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agomez |
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#include "catchinkilos.h" |
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#include "readfunc.h" |
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#include "readword.h" |
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#include "readaggregation.h" |
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#include "errorhandler.h" |
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#include "areatime.h" |
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#include "fleet.h" |
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#include "stock.h" |
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#include "gadget.h" |
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#include "global.h" |
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CatchInKilos::CatchInKilos(CommentStream& infile, const AreaClass* const Area,
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const TimeClass* const TimeInfo, double weight, const char* name)
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: Likelihood(CATCHINKILOSLIKELIHOOD, weight, name) {
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int i, j;
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int numarea = 0;
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int readfile = 0;
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char text[MaxStrLength];
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char datafilename[MaxStrLength];
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char aggfilename[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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strncpy(datafilename, "", MaxStrLength);
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strncpy(aggfilename, "", MaxStrLength);
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ifstream datafile;
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CommentStream subdata(datafile);
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functionname = new char[MaxStrLength];
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strncpy(functionname, "", MaxStrLength);
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readWordAndValue(infile, "datafile", datafilename);
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readWordAndValue(infile, "function", functionname);
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yearly = 0;
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epsilon = 10.0;
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timeindex = 0;
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functionnumber = 0;
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if (strcasecmp(functionname, "sumofsquares") == 0)
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functionnumber = 1;
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else
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handle.logFileMessage(LOGFAIL, "\nError in catchinkilos - unrecognised function", functionname);
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infile >> ws;
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char c = infile.peek();
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if ((c == 'a') || (c == 'A')) {
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//we have found either aggregationlevel or areaaggfile ...
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streampos pos = infile.tellg();
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infile >> text >> ws;
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if ((strcasecmp(text, "aggregationlevel") == 0))
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infile >> yearly >> ws;
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else if (strcasecmp(text, "areaaggfile") == 0)
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infile.seekg(pos);
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else
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handle.logFileUnexpected(LOGFAIL, "areaaggfile", text);
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//JMB - peek at the next char
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c = infile.peek();
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if (yearly != 0 && yearly != 1)
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handle.logFileMessage(LOGFAIL, "\nError in catchinkilos - aggregationlevel must be 0 or 1");
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}
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//JMB - changed to make the reading of epsilon optional
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c = infile.peek();
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if ((c == 'e') || (c == 'E')) {
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readWordAndVariable(infile, "epsilon", epsilon);
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if (epsilon < verysmall) {
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handle.logFileMessage(LOGWARN, "epsilon should be a positive number - set to default value 10");
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epsilon = 10.0;
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}
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}
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readWordAndValue(infile, "areaaggfile", aggfilename);
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datafile.open(aggfilename, ios::in);
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handle.checkIfFailure(datafile, aggfilename);
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handle.Open(aggfilename);
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numarea = readAggregation(subdata, areas, areaindex);
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handle.Close();
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datafile.close();
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datafile.clear();
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//Must change from outer areas to inner areas.
