++)
|
| 162 : |
|
|
maxcons[inarea][predl] = tmp * pow(LgrpDiv->meanLength(predl), consParam[3]);
|
| 163 : |
|
|
|
| 164 : |
|
|
} else if (functionnumber == 2) {
|
| 165 : |
|
|
double max1, max2, max3, l;
|
| 166 : |
|
|
for (predl = 0; predl < LgrpDiv->numLengthGroups(); predl++) {
|
| 167 : |
|
|
l = LgrpDiv->meanLength(predl);
|
| 168 : |
|
|
max1 = max(0.0, consParam[6] * (consParam[7] + consParam[8] * l));
|
| 169 : |
|
|
max2 = max(0.0, consParam[9] * (consParam[10] + consParam[11] * l));
|
| 170 : |
|
|
max3 = max(0.0, consParam[12] * (consParam[13] + consParam[14] * l));
|
| 171 : |
|
|
tmp = consParam[2] * pow(prednumber[inarea][predl].W, consParam[3])
|
| 172 : |
|
|
+ consParam[4] * pow(l, consParam[5]) + max1 + max2 + max3;
|
| 173 : |
|
|
maxcons[inarea][predl] = consParam[0] * consParam[1] * tmp;
|
| 174 : |
|
|
}
|
| 175 : |
|
|
|
| 176 : |
|
|
} else
|
| 177 : |
|
|
handle.logMessage(LOGWARN, "Warning in stockpredator - unrecognised consumption format");
|
| 178 : |
|
|
|
| 179 : |
|
|
} else {
|
| 180 : |
|
|
//this is not the first substep of the timestep so only reset Phi
|
| 181 : |
|
|
for (predl = 0; predl < LgrpDiv->numLengthGroups(); predl++)
|
| 182 : |
|
|
Phi[inarea][predl] = 0.0;
|
| 183 : |
|
|
}
|
| 184 : |
|
|
|
| 185 : |
|
|
//Now maxcons contains the maximum consumption by length
|
| 186 : |
|
|
//Calculating Phi(L) and O(l,L,prey) based on energy requirements
|
| 187 : |
|
|
for (prey = 0; prey < this->numPreys(); prey++) {
|
| 188 : |
|
|
check = 0;
|
| 189 : |
|
|
if (isEqual(preference[prey], 1.0))
|
| 190 : |
|
|
check = 1;
|
| 191 : |
|
|
|
| 192 : |
|
|
if ((this->getPrey(prey)->isPreyArea(area)) && (!(isZero(this->getPrey(prey)->getEnergy())))) {
|
| 193 : |
|
|
for (predl = 0; predl < LgrpDiv->numLengthGroups(); predl++) {
|
| 194 : |
|
|
for (preyl = 0; preyl < (*cons[inarea][prey])[predl].Size(); preyl++) {
|
| 195 : |
|
|
tmp = this->getSuitability(prey)[predl][preyl] * this->getPrey(prey)->getEnergy()
|
| 196 : |
|
|
* this->getPrey(prey)->getBiomass(area, preyl);
|
| 197 : |
|
|
|
| 198 : |
|
|
//JMB - dont take the power if we dont have to
|
| 199 : |
|
|
if (!check)
|
| 200 : |
|
|
tmp = pow(tmp, preference[prey]);
|
| 201 : |
|
|
(*cons[inarea][prey])[predl][preyl] = tmp;
|
| 202 : |
|
|
Phi[inarea][predl] += tmp;
|
| 203 : |
|
|
}
|
| 204 : |
|
|
}
|
| 205 : |
|
|
|
| 206 : |
|
|
} else {
|
| 207 : |
|
|
for (predl = 0; predl < LgrpDiv->numLengthGroups(); predl++)
|
| 208 : |
|
|
for (preyl = 0; preyl < (*cons[inarea][prey])[predl].Size(); preyl++)
|
| 209 : |
|
|
(*cons[inarea][prey])[predl][preyl] = 0.0;
|
| 210 : |
|
|
}
|
| 211 : |
