| 1 : |
agomez |
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#include "renewal.h" |
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#include "errorhandler.h" |
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#include "readfunc.h" |
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#include "keeper.h" |
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#include "readword.h" |
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#include "gadget.h" |
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#include "global.h" |
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RenewalData::RenewalData(CommentStream& infile, const IntVector& Areas,
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const AreaClass* const Area, const TimeClass* const TimeInfo, Keeper* const keeper,
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const char* refWeightFile, const char* givenname, int minage, int maxage, double DL)
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: HasName(givenname), LivesOnAreas(Areas), CI(0), LgrpDiv(0) {
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keeper->addString("renewaldata");
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ifstream subfile;
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CommentStream subcomment(subfile);
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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index = 0;
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int i, j;
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double minlength, maxlength, dl;
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readWordAndVariable(infile, "minlength", minlength);
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readWordAndVariable(infile, "maxlength", maxlength);
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//JMB - changed to make the reading of dl optional
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//if it isnt specifed here, it will default to the dl value of the stock
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infile >> ws;
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char c = infile.peek();
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if ((c == 'd') || (c == 'D'))
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| 31 : |
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readWordAndVariable(infile, "dl", dl);
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else
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dl = DL;
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LgrpDiv = new LengthGroupDivision(minlength, maxlength, dl);
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if (LgrpDiv->Error())
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handle.logMessage(LOGFAIL, "Error in renewal - failed to create length group");
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infile >> text >> ws;
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if ((strcasecmp(text, "normalcondfile") == 0)) {
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| 41 : |
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//read renewal data in mean length format, using the reference weight file
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readoption = 0;
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infile >> text >> ws;
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subfile.open(text, ios::in);
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handle.checkIfFailure(subfile, text);
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handle.Open(text);
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| 47 : |
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this->readNormalConditionData(subcomment, keeper, TimeInfo, Area, minage, maxage);
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handle.Close();
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subfile.close();
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subfile.clear();
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//read information on reference weights.
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DoubleMatrix tmpRefW;
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keeper->addString("referenceweights");
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subfile.open(refWeightFile, ios::in);
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handle.checkIfFailure(subfile, refWeightFile);
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handle.Open(refWeightFile);
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readRefWeights(subcomment, tmpRefW);
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handle.Close();
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subfile.close();
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subfile.clear();
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//Interpolate the reference weights. First there are some error checks.
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if (LgrpDiv->meanLength(0) < tmpRefW[0][0] ||
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LgrpDiv->meanLength(LgrpDiv->numLengthGroups() - 1) > tmpRefW[tmpRefW.Nrow() - 1][0])
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handle.logFileMessage(LOGFAIL, "lengths for reference weights must span the range of initial condition lengths");
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//Aggregate the reference weight data to be the same format
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double ratio, tmplen;
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refWeight.resize(LgrpDiv->numLengthGroups(), 0.0);
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int pos = 0;
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for (j = 0; j < LgrpDiv->numLengthGroups(); j++) {
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tmplen = LgrpDiv->meanLength(j);
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for (i = pos; i < tmpRefW.Nrow() - 1; i++) {
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if (((tmplen > tmpRefW[i][0]) || (isEqual(tmplen, tmpRefW[i][0]))) &&