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for (i = 0; i < areas.Nrow(); i++)
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for (j = 0; j < areas.Ncol(i); j++)
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areas[i][j] = Area->getInnerArea(areas[i][j]);
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//read in the fleetnames
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i = 0;
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infile >> text >> ws;
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if (strcasecmp(text, "fleetnames") != 0)
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handle.logFileUnexpected(LOGFAIL, "fleetnames", text);
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infile >> text >> ws;
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while (!infile.eof() && (strcasecmp(text, "stocknames") != 0)) {
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fleetnames.resize(new char[strlen(text) + 1]);
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strcpy(fleetnames[i++], text);
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infile >> text >> ws;
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}
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if (fleetnames.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in catchinkilos - failed to read fleets");
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handle.logMessage(LOGMESSAGE, "Read fleet data - number of fleets", fleetnames.Size());
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//read in the stocknames
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i = 0;
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if (strcasecmp(text, "stocknames") != 0)
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handle.logFileUnexpected(LOGFAIL, "stocknames", text);
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infile >> text;
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while (!infile.eof() && (strcasecmp(text, "[component]") != 0)) {
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infile >> ws;
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stocknames.resize(new char[strlen(text) + 1]);
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strcpy(stocknames[i++], text);
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infile >> text;
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}
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if (stocknames.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in catchinkilos - failed to read stocks");
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handle.logMessage(LOGMESSAGE, "Read stock data - number of stocks", stocknames.Size());
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//We have now read in all the data from the main likelihood file
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//But we have to read in the statistics data from datafilename
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datafile.open(datafilename, ios::in);
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handle.checkIfFailure(datafile, datafilename);
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handle.Open(datafilename);
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readCatchInKilosData(subdata, TimeInfo, numarea);
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handle.Close();
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datafile.close();
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datafile.clear();
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}
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void CatchInKilos::Reset(const Keeper* const keeper) {
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Likelihood::Reset(keeper);
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if (isZero(weight))
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handle.logMessage(LOGWARN, "Warning in catchinkilos - zero weight for", this->getName());
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modelDistribution.setToZero();
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if (handle.getLogLevel() >= LOGMESSAGE)
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handle.logMessage(LOGMESSAGE, "Reset catchinkilos component", this->getName());
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}
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void CatchInKilos::Print(ofstream& outfile) const {
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int i;
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outfile << "\nCatch in Kilos " << this->getName() << " - likelihood value " << likelihood
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<< "\n\tFunction " << functionname;
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outfile << "\n\tStock names:";
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for (i = 0; i < stocknames.Size(); i++)
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outfile << sep << stocknames[i];
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outfile << "\n\tFleet names:";
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for (i = 0; i < fleetnames.Size(); i++)
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outfile << sep << fleetnames[i];
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outfile << endl;
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outfile.flush();
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}
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double CatchInKilos::calcLikSumSquares(const TimeClass* const TimeInfo) {
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int r, a, f, p;
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double totallikelihood = 0.0;
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for (r = 0; r < areas.Nrow(); r++) {