|
|
}
|
| 212 : |
|
|
|
| 213 : |
|
|
tmp = TimeInfo->getTimeStepLength() / TimeInfo->numSubSteps();
|
| 214 : |
|
|
if (functionnumber == 1)
|
| 215 : |
|
|
tmp *= consParam[4];
|
| 216 : |
|
|
else if (functionnumber == 2)
|
| 217 : |
|
|
tmp *= consParam[15];
|
| 218 : |
|
|
else
|
| 219 : |
|
|
handle.logMessage(LOGWARN, "Warning in stockpredator - unrecognised consumption format");
|
| 220 : |
|
|
|
| 221 : |
|
|
//Calculating fphi(L) and totalcons of predator in area
|
| 222 : |
|
|
for (predl = 0; predl < LgrpDiv->numLengthGroups(); predl++) {
|
| 223 : |
|
|
if (isZero(tmp)) {
|
| 224 : |
|
|
subfphi[inarea][predl] = 1.0;
|
| 225 : |
|
|
totalcons[inarea][predl] = maxcons[inarea][predl] * prednumber[inarea][predl].N;
|
| 226 : |
|
|
} else if (isZero(Phi[inarea][predl]) || isZero(Phi[inarea][predl] + tmp)) {
|
| 227 : |
|
|
subfphi[inarea][predl] = 0.0;
|
| 228 : |
|
|
totalcons[inarea][predl] = 0.0;
|
| 229 : |
|
|
} else {
|
| 230 : |
|
|
subfphi[inarea][predl] = Phi[inarea][predl] / (Phi[inarea][predl] + tmp);
|
| 231 : |
|
|
totalcons[inarea][predl] = subfphi[inarea][predl]
|
| 232 : |
|
|
* maxcons[inarea][predl] * prednumber[inarea][predl].N;
|
| 233 : |
|
|
}
|
| 234 : |
|
|
}
|
| 235 : |
|
|
|
| 236 : |
|
|
//Distributing the total consumption on the preys and converting to biomass
|
| 237 : |
|
|
for (prey = 0; prey < this->numPreys(); prey++) {
|
| 238 : |
|
|
if ((this->getPrey(prey)->isPreyArea(area)) && (!(isZero(this->getPrey(prey)->getEnergy())))) {
|
| 239 : |
|
|
for (predl = 0; predl < LgrpDiv->numLengthGroups(); predl++) {
|
| 240 : |
|
|
if (!(isZero(Phi[inarea][predl]))) {
|
| 241 : |
|
|
tmp = totalcons[inarea][predl] / (Phi[inarea][predl] * this->getPrey(prey)->getEnergy());
|
| 242 : |
|
|
for (preyl = 0; preyl < (*cons[inarea][prey])[predl].Size(); preyl++)
|
| 243 : |
|
|
(*cons[inarea][prey])[predl][preyl] *= tmp;
|
| 244 : |
|
|
|
| 245 : |
|
|
//set the multiplicative constant
|
| 246 : |
|
|
(*predratio[inarea])[prey][predl] += tmp;
|
| 247 : |
|
|
}
|
| 248 : |
|
|
}
|
| 249 : |
|
|
}
|
| 250 : |
|
|
}
|
| 251 : |
|
|
|
| 252 : |
|
|
//Add the calculated consumption to the preys in question
|
| 253 : |
|
|
for (prey = 0; prey < this->numPreys(); prey++)
|
| 254 : |
|
|
if (this->getPrey(prey)->isPreyArea(area))
|
| 255 : |
|
|
for (predl = 0; predl < LgrpDiv->numLengthGroups(); predl++)
|
| 256 : |
|
|
this->getPrey(prey)->addBiomassConsumption(area, (*cons[inarea][prey])[predl]);
|
| 257 : |
|
|
}
|
| 258 : |
|
|
|
| 259 : |
|
|
//Check if any of the preys of the predator are eaten up.
|
| 260 : |
|
|
//adjust the consumption according to that.