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| 76 : |
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((tmplen < tmpRefW[i + 1][0]) || (isEqual(tmplen, tmpRefW[i + 1][0])))) {
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ratio = (tmplen - tmpRefW[i][0]) / (tmpRefW[i + 1][0] - tmpRefW[i][0]);
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refWeight[j] = tmpRefW[i][1] + ratio * (tmpRefW[i + 1][1] - tmpRefW[i][1]);
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pos = i;
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}
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}
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}
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keeper->clearLast();
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} else if ((strcasecmp(text, "renewaldatafile") == 0) || (strcasecmp(text, "normalparamfile") == 0)) {
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| 87 : |
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//read renewal data in mean length format, using a length weight relationship
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| 88 : |
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readoption = 1;
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| 89 : |
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infile >> text >> ws;
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| 90 : |
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subfile.open(text, ios::in);
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handle.checkIfFailure(subfile, text);
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handle.Open(text);
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this->readNormalParameterData(subcomment, keeper, TimeInfo, Area, minage, maxage);
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handle.Close();
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subfile.close();
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subfile.clear();
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} else if ((strcasecmp(text, "numberfile") == 0)) {
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//read renewal data in number format
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readoption = 2;
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infile >> text >> ws;
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subfile.open(text, ios::in);
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handle.checkIfFailure(subfile, text);
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handle.Open(text);
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this->readNumberData(subcomment, keeper, TimeInfo, Area, minage, maxage);
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handle.Close();
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subfile.close();
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subfile.clear();
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} else
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handle.logFileMessage(LOGFAIL, "unrecognised renewal data format", text);
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keeper->clearLast();
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}
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void RenewalData::readNormalParameterData(CommentStream& infile, Keeper* const keeper,
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const TimeClass* const TimeInfo, const AreaClass* const Area, int minage, int maxage) {
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| 118 : |
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char c;
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int year, step, area, age, keepdata, count, reject;
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PopInfoIndexVector poptmp(LgrpDiv->numLengthGroups(), 0);
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//We now expect to find the renewal data in the following format
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//year, step, area, age, number, mean, sdev, alpha, beta
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infile >> ws;
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if (countColumns(infile) != 9)
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 9");
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year = step = area = age = count = reject = 0;
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while (!infile.eof()) {
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//crude check to see if something has gone wrong and avoid infinite loops
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if (!(isdigit(infile.peek())))
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| 133 : |
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handle.logFileMessage(LOGFAIL, "failed to read data from file");
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| 134 : |
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keepdata = 1;
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infile >> year >> step >> area >> age >> ws;
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if (!(TimeInfo->isWithinPeriod(year, step)))
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keepdata = 0;
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if (!(this->isInArea(Area->getInnerArea(area))))
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keepdata = 0;
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if ((age < minage) || (age > maxage))
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keepdata = 0;
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if (keepdata == 1) {
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//renewal data is required, so store it
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renewalTime.resize(1, TimeInfo->calcSteps(year, step));
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renewalArea.resize(1, Area->getInnerArea(area));
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renewalAge.resize(1, age);
