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agomez |
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#include "grower.h" |
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#include "errorhandler.h" |
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#include "readfunc.h" |
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#include "readword.h" |
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#include "keeper.h" |
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#include "areatime.h" |
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#include "growthcalc.h" |
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#include "gadget.h" |
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#include "global.h" |
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Grower::Grower(CommentStream& infile, const LengthGroupDivision* const OtherLgrpDiv,
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const LengthGroupDivision* const GivenLgrpDiv, const IntVector& Areas,
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const TimeClass* const TimeInfo, Keeper* const keeper, const char* refWeight,
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const char* givenname, const AreaClass* const Area, const CharPtrVector& lenindex)
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: HasName(givenname), LivesOnAreas(Areas), LgrpDiv(0), CI(0), growthcalc(0) {
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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int i;
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keeper->addString("grower");
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fixedweights = 0;
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functionnumber = 0;
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LgrpDiv = new LengthGroupDivision(*GivenLgrpDiv);
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if (LgrpDiv->Error())
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handle.logMessage(LOGFAIL, "Error in grower - failed to create length group");
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CI = new ConversionIndex(OtherLgrpDiv, LgrpDiv, 1);
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if (CI->Error())
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handle.logMessage(LOGFAIL, "Error in grower - error when checking length structure");
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readWordAndValue(infile, "growthfunction", text);
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if (strcasecmp(text, "multspec") == 0) {
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functionnumber = 1;
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growthcalc = new GrowthCalcA(infile, areas, TimeInfo, keeper);
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} else if (strcasecmp(text, "fromfile") == 0) {
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functionnumber = 2;
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growthcalc = new GrowthCalcB(infile, areas, TimeInfo, keeper, Area, lenindex);
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} else if (strcasecmp(text, "weightvb") == 0) {
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functionnumber = 3;
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growthcalc = new GrowthCalcC(infile, areas, TimeInfo, LgrpDiv, keeper, refWeight);
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} else if (strcasecmp(text, "weightjones") == 0) {
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functionnumber = 4;
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growthcalc = new GrowthCalcD(infile, areas, TimeInfo, LgrpDiv, keeper, refWeight);
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} else if (strcasecmp(text, "weightvbexpanded") == 0) {
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functionnumber = 5;
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growthcalc = new GrowthCalcE(infile, areas, TimeInfo, LgrpDiv, keeper, refWeight);
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} else if (strcasecmp(text, "lengthvb") == 0) {
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functionnumber = 6;
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fixedweights = 1;
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growthcalc = new GrowthCalcF(infile, areas, TimeInfo, keeper, Area, lenindex);
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} else if (strcasecmp(text, "lengthpower") == 0) {
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functionnumber = 7;
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fixedweights = 1;
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growthcalc = new GrowthCalcG(infile, areas, TimeInfo, keeper, Area, lenindex);
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} else if (strcasecmp(text, "lengthvbsimple") == 0) {
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functionnumber = 8;
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growthcalc = new GrowthCalcH(infile, areas, TimeInfo, keeper);
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} else if (strcasecmp(text, "weightjonessimple") == 0) {
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functionnumber = 9;
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growthcalc = new GrowthCalcI(infile, areas, TimeInfo, keeper);
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} else if (strcasecmp(text, "lengthvpsimplet0") == 0) {
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functionnumber = 10;
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growthcalc = new GrowthCalcJ(infile, areas, TimeInfo, keeper);
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} else if (strcasecmp(text, "lengthgompertz") == 0) {
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functionnumber = 11;
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growthcalc = new GrowthCalcK(infile, areas, TimeInfo, keeper);
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} else {
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handle.logFileMessage(LOGFAIL, "unrecognised growth function", text);
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}
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infile >> ws >> text;
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if (strcasecmp(text, "beta") == 0) {
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//Beta binomial growth distribution code is used
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infile >> beta;
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beta.Inform(keeper);
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readWordAndVariable(infile, "maxlengthgroupgrowth", maxlengthgroupgrowth);
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if (maxlengthgroupgrowth > LgrpDiv->numLengthGroups()) {
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handle.logMessage(LOGWARN, "Warning in grower - maxlengthgroupgrowth is greater than number of length groups");
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maxlengthgroupgrowth = LgrpDiv->numLengthGroups();
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}
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part1.resize(maxlengthgroupgrowth + 1, 0.0);
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part2.resize(maxlengthgroupgrowth + 1, 0.0);
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part4.resize(maxlengthgroupgrowth + 1, 0.0);
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} else if (strcasecmp(text, "meanvarianceparameters") == 0) {
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handle.logFileMessage(LOGFAIL, "\nThe mean variance parameters implementation of the growth is no longer supported\nUse the beta-binomial distribution implementation of the growth instead");
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} else
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handle.logFileUnexpected(LOGFAIL, "beta", text);
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//Finished reading from input files.