|
| 261 : |
|
|
void StockPredator::adjustConsumption(int area, const TimeClass* const TimeInfo) {
|
| 262 : |
|
|
int inarea = this->areaNum(area);
|
| 263 : |
|
|
int numlen = LgrpDiv->numLengthGroups();
|
| 264 : |
|
|
int preyl, predl, prey;
|
| 265 : |
|
|
double maxRatio, tmp;
|
| 266 : |
|
|
|
| 267 : |
|
|
maxRatio = TimeInfo->getMaxRatioConsumed();
|
| 268 : |
|
|
for (predl = 0; predl < numlen; predl++)
|
| 269 : |
|
|
overcons[inarea][predl] = 0.0;
|
| 270 : |
|
|
|
| 271 : |
|
|
for (prey = 0; prey < this->numPreys(); prey++) {
|
| 272 : |
|
|
if (this->getPrey(prey)->isOverConsumption(area)) {
|
| 273 : |
|
|
hasoverconsumption[inarea] = 1;
|
| 274 : |
|
|
DoubleVector ratio = this->getPrey(prey)->getRatio(area);
|
| 275 : |
|
|
for (predl = 0; predl < numlen; predl++) {
|
| 276 : |
|
|
for (preyl = 0; preyl < (*cons[inarea][prey])[predl].Size(); preyl++) {
|
| 277 : |
|
|
if (ratio[preyl] > maxRatio) {
|
| 278 : |
|
|
tmp = maxRatio / ratio[preyl];
|
| 279 : |
|
|
overcons[inarea][predl] += (1.0 - tmp) * (*cons[inarea][prey])[predl][preyl];
|
| 280 : |
|
|
(*cons[inarea][prey])[predl][preyl] *= tmp;
|
| 281 : |
|
|
(*usesuit[inarea][prey])[predl][preyl] *= tmp;
|
| 282 : |
|
|
}
|
| 283 : |
|
|
}
|
| 284 : |
|
|
}
|
| 285 : |
|
|
}
|
| 286 : |
|
|
}
|
| 287 : |
|
|
|
| 288 : |
|
|
if (hasoverconsumption[inarea]) {
|
| 289 : |
|
|
for (predl = 0; predl < numlen; predl++) {
|
| 290 : |
|
|
overconsumption[inarea][predl] += overcons[inarea][predl];
|
| 291 : |
|
|
if (totalcons[inarea][predl] > verysmall) {
|
| 292 : |
|
|
tmp = 1.0 - (overcons[inarea][predl] / totalcons[inarea][predl]);
|
| 293 : |
|
|
subfphi[inarea][predl] *= tmp;
|
| 294 : |
|
|
totalcons[inarea][predl] -= overcons[inarea][predl];
|
| 295 : |
|
|
}
|
| 296 : |
|
|
}
|
| 297 : |
|
|
}
|
| 298 : |
|
|
|
| 299 : |
|
|
for (predl = 0; predl < numlen; predl++)
|
| 300 : |
|
|
totalconsumption[inarea][predl] += totalcons[inarea][predl];
|
| 301 : |
|
|
|
| 302 : |
|
|
if (TimeInfo->numSubSteps() != 1) {
|
| 303 : |
|
|
double ratio1, ratio2;
|
| 304 : |
|
|
ratio2 = 1.0 / TimeInfo->getSubStep();
|
| 305 : |
|
|
ratio1 = 1.0 - ratio2;
|
| 306 : |
|
|
for (predl = 0; predl < numlen; predl++)
|
| 307 : |
|
|
fphi[inarea][predl] = (ratio2 * subfphi[inarea][predl]) + (ratio1 * fphi[inarea][predl]);
|
| 308 : |
|
|
|
| 309 : |
|
|
} else
|
| 310 : |
|
|
for (predl = 0; predl < numlen; predl++)
|
| 311 : |
|
|
fphi[inarea][predl] = subfphi[inarea][predl];
|
| 312 : |
|
|
|
| 313 : |
|
|
for (prey = 0; prey < this->numPreys(); prey++)
|
| 314 : |
|
|
if (this->getPrey(prey)->isPreyArea(area))
|
| 315 : |
|
|
for (predl = 0; predl < numlen; predl++)
|
| 316 : |
|
|
for (preyl = 0; preyl < (*cons[inarea][prey])[predl].Size(); preyl++)
|
| 317 : |
|
|
(*consumption[inarea][prey])[predl][preyl] += (*cons[inarea][prey])[predl][preyl];
|
| 318 : |
|
|
}
|
Parent Directory
Revision Log