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renewalMult.resize(1, keeper);
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meanLength.resize(1, keeper);
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sdevLength.resize(1, keeper);
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alpha.resize(1, keeper);
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beta.resize(1, keeper);
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renewalDistribution.resize(1, new AgeBandMatrix(age, poptmp));
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infile >> renewalMult[count] >> ws;
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infile >> meanLength[count] >> ws;
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infile >> sdevLength[count] >> ws;
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infile >> alpha[count] >> ws;
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infile >> beta[count] >> ws;
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renewalMult[count].Inform(keeper);
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meanLength[count].Inform(keeper);
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sdevLength[count].Inform(keeper);
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alpha[count].Inform(keeper);
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beta[count].Inform(keeper);
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count++;
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} else { //renewal data not required - skip rest of line
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reject++;
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infile.get(c);
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| 176 : |
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while (c != '\n' && !infile.eof())
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infile.get(c);
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infile >> ws;
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}
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}
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if (count == 0)
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handle.logMessage(LOGWARN, "Warning in renewal - found no data in the data file");
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if (reject != 0)
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handle.logMessage(LOGMESSAGE, "Discarded invalid renewal data - number of invalid entries", reject);
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handle.logMessage(LOGMESSAGE, "Read renewal data file - number of entries", count);
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}
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void RenewalData::readNormalConditionData(CommentStream& infile, Keeper* const keeper,
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const TimeClass* const TimeInfo, const AreaClass* const Area, int minage, int maxage) {
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| 191 : |
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| 192 : |
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char c;
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| 193 : |
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int year, step, area, age, keepdata, count, reject;
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| 194 : |
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PopInfoIndexVector poptmp(LgrpDiv->numLengthGroups(), 0);
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| 195 : |
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| 196 : |
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//We now expect to find the renewal data in the following format
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//year, step, area, age, number, mean, sdev, cond
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infile >> ws;
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if (countColumns(infile) != 8)
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 8");
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year = step = area = age = count = reject = 0;
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| 203 : |
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while (!infile.eof()) {
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| 204 : |
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//crude check to see if something has gone wrong and avoid infinite loops
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| 205 : |
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if (!(isdigit(infile.peek())))
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| 206 : |
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handle.logFileMessage(LOGFAIL, "failed to read data from file");
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| 207 : |
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keepdata = 1;
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| 209 : |
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infile >> year >> step >> area >> age >> ws;
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| 210 : |
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| 211 : |
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if (!(TimeInfo->isWithinPeriod(year, step)))
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| 212 : |
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keepdata = 0;
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| 213 : |
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| 214 : |
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if (!(this->isInArea(Area->getInnerArea(area))))
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| 215 : |
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keepdata = 0;
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| 216 : |
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| 217 : |
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if ((age < minage) || (age > maxage))