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likelihoodValues[timeindex][r] = 0.0;
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for (a = 0; a < areas.Ncol(r); a++)
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for (f = 0; f < predators.Size(); f++)
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for (p = 0; p < preyindex.Ncol(f); p++)
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modelDistribution[timeindex][r] += predators[f]->getConsumptionBiomass(preyindex[f][p], areas[r][a]);
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if ((!yearly) || (TimeInfo->getStep() == TimeInfo->numSteps())) {
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likelihoodValues[timeindex][r] +=
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(log(modelDistribution[timeindex][r] + epsilon) - log(obsDistribution[timeindex][r] + epsilon))
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* (log(modelDistribution[timeindex][r] + epsilon) - log(obsDistribution[timeindex][r] + epsilon));
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totallikelihood += likelihoodValues[timeindex][r];
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}
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}
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return totallikelihood;
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}
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void CatchInKilos::addLikelihood(const TimeClass* const TimeInfo) {
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if ((!(AAT.atCurrentTime(TimeInfo))) || (isZero(weight)))
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return;
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if ((handle.getLogLevel() >= LOGMESSAGE) && ((!yearly) || (TimeInfo->getStep() == TimeInfo->numSteps())))
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handle.logMessage(LOGMESSAGE, "Calculating likelihood score for catchinkilos component", this->getName());
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int i;
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if (yearly) {
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for (i = 0; i < Years.Size(); i++)
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if (Years[i] == TimeInfo->getYear())
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timeindex = i;
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} else {
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for (i = 0; i < Years.Size(); i++)
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if ((Years[i] == TimeInfo->getYear()) && (Steps[i] == TimeInfo->getStep()))
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timeindex = i;
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}
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double l = 0.0;
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switch (functionnumber) {
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case 1:
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l = calcLikSumSquares(TimeInfo);
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break;
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default:
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handle.logMessage(LOGWARN, "Warning in catchinkilos - unrecognised function", functionname);
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break;
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}
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if ((!yearly) || (TimeInfo->getStep() == TimeInfo->numSteps())) {
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likelihood += l;
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if (handle.getLogLevel() >= LOGMESSAGE)
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handle.logMessage(LOGMESSAGE, "The likelihood score for this component on this timestep is", l);
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}
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}
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CatchInKilos::~CatchInKilos() {
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int i;
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for (i = 0; i < stocknames.Size(); i++)
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delete[] stocknames[i];
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for (i = 0; i < fleetnames.Size(); i++)
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delete[] fleetnames[i];
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for (i = 0; i < areaindex.Size(); i++)
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delete[] areaindex[i];
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delete[] functionname;
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}
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void CatchInKilos::setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks) {
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| 222 : |
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int i, j, k, found;
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StockPtrVector stocks;
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| 224 : |
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FleetPtrVector fleets;
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| 225 : |
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for (i = 0; i < fleetnames.Size(); i++) {
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| 227 : |
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found = 0;
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| 228 : |
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for (j = 0; j < Fleets.Size(); j++) {
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| 229 : |
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if (strcasecmp(fleetnames[i], Fleets[j]->getName()) == 0) {
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found++;