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keeper->clearLast();
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int noareas = areas.Size();
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int len = LgrpDiv->numLengthGroups();
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int otherlen = OtherLgrpDiv->numLengthGroups();
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PopInfo nullpop;
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numGrow.AddRows(noareas, len, nullpop);
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//setting storage spaces for growth
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calcLengthGrowth.AddRows(noareas, len, 0.0);
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calcWeightGrowth.AddRows(noareas, len, 0.0);
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interpLengthGrowth.AddRows(noareas, otherlen, 0.0);
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interpWeightGrowth.AddRows(noareas, otherlen, 0.0);
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dummyfphi.resize(len, 0.0);
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for (i = 0; i < noareas; i++) {
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lgrowth.resize(new DoubleMatrix(maxlengthgroupgrowth + 1, otherlen, 0.0));
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wgrowth.resize(new DoubleMatrix(maxlengthgroupgrowth + 1, otherlen, 0.0));
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}
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}
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Grower::~Grower() {
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int i;
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for (i = 0; i < lgrowth.Size(); i++) {
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delete lgrowth[i];
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delete wgrowth[i];
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}
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delete CI;
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delete LgrpDiv;
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delete growthcalc;
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}
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void Grower::Print(ofstream& outfile) const {
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int i, j, area;
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outfile << "\nGrower\n\t";
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LgrpDiv->Print(outfile);
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for (area = 0; area < areas.Size(); area++) {
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outfile << "\tLength increase on internal area " << areas[area] << ":\n\t";
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for (i = 0; i < calcLengthGrowth.Ncol(area); i++)
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outfile << sep << calcLengthGrowth[area][i];
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outfile << "\n\tWeight increase on internal area " << areas[area] << ":\n\t";
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for (i = 0; i < calcWeightGrowth.Ncol(area); i++)
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outfile << sep << calcWeightGrowth[area][i];
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outfile << "\n\tDistributed length increase on internal area " << areas[area] << ":\n";
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for (i = 0; i < lgrowth[area]->Nrow(); i++) {
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outfile << TAB;
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for (j = 0; j < lgrowth[area]->Ncol(i); j++)
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outfile << sep << (*lgrowth[area])[i][j];
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outfile << endl;
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}
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outfile << "\tDistributed weight increase on internal area " << areas[area] << ":\n";
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for (i = 0; i < wgrowth[area]->Nrow(); i++) {
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outfile << TAB;
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for (j = 0; j < wgrowth[area]->Ncol(i); j++)
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outfile << sep << (*wgrowth[area])[i][j];
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outfile << endl;
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}
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}
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}
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void Grower::Sum(const PopInfoVector& NumberInArea, int area) {
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numGrow[this->areaNum(area)].Sum(&NumberInArea, *CI);
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}
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void Grower::calcGrowth(int area,
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const AreaClass* const Area, const TimeClass* const TimeInfo) {
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this->calcGrowth(area, Area, TimeInfo, dummyfphi, dummyfphi);
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}
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void Grower::calcGrowth(int area,
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const AreaClass* const Area, const TimeClass* const TimeInfo,
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const DoubleVector& FPhi, const DoubleVector& MaxCon) {
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int inarea = this->areaNum(area);
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growthcalc->calcGrowth(area, calcLengthGrowth[inarea], calcWeightGrowth[inarea],
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numGrow[inarea], Area, TimeInfo, FPhi, MaxCon, LgrpDiv);
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CI->interpolateLengths(interpLengthGrowth[inarea], calcLengthGrowth[inarea]);
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switch (functionnumber) {
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case 1:
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case 2:
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case 3:
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case 4:
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case 5:
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case 6:
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case 7:
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case 9:
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CI->interpolateLengths(interpWeightGrowth[inarea], calcWeightGrowth[inarea]);
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break;
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case 8:
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case 10:
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case 11:
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break;
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default:
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handle.logMessage(LOGFAIL, "Error in grower - unrecognised growth function", functionnumber);
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break;
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}
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}
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void Grower::Reset() {
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int i, j, area;
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double factorialx, tmppart, tmpmax;
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calcLengthGrowth.setToZero();
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calcWeightGrowth.setToZero();
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interpLengthGrowth.setToZero();
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for (area = 0; area < areas.Size(); area++) {
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(*lgrowth[area]).setToZero();
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++)
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numGrow[area][i].setToZero();
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}
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switch (functionnumber) {
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case 1:
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case 2:
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case 3:
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case 4:
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case 5:
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case 6:
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case 7:
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case 9:
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interpWeightGrowth.setToZero();
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for (area = 0; area < areas.Size(); area++)
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(*wgrowth[area]).setToZero();
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break;
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case 8:
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case 10:
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case 11:
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break;
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default:
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handle.logMessage(LOGFAIL, "Error in grower - unrecognised growth function", functionnumber);
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break;
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}
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tmpmax = double(maxlengthgroupgrowth);
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part1[0] = 1.0;
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part1[1] = tmpmax;
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factorialx = 1.0;
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tmppart = tmpmax;
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if (maxlengthgroupgrowth > 1) {
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for (i = 2; i < maxlengthgroupgrowth + 1; i++) {
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tmppart *= (tmpmax - i + 1);
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factorialx *= double(i);
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part1[i] = (tmppart / factorialx);
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}
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}
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part2[maxlengthgroupgrowth] = 1.0;
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part2[maxlengthgroupgrowth - 1] = beta;
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if (maxlengthgroupgrowth > 1)
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for (i = maxlengthgroupgrowth - 2; i >= 0; i--)
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part2[i] = part2[i + 1] * (beta + tmpmax - i - 1);
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//JMB this will never change so we can set it once
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part4[0] = 1.0;
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if (handle.getLogLevel() >= LOGMESSAGE)
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handle.logMessage(LOGMESSAGE, "Reset grower data for stock", this->getName());
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}
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