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| 218 : |
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keepdata = 0;
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| 219 : |
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| 220 : |
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if (keepdata == 1) {
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| 221 : |
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//renewal data is required, so store it
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| 222 : |
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renewalTime.resize(1, TimeInfo->calcSteps(year, step));
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| 223 : |
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renewalArea.resize(1, Area->getInnerArea(area));
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| 224 : |
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renewalAge.resize(1, age);
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| 225 : |
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| 226 : |
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renewalMult.resize(1, keeper);
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| 227 : |
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meanLength.resize(1, keeper);
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| 228 : |
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sdevLength.resize(1, keeper);
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| 229 : |
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relCond.resize(1, keeper);
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| 230 : |
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renewalDistribution.resize(1, new AgeBandMatrix(age, poptmp));
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| 231 : |
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| 232 : |
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infile >> renewalMult[count] >> ws;
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| 233 : |
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infile >> meanLength[count] >> ws;
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| 234 : |
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infile >> sdevLength[count] >> ws;
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| 235 : |
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infile >> relCond[count] >> ws;
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| 236 : |
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| 237 : |
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renewalMult[count].Inform(keeper);
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| 238 : |
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meanLength[count].Inform(keeper);
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| 239 : |
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sdevLength[count].Inform(keeper);
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| 240 : |
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relCond[count].Inform(keeper);
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| 241 : |
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count++;
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| 242 : |
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| 243 : |
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} else { //renewal data not required - skip rest of line
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| 244 : |
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reject++;
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| 245 : |
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infile.get(c);
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| 246 : |
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while (c != '\n' && !infile.eof())
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| 247 : |
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infile.get(c);
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| 248 : |
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infile >> ws;
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| 249 : |
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}
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| 250 : |
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}
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| 251 : |
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| 252 : |
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if (count == 0)
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| 253 : |
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handle.logMessage(LOGWARN, "Warning in renewal - found no data in the data file");
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| 254 : |
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if (reject != 0)
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| 255 : |
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handle.logMessage(LOGMESSAGE, "Discarded invalid renewal data - number of invalid entries", reject);
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| 256 : |
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handle.logMessage(LOGMESSAGE, "Read renewal data file - number of entries", count);
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| 257 : |
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}
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| 258 : |
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| 259 : |
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void RenewalData::readNumberData(CommentStream& infile, Keeper* const keeper,
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| 260 : |
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const TimeClass* const TimeInfo, const AreaClass* const Area, int minage, int maxage) {
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| 261 : |
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| 262 : |
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char c;