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fleets.resize(Fleets[j]);
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}
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| 233 : |
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}
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if (found == 0)
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handle.logMessage(LOGFAIL, "Error in catchinkilos - unrecognised fleet", fleetnames[i]);
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}
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for (i = 0; i < fleets.Size(); i++)
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for (j = 0; j < fleets.Size(); j++)
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| 240 : |
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if ((strcasecmp(fleets[i]->getName(), fleets[j]->getName()) == 0) && (i != j))
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| 241 : |
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handle.logMessage(LOGFAIL, "Error in catchinkilos - repeated fleet", fleets[i]->getName());
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| 242 : |
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for (i = 0; i < stocknames.Size(); i++) {
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| 244 : |
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found = 0;
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| 245 : |
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for (j = 0; j < Stocks.Size(); j++) {
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| 246 : |
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if (Stocks[j]->isEaten()) {
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| 247 : |
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if (strcasecmp(stocknames[i], Stocks[j]->getName()) == 0) {
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| 248 : |
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found++;
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| 249 : |
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stocks.resize(Stocks[j]);
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| 250 : |
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}
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| 251 : |
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}
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| 252 : |
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}
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| 253 : |
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if (found == 0)
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| 254 : |
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handle.logMessage(LOGFAIL, "Error in catchinkilos - unrecognised stock", stocknames[i]);
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| 255 : |
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}
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| 256 : |
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| 257 : |
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for (i = 0; i < stocks.Size(); i++)
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| 258 : |
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for (j = 0; j < stocks.Size(); j++)
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| 259 : |
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if ((strcasecmp(stocks[i]->getName(), stocks[j]->getName()) == 0) && (i != j))
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| 260 : |
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handle.logMessage(LOGFAIL, "Error in catchinkilos - repeated stock", stocks[i]->getName());
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| 261 : |
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| 262 : |
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//check fleet and stock areas
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| 263 : |
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if (handle.getLogLevel() >= LOGWARN) {
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| 264 : |
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for (j = 0; j < areas.Nrow(); j++) {
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| 265 : |
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found = 0;
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| 266 : |
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for (i = 0; i < fleets.Size(); i++)
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| 267 : |
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for (k = 0; k < areas.Ncol(j); k++)
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| 268 : |
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if (fleets[i]->isInArea(areas[j][k]))
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| 269 : |
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found++;
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| 270 : |
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if (found == 0)
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| 271 : |
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handle.logMessage(LOGWARN, "Warning in catchinkilos - fleet not defined on all areas");
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| 272 : |
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}
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| 273 : |
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| 274 : |
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for (j = 0; j < areas.Nrow(); j++) {
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| 275 : |
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found = 0;
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| 276 : |
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for (i = 0; i < stocks.Size(); i++)