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| 263 : |
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double length;
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| 264 : |
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int i, year, step, area, age, keepdata, count, id, lengthid, reject;
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| 265 : |
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int numlen = LgrpDiv->numLengthGroups();
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| 266 : |
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PopInfoIndexVector poptmp(numlen, 0);
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| 267 : |
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| 268 : |
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//We now expect to find the renewal data in the following format
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| 269 : |
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//year, step, area, age, length, number, mean weight
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| 270 : |
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infile >> ws;
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| 271 : |
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if (countColumns(infile) != 7)
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| 272 : |
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 7");
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| 273 : |
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| 274 : |
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year = step = area = age = count = reject = 0;
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| 275 : |
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while (!infile.eof()) {
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| 276 : |
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//crude check to see if something has gone wrong and avoid infinite loops
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| 277 : |
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if (!(isdigit(infile.peek())))
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| 278 : |
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handle.logFileMessage(LOGFAIL, "failed to read data from file");
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| 279 : |
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| 280 : |
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keepdata = 1;
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| 281 : |
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infile >> year >> step >> area >> age >> length >> ws;
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| 282 : |
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| 283 : |
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if (!(TimeInfo->isWithinPeriod(year, step)))
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| 284 : |
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keepdata = 0;
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| 285 : |
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| 286 : |
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if (!(this->isInArea(Area->getInnerArea(area))))
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| 287 : |
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keepdata = 0;
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| 288 : |
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| 289 : |
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if ((age < minage) || (age > maxage))
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| 290 : |
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keepdata = 0;
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| 291 : |
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| 292 : |
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lengthid = -1;
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| 293 : |
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for (i = 0; i < numlen; i++)
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| 294 : |
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if (isEqual(length, LgrpDiv->minLength(i)))
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| 295 : |
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lengthid = i;
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| 296 : |
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| 297 : |
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//OK the length doesnt match a minimum length so find the length group it is in
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| 298 : |
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if ((lengthid == -1) && (length > LgrpDiv->minLength()) && (length < LgrpDiv->maxLength())) {
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| 299 : |
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for (i = 1; i < numlen; i++) {
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| 300 : |
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if (length < LgrpDiv->minLength(i)) {
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| 301 : |
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lengthid = i - 1;
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| 302 : |
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break;
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| 303 : |
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}
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| 304 : |
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}
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| 305 : |
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if (lengthid == -1)
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| 306 : |
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lengthid = numlen - 1; //then this must be the last length group
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| 307 : |
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}
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| 308 : |
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| 309 : |
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if (lengthid == -1)
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| 310 : |
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keepdata = 0;
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| 311 : |
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| 312 : |
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if (keepdata == 1) {
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| 313 : |
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//renewal data is required, so store it
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| 314 : |
|
|
id = -1;
|
| 315 : |
|
|
for (i = 0; i < renewalTime.Size(); i++)
|
| 316 : |
|
|
if ((renewalTime[i] == TimeInfo->calcSteps(year, step))
|
| 317 : |
|
|
&& (renewalArea[i] == Area->getInnerArea(area))
|
| 318 : |
|
|
&& (renewalAge[i] == age))
|
| 319 : |
|
|
id = i;
|
| 320 : |
|
|
|
| 321 : |
|
|
if (id == -1) {
|
| 322 : |
|
|
//this is a new timestep/area combination
|
| 323 : |
|
|
renewalTime.resize(1, TimeInfo->calcSteps(year, step));
|
| 324 : |
|
|
renewalArea.resize(1, Area->getInnerArea(area));
|
| 325 : |
|
|
renewalAge.resize(1, age);
|
| 326 : |
|
|
id = renewalTime.Size() - 1;
|
| 327 : |
|
|
|
| 328 : |
|
|
renewalDistribution.resize(1, new AgeBandMatrix(age, poptmp));
|
| 329 : |
|
|
renewalNumber.resize(new FormulaMatrix(maxage - minage + 1, numlen, 0.0));
|
| 330 : |
|
|
}
|
| 331 : |
|
|
|
| 332 : |
|
|
renewalDistribution[id][age][lengthid].N = 0.0;
|
| 333 : |
|
|
infile >> (*renewalNumber[id])[age - minage][lengthid] >> ws;
|
| 334 : |
|
|
infile >> renewalDistribution[id][age][lengthid].W >> ws;
|
| 335 : |
|
|
count++;
|
| 336 : |
|
|
|
| 337 : |
|
|
} else { //renewal data not required - skip rest of line
|
| 338 : |
|
|
reject++;
|
| 339 : |
|
|
infile.get(c);
|
| 340 : |
|
|
while (c != '\n' && !infile.eof())
|
| 341 : |
|
|
infile.get(c);
|
| 342 : |
|
|
infile >> ws;
|
| 343 : |
|
|
}
|
| 344 : |
|
|
}
|
| 345 : |
|
|
|
| 346 : |
|
|
for (i = 0; i < renewalNumber.Size(); i++)
|
| 347 : |
|
|
(*renewalNumber[i]).Inform(keeper);
|
| 348 : |
|
|
|
| 349 : |
|
|
if (count == 0)
|
| 350 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - found no data in the data file");
|
| 351 : |
|
|
if (reject != 0)
|
| 352 : |
|
|
handle.logMessage(LOGMESSAGE, "Discarded invalid renewal data - number of invalid entries", reject);
|
| 353 : |
|
|
handle.logMessage(LOGMESSAGE, "Read renewal data file - number of entries", count);
|
| 354 : |
|
|
}
|
| 355 : |
|
|
|
| 356 : |
|
|
RenewalData::~RenewalData() {
|
| 357 : |
|
|
int i;
|
| 358 : |
|
|
delete LgrpDiv;
|
| 359 : |
|
|
delete CI;
|
| 360 : |
|
|
for (i = 0; i < renewalNumber.Size(); i++)
|
| 361 : |
|
|
delete renewalNumber[i];
|
| 362 : |
|
|
}
|
| 363 : |
|
|
|
| 364 : |
|
|
void RenewalData::setCI(const LengthGroupDivision* const GivenLDiv) {
|
| 365 : |
|
|
if (!checkLengthGroupStructure(GivenLDiv, LgrpDiv))
|
| 366 : |
|
|
handle.logMessage(LOGFAIL, "Error in renewal - invalid length group structure for stock", this->getName());
|
| 367 : |
|
|
//check minimum and maximum lengths
|
| 368 : |
|
|
if (LgrpDiv->minLength() < GivenLDiv->minLength())
|
| 369 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - minimum length less than stock length for stock", this->getName());
|
| 370 : |
|
|
if (LgrpDiv->maxLength() > GivenLDiv->maxLength())
|
| 371 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - maximum length greater than stock length for stock", this->getName());
|
| 372 : |
|
|
CI = new ConversionIndex(LgrpDiv, GivenLDiv);
|
| 373 : |
|
|
if (CI->Error())
|
| 374 : |
|
|
handle.logMessage(LOGFAIL, "Error in renewal - error when checking length structure");
|
| 375 : |
|
|
}
|
| 376 : |
|
|
|
| 377 : |
|
|
void RenewalData::Print(ofstream& outfile) const {
|
| 378 : |
|
|
int i;
|
| 379 : |
|
|
outfile << "\nRenewal data\n\t";
|
| 380 : |
|
|
LgrpDiv->Print(outfile);
|
| 381 : |
|
|
//need to find all areas and ages for current index value ...
|
| 382 : |
|
|
for (i = 0; i < renewalTime.Size(); i++) {
|
| 383 : |
|
|
if (renewalTime[i] == renewalTime[index]) {
|
| 384 : |
|
|
outfile << "\tInternal area " << renewalArea[i] << " age " << renewalAge[i];
|
| 385 : |
|
|
|
| 386 : |
|
|
if (readoption == 2)
|
| 387 : |
|
|
outfile << "\n\tNumbers\n";
|
| 388 : |
|
|
else
|
| 389 : |
|
|
outfile << " multiplier " << renewalMult[i] << "\n\tNumbers\n";
|
| 390 : |
|
|
|
| 391 : |
|
|
renewalDistribution[i].printNumbers(outfile);
|
| 392 : |
|
|
outfile << "\tMean weights\n";
|
| 393 : |
|
|
renewalDistribution[i].printWeights(outfile);
|
| 394 : |
|
|
}
|
| 395 : |
|
|
}
|
| 396 : |
|
|
outfile.flush();
|
| 397 : |
|
|
}
|
| 398 : |
|
|
|
| 399 : |
|
|
void RenewalData::Reset() {
|
| 400 : |
|
|
int i, age, l, minage;
|
| 401 : |
|
|
double sum, mult, dnorm;
|
| 402 : |
|
|
|
| 403 : |
|
|
index = 0;
|
| 404 : |
|
|
if (readoption == 0) {
|
| 405 : |
|
|
for (i = 0; i < renewalTime.Size(); i++) {
|
| 406 : |
|
|
age = renewalAge[i];
|
| 407 : |
|
|
|
| 408 : |
|
|
//JMB check that the length data is valid
|
| 409 : |
|
|
if (isZero(meanLength[i]) || sdevLength[i] < 0.04) {
|
| 410 : |
|
|
//JMB the limit has been set at 0.04 to keep the exponential calculation sane
|
| 411 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - invalid length data");
|
| 412 : |
|
|
|
| 413 : |
|
|
//JMB set the population to zero
|
| 414 : |
|
|
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++)
|
| 415 : |
|
|
renewalDistribution[i][age][l].setToZero();
|
| 416 : |
|
|
|
| 417 : |
|
|
} else {
|
| 418 : |
|
|
//JMB check that the mean length is within the length group range
|
| 419 : |
|
|
if (meanLength[i] < LgrpDiv->minLength())
|
| 420 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - mean length is less than minimum length for stock", this->getName());
|
| 421 : |
|
|
if (meanLength[i] > LgrpDiv->maxLength())
|
| 422 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - mean length is greater than maximum length for stock", this->getName());