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| 277 : |
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for (k = 0; k < areas.Ncol(j); k++)
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| 278 : |
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if (stocks[i]->isInArea(areas[j][k]))
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| 279 : |
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found++;
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| 280 : |
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if (found == 0)
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| 281 : |
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handle.logMessage(LOGWARN, "Warning in catchinkilos - stock not defined on all areas");
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| 282 : |
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}
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| 283 : |
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}
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| 284 : |
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| 285 : |
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//JMB its simpler to just store pointers to the predators rather than the fleets
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| 286 : |
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for (i = 0; i < fleets.Size(); i++)
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| 287 : |
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predators.resize(fleets[i]->getPredator());
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| 288 : |
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| 289 : |
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for (i = 0; i < predators.Size(); i++) {
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| 290 : |
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found = 0;
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| 291 : |
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preyindex.AddRows(1, 0, 0);
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| 292 : |
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for (j = 0; j < predators[i]->numPreys(); j++)
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| 293 : |
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for (k = 0; k < stocknames.Size(); k++)
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| 294 : |
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if (strcasecmp(stocknames[k], predators[i]->getPrey(j)->getName()) == 0) {
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| 295 : |
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found++;
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| 296 : |
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preyindex[i].resize(1, j);
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| 297 : |
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}
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| 298 : |
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| 299 : |
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if (found == 0)
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| 300 : |
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handle.logMessage(LOGWARN, "Warning in catchinkilos - found no stocks for fleet", fleetnames[i]);
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| 301 : |
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}
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| 302 : |
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}
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| 303 : |
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| 304 : |
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void CatchInKilos::readCatchInKilosData(CommentStream& infile,
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| 305 : |
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const TimeClass* TimeInfo, int numarea) {
|
| 306 : |
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| 307 : |
|
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int i, year, step, count, reject;
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| 308 : |
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double tmpnumber = 0.0;
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| 309 : |
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char tmparea[MaxStrLength];
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| 310 : |
|
|
char tmpfleet[MaxStrLength];
|
| 311 : |
|
|
strncpy(tmparea, "", MaxStrLength);
|
| 312 : |
|
|
strncpy(tmpfleet, "", MaxStrLength);
|
| 313 : |
|
|
int keepdata, timeid, areaid, fleetid, check;
|
| 314 : |
|
|
|
| 315 : |
|
|
//Check the number of columns in the inputfile
|
| 316 : |
|
|
infile >> ws;
|
| 317 : |
|
|
check = countColumns(infile);
|
| 318 : |
|
|
if (!(((yearly) && ((check == 4) || (check == 5))) || ((!yearly) && (check == 5))))
|
| 319 : |
|
|
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 4 or 5");
|
| 320 : |
|
|
|
| 321 : |
|
|
step = 1; //default value in case there are only 4 columns in the datafile
|
| 322 : |
|
|
year = count = reject = 0;
|
| 323 : |
|
|
while (!infile.eof()) {
|
| 324 : |
|
|
keepdata = 1;
|
| 325 : |
|
|
if ((yearly) && (check == 4))
|
| 326 : |
|
|
infile >> year >> tmparea >> tmpfleet >> tmpnumber >> ws;
|
| 327 : |
|
|
else
|
| 328 : |
|
|
infile >> year >> step >> tmparea >> tmpfleet >> tmpnumber >> ws;
|
| 329 : |
|
|
|
| 330 : |
|
|
//crude check to see if something has gone wrong and avoid infinite loops
|
| 331 : |
|
|
if (strlen(tmparea) == 0)
|
| 332 : |
|
|
handle.logFileMessage(LOGFAIL, "failed to read data from file");
|
| 333 : |
|
|
|
| 334 : |
|
|
//if tmparea is in areaindex find areaid, else dont keep the data
|
| 335 : |