|
| 423 : |
|
|
|
| 424 : |
|
|
sum = 0.0;
|
| 425 : |
|
|
mult = 1.0 / sdevLength[i];
|
| 426 : |
|
|
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
|
| 427 : |
|
|
dnorm = (LgrpDiv->meanLength(l) - meanLength[i]) * mult;
|
| 428 : |
|
|
renewalDistribution[i][age][l].N = exp(-(dnorm * dnorm) * 0.5);
|
| 429 : |
|
|
sum += renewalDistribution[i][age][l].N;
|
| 430 : |
|
|
}
|
| 431 : |
|
|
|
| 432 : |
|
|
if (isZero(sum)) {
|
| 433 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - calculated zero recruits for stock", this->getName());
|
| 434 : |
|
|
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++)
|
| 435 : |
|
|
renewalDistribution[i][age][l].setToZero();
|
| 436 : |
|
|
|
| 437 : |
|
|
} else {
|
| 438 : |
|
|
sum = 10000.0 / sum;
|
| 439 : |
|
|
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
|
| 440 : |
|
|
renewalDistribution[i][age][l].N *= sum;
|
| 441 : |
|
|
renewalDistribution[i][age][l].W = refWeight[l] * relCond[i];
|
| 442 : |
|
|
if ((handle.getLogLevel() >= LOGWARN) && (isZero(renewalDistribution[i][age][l].W)) && (renewalDistribution[i][age][l].N > 0.0))
|
| 443 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - zero mean weight for stock", this->getName());
|
| 444 : |
|
|
}
|
| 445 : |
|
|
}
|
| 446 : |
|
|
}
|
| 447 : |
|
|
}
|
| 448 : |
|
|
|
| 449 : |
|
|
} else if (readoption == 1) {
|
| 450 : |
|
|
for (i = 0; i < renewalTime.Size(); i++) {
|
| 451 : |
|
|
age = renewalAge[i];
|
| 452 : |
|
|
|
| 453 : |
|
|
//JMB check that the length data is valid
|
| 454 : |
|
|
if (isZero(meanLength[i]) || sdevLength[i] < 0.04) {
|
| 455 : |
|
|
//JMB the limit has been set at 0.04 to keep the exponential calculation sane
|
| 456 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - invalid length data");
|
| 457 : |
|
|
|
| 458 : |
|
|
//JMB set the population to zero
|
| 459 : |
|
|
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++)
|
| 460 : |
|
|
renewalDistribution[i][age][l].setToZero();
|
| 461 : |
|
|
|
| 462 : |
|
|
} else {
|
| 463 : |
|
|
//JMB check that the mean length is within the length group range
|
| 464 : |
|
|
if (meanLength[i] < LgrpDiv->minLength())
|
| 465 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - mean length is less than minimum length for stock", this->getName());
|
| 466 : |
|
|
if (meanLength[i] > LgrpDiv->maxLength())
|
| 467 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - mean length is greater than maximum length for stock", this->getName());
|
| 468 : |
|
|
|
| 469 : |
|
|
sum = 0.0;
|
| 470 : |
|
|
mult = 1.0 / sdevLength[i];
|
| 471 : |
|
|
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
|
| 472 : |
|
|
dnorm = (LgrpDiv->meanLength(l) - meanLength[i]) * mult;
|
| 473 : |
|
|
renewalDistribution[i][age][l].N = exp(-(dnorm * dnorm) * 0.5);
|
| 474 : |
|
|
sum += renewalDistribution[i][age][l].N;
|
| 475 : |
|
|
}
|
| 476 : |
|
|
|
| 477 : |
|
|
if (isZero(sum)) {
|
| 478 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - calculated zero recruits for stock", this->getName());
|
| 479 : |
|
|
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++)
|
| 480 : |
|
|
renewalDistribution[i][age][l].setToZero();
|
| 481 : |
|
|
|
| 482 : |
|
|
} else {
|
| 483 : |
|
|
sum = 10000.0 / sum;
|
| 484 : |
|
|
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
|
| 485 : |
|
|
renewalDistribution[i][age][l].N *= sum;
|
| 486 : |
|
|
renewalDistribution[i][age][l].W = alpha[i] * pow(LgrpDiv->meanLength(l), beta[i]);
|
| 487 : |
|
|
if ((handle.getLogLevel() >= LOGWARN) && (isZero(renewalDistribution[i][age][l].W)) && (renewalDistribution[i][age][l].N > 0.0))
|
| 488 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - zero mean weight for stock", this->getName());
|
| 489 : |
|
|
}
|
| 490 : |
|
|
}
|
| 491 : |
|
|
}
|
| 492 : |
|
|
}
|
| 493 : |
|
|
|
| 494 : |
|
|
} else if (readoption == 2) {
|
| 495 : |
|
|
for (i = 0; i < renewalTime.Size(); i++) {
|
| 496 : |
|
|
age = renewalAge[i];
|
| 497 : |
|
|
minage = renewalDistribution[i].minAge();
|
| 498 : |
|
|
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
|
| 499 : |
|
|
renewalDistribution[i][age][l].N = (*renewalNumber[i])[age - minage][l];
|
| 500 : |
|
|
if (handle.getLogLevel() >= LOGWARN) {
|
| 501 : |
|
|
if (renewalDistribution[i][age][l].N < 0.0)
|
| 502 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - negative number of recruits", renewalDistribution[i][age][l].N);
|
| 503 : |
|
|
if ((isZero(renewalDistribution[i][age][l].W)) && (renewalDistribution[i][age][l].N > 0.0))
|
| 504 : |
|
|
handle.logMessage(LOGWARN, "Warning in renewal - zero mean weight for stock", this->getName());
|
| 505 : |
|
|
}
|
| 506 : |
|
|
}
|
| 507 : |
|
|
}
|
| 508 : |
|
|
|
| 509 : |
|
|
} else
|
| 510 : |
|
|
handle.logMessage(LOGFAIL, "Error in renewal - unrecognised data format");
|
| 511 : |
|
|
|
| 512 : |
|
|
if (handle.getLogLevel() >= LOGMESSAGE)
|
| 513 : |
|
|
handle.logMessage(LOGMESSAGE, "Reset renewal data for stock", this->getName());
|
| 514 : |
|
|
}
|
| 515 : |
|
|
|
| 516 : |
|
|
int RenewalData::isRenewalStepArea(int area, const TimeClass* const TimeInfo) {
|
| 517 : |
|
|
int i;
|
| 518 : |
|
|
for (i = 0; i < renewalTime.Size(); i++)
|
| 519 : |
|
|
if ((renewalTime[i] == TimeInfo->getTime()) && (renewalArea[i] == area))
|
| 520 : |
|
|
return 1;
|
| 521 : |
|
|
return 0;
|
| 522 : |
|
|
}
|
| 523 : |
|
|
|
| 524 : |
|
|
void RenewalData::addRenewal(AgeBandMatrix& Alkeys, int area, const TimeClass* const TimeInfo) {
|
| 525 : |
|
|
int i;
|
| 526 : |
|
|
for (i = 0; i < renewalTime.Size(); i++) {
|
| 527 : |
|
|
if ((renewalTime[i] == TimeInfo->getTime()) && (renewalArea[i] == area)) {
|
| 528 : |
|
|
index = i;
|
| 529 : |
|
|
if (readoption == 2)
|
| 530 : |
|
|
Alkeys.Add(renewalDistribution[i], *CI);
|
| 531 : |
|
|
else if (renewalMult[i] > verysmall)
|
| 532 : |
|
|
Alkeys.Add(renewalDistribution[i], *CI, renewalMult[i]);
|
| 533 : |
|
|
}
|
| 534 : |
|
|
}
|
| 535 : |
|
|
}
|
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