|
|
areaid = -1;
|
| 336 : |
|
|
for (i = 0; i < areaindex.Size(); i++)
|
| 337 : |
|
|
if (strcasecmp(areaindex[i], tmparea) == 0)
|
| 338 : |
|
|
areaid = i;
|
| 339 : |
|
|
|
| 340 : |
|
|
if (areaid == -1)
|
| 341 : |
|
|
keepdata = 0;
|
| 342 : |
|
|
|
| 343 : |
|
|
//if tmpfleet is a required fleet keep the data, else ignore it
|
| 344 : |
|
|
fleetid = -1;
|
| 345 : |
|
|
for (i = 0; i < fleetnames.Size(); i++)
|
| 346 : |
|
|
if (strcasecmp(fleetnames[i], tmpfleet) == 0)
|
| 347 : |
|
|
fleetid = i;
|
| 348 : |
|
|
|
| 349 : |
|
|
if (fleetid == -1)
|
| 350 : |
|
|
keepdata = 0;
|
| 351 : |
|
|
|
| 352 : |
|
|
//check if the year and step are in the simulation
|
| 353 : |
|
|
timeid = -1;
|
| 354 : |
|
|
if ((TimeInfo->isWithinPeriod(year, step)) && (keepdata == 1)) {
|
| 355 : |
|
|
//if this is a new timestep, resize to store the data
|
| 356 : |
|
|
for (i = 0; i < Years.Size(); i++)
|
| 357 : |
|
|
if ((Years[i] == year) && (yearly || (Steps[i] == step)))
|
| 358 : |
|
|
timeid = i;
|
| 359 : |
|
|
|
| 360 : |
|
|
if (timeid == -1) {
|
| 361 : |
|
|
Years.resize(1, year);
|
| 362 : |
|
|
if (!(yearly))
|
| 363 : |
|
|
Steps.resize(1, step);
|
| 364 : |
|
|
timeid = (Years.Size() - 1);
|
| 365 : |
|
|
obsDistribution.AddRows(1, numarea, 0.0);
|
| 366 : |
|
|
modelDistribution.AddRows(1, numarea, 0.0);
|
| 367 : |
|
|
likelihoodValues.AddRows(1, numarea, 0.0);
|
| 368 : |
|
|
}
|
| 369 : |
|
|
|
| 370 : |
|
|
} else
|
| 371 : |
|
|
keepdata = 0;
|
| 372 : |
|
|
|
| 373 : |
|
|
if (keepdata == 1) {
|
| 374 : |
|
|
//distribution data is required, so store it
|
| 375 : |
|
|
count++;
|
| 376 : |
|
|
//note that we use += to sum the data over all fleets (and possibly time)
|
| 377 : |
|
|
obsDistribution[timeid][areaid] += tmpnumber;
|
| 378 : |
|
|
} else
|
| 379 : |
|
|
reject++; //count number of rejected data points read from file
|
| 380 : |
|
|
}
|
| 381 : |
|
|
|
| 382 : |
|
|
if (yearly)
|
| 383 : |
|
|
AAT.addActionsAllSteps(Years, TimeInfo);
|
| 384 : |
|
|
else
|
| 385 : |
|
|
AAT.addActions(Years, Steps, TimeInfo);
|
| 386 : |
|
|
|
| 387 : |
|
|
if (count == 0)
|
| 388 : |
|
|
handle.logMessage(LOGWARN, "Warning in catchinkilos - found no data in the data file for", this->getName());
|
| 389 : |
|
|
if (reject != 0)
|
| 390 : |
|
|
handle.logMessage(LOGMESSAGE, "Discarded invalid catchinkilos data - number of invalid entries", reject);
|
| 391 : |
|
|
handle.logMessage(LOGMESSAGE, "Read catchinkilos data file - number of entries", count);
|
| 392 : |
|
|
}
|
| 393 : |
|
|
|
| 394 : |
|
|
void CatchInKilos::printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo) {
|
| 395 : |
|
|
if (!AAT.atCurrentTime(TimeInfo))
|
| 396 : |
|
|
return;
|
| 397 : |
|
|
|
| 398 : |
|
|
if ((yearly) && (TimeInfo->getStep() != TimeInfo->numSteps()))
|
| 399 : |
|
|
return; //if data is aggregated into years then we need the last timestep
|
| 400 : |
|
|
|
| 401 : |
|
|
int i, area, age, len;
|
| 402 : |
|
|
timeindex = -1;
|
| 403 : |
|
|
if (yearly) {
|
| 404 : |
|
|
for (i = 0; i < Years.Size(); i++)
|
| 405 : |
|
|
if (Years[i] == TimeInfo->getYear())
|
| 406 : |
|
|
timeindex = i;
|
| 407 : |
|
|
} else {
|
| 408 : |
|
|
for (i = 0; i < Years.Size(); i++)
|
| 409 : |
|
|
if ((Years[i] == TimeInfo->getYear()) && (Steps[i] == TimeInfo->getStep()))
|
| 410 : |
|
|
timeindex = i;
|
| 411 : |
|
|
}
|
| 412 : |
|
|
|
| 413 : |
|
|
if (timeindex == -1)
|
| 414 : |
|
|
handle.logMessage(LOGFAIL, "Error in catchinkilos - invalid timestep");
|
| 415 : |
|
|
|
| 416 : |
|
|
for (area = 0; area < modelDistribution.Ncol(timeindex); area++) {
|
| 417 : |
|
|
if (yearly)
|
| 418 : |
|
|
outfile << setw(lowwidth) << Years[timeindex] << " all "
|
| 419 : |
|
|
<< setw(printwidth) << areaindex[area];
|
| 420 : |
|
|
else
|
| 421 : |
|
|
outfile << setw(lowwidth) << Years[timeindex] << sep << setw(lowwidth)
|
| 422 : |
|
|
<< Steps[timeindex] << sep << setw(printwidth) << areaindex[area];
|
| 423 : |
|
|
|
| 424 : |
|
|
if (fleetnames.Size() == 1)
|
| 425 : |
|
|
outfile << sep << setw(printwidth) << fleetnames[0] << sep;
|
| 426 : |
|
|
else
|
| 427 : |
|
|
outfile << " all ";
|
| 428 : |
|
|
|
| 429 : |
|
|
//JMB crude filter to remove the 'silly' values from the output
|
| 430 : |
|
|
if (modelDistribution[timeindex][area] < rathersmall)
|
| 431 : |
|
|
outfile << setw(largewidth) << 0 << endl;
|
| 432 : |
|
|
else
|
| 433 : |
|
|
outfile << setprecision(largeprecision) << setw(largewidth)
|
| 434 : |
|
|
<< modelDistribution[timeindex][area] << endl;
|
| 435 : |
|
|
}
|
| 436 : |
|
|
}
|
| 437 : |
|
|
|
| 438 : |
|
|
void CatchInKilos::printSummary(ofstream& outfile) {
|
| 439 : |
|
|
int year, area;
|
| 440 : |
|
|
|
| 441 : |
|
|
for (year = 0; year < likelihoodValues.Nrow(); year++) {
|
| 442 : |
|
|
for (area = 0; area < likelihoodValues.Ncol(year); area++) {
|
| 443 : |
|
|
if (yearly) {
|
| 444 : |
|
|
outfile << setw(lowwidth) << Years[year] << " all "
|
| 445 : |
|
|
<< setw(printwidth) << areaindex[area] << sep
|
| 446 : |
|
|
<< setw(largewidth) << this->getName() << sep << setprecision(smallprecision)
|
| 447 : |
|
|
<< setw(smallwidth) << weight << sep << setprecision(largeprecision)
|
| 448 : |
|
|
<< setw(largewidth) << likelihoodValues[year][area] << endl;
|
| 449 : |
|
|
} else {
|
| 450 : |
|
|
outfile << setw(lowwidth) << Years[year] << sep << setw(lowwidth)
|
| 451 : |
|
|
<< Steps[year] << sep << setw(printwidth) << areaindex[area] << sep
|
| 452 : |
|
|
<< setw(largewidth) << this->getName() << sep << setprecision(smallprecision)
|
| 453 : |
|
|
<< setw(smallwidth) << weight << sep << setprecision(largeprecision)
|
| 454 : |
|
|
<< setw(largewidth) << likelihoodValues[year][area] << endl;
|
| 455 : |
|
|
}
|
| 456 : |
|
|
}
|
| 457 : |
|
|
}
|
| 458 : |
|
|
outfile.flush();
|
| 459 : |
|
|
}
|
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