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agomez |
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#include "migrationproportion.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 "mathfunc.h" |
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#include "stockprey.h" |
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#include "gadget.h" |
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#include "global.h" |
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MigrationProportion::MigrationProportion(CommentStream& infile, const AreaClass* const Area,
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const TimeClass* const TimeInfo, double weight, const char* name)
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: Likelihood(MIGRATIONPROPORTIONLIKELIHOOD, weight, name) {
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int i, j;
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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int numarea = 0, numage = 0, numlen = 0;
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char datafilename[MaxStrLength];
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char aggfilename[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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timeindex = 0;
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biomass = 1; // default is to use the biomass to calculate the likelihood score
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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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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 migrationproportion - unrecognised function", functionname);
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char c = infile.peek();
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if ((c == 'b') || (c == 'B'))
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readWordAndVariable(infile, "biomass", biomass);
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if (biomass != 0 && biomass != 1)
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handle.logFileMessage(LOGFAIL, "\nError in migrationproportion - biomass must be 0 or 1");
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//read in area aggregation from file
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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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if (areaindex.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in migrationproportion - failed to read areas");
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if (areaindex.Size() == 1)
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handle.logFileMessage(LOGWARN, "\nWarning in migrationproportion - only read one area");
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handle.logMessage(LOGMESSAGE, "Read area data - number of areas", areaindex.Size());
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//read in the stocknames
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i = 0;
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infile >> text >> ws;
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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 migrationproportion - 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 migration proportion 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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readProportionData(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 MigrationProportion::readProportionData(CommentStream& infile,
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const TimeClass* TimeInfo, int numarea) {
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int i, year, step;
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double tmpnumber;
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char tmparea[MaxStrLength];
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strncpy(tmparea, "", MaxStrLength);
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int keepdata, timeid, areaid, count, reject;
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//Check the number of columns in the inputfile
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infile >> ws;
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if (countColumns(infile) != 4)
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 4");
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year = step = count = reject = 0;
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while (!infile.eof()) {
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keepdata = 1;
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infile >> year >> step >> tmparea >> tmpnumber >> ws;
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//crude check to see if something has gone wrong and avoid infinite loops
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if (strlen(tmparea) == 0)
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handle.logFileMessage(LOGFAIL, "failed to read data from file");
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//if tmparea is in areaindex find areaid, else dont keep the data
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areaid = -1;
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for (i = 0; i < areaindex.Size(); i++)
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if (strcasecmp(areaindex[i], tmparea) == 0)
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areaid = i;
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if (areaid == -1)
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keepdata = 0;
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//check if the year and step are in the simulation
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timeid = -1;
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if ((TimeInfo->isWithinPeriod(year, step)) && (keepdata == 1)) {
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//if this is a new timestep, resize to store the data
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for (i = 0; i < Years.Size(); i++)
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if ((Years[i] == year) && (Steps[i] == step))
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timeid = i;
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if (timeid == -1) {
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Years.resize(1, year);
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Steps.resize(1, step);
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timeid = (Years.Size() - 1);
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obsDistribution.AddRows(1, numarea, 0.0);
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modelDistribution.AddRows(1, numarea, 0.0);
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likelihoodValues.resize(1, 0.0);
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}
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} else
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keepdata = 0;
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if (keepdata == 1) {
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//distribution data is required, so store it
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count++;
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obsDistribution[timeid][areaid] = tmpnumber;
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} else
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reject++; //count number of rejected data points read from file
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}
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AAT.addActions(Years, Steps, TimeInfo);
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if (count == 0)
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handle.logMessage(LOGWARN, "Warning in migrationproportion - found no data in the data file for", this->getName());
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if (reject != 0)
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handle.logMessage(LOGMESSAGE, "Discarded invalid migrationproportion data - number of invalid entries", reject);
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handle.logMessage(LOGMESSAGE, "Read migrationproportion data file - number of entries", count);
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}
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MigrationProportion::~MigrationProportion() {
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int i, j;
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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 < 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 MigrationProportion::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 migrationproportion - 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 migrationproportion component", this->getName());
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}
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void MigrationProportion::Print(ofstream& outfile) const {
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int i;
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outfile << "\nMigration Proportion " << this->getName() << " - likelihood value " << likelihood
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<< "\n\tFunction " << functionname << "\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 << endl;
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outfile.flush();
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}
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void MigrationProportion::printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo) {
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if (!AAT.atCurrentTime(TimeInfo))
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return;
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int i, area;
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timeindex = -1;
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| 202 : |
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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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if (timeindex == -1)
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handle.logMessage(LOGFAIL, "Error in migrationproportion - invalid timestep");
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for (area = 0; area < modelDistribution.Ncol(timeindex); area++) {
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outfile << setw(lowwidth) << Years[timeindex] << sep << setw(lowwidth)
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| 210 : |
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<< Steps[timeindex] << sep << setw(printwidth) << areaindex[area] << sep;
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| 211 : |
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//JMB crude filter to remove the 'silly' values from the output
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if (modelDistribution[timeindex][area] < rathersmall)
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outfile << setw(largewidth) << 0 << endl;
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else
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outfile << setprecision(largeprecision) << setw(largewidth)
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<< modelDistribution[timeindex][area] << endl;
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}
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}
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| 220 : |
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void MigrationProportion::setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks) {
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| 222 : |
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int i, j, k, found;
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| 223 : |
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| 224 : |
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for (i = 0; i < stocknames.Size(); i++) {
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found = 0;
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| 226 : |
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for (j = 0; j < Stocks.Size(); j++) {
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| 227 : |
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if (strcasecmp(stocknames[i], Stocks[j]->getName()) == 0) {
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| 228 : |
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found++;
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| 229 : |
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stocks.resize(Stocks[j]);
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| 230 : |
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}
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}
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| 232 : |
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if (found == 0)
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handle.logMessage(LOGFAIL, "Error in migrationproportion - unrecognised stock", stocknames[i]);
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}
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for (i = 0; i < stocks.Size(); i++)
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for (j = 0; j < stocks.Size(); j++)
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| 238 : |
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if ((strcasecmp(stocks[i]->getName(), stocks[j]->getName()) == 0) && (i != j))
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| 239 : |
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handle.logMessage(LOGFAIL, "Error in migrationproportion - repeated stock", stocks[i]->getName());
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| 240 : |
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| 241 : |
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if (handle.getLogLevel() >= LOGWARN) {
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| 242 : |
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for (j = 0; j < areas.Nrow(); j++) {
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| 243 : |
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found = 0;
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| 244 : |
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for (i = 0; i < stocks.Size(); i++)
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| 245 : |
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for (k = 0; k < areas.Ncol(j); k++)
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| 246 : |
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if (stocks[i]->isInArea(areas[j][k]))
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| 247 : |
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found++;
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| 248 : |
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if (found == 0)
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| 249 : |
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handle.logMessage(LOGWARN, "Warning in migrationproportion - stock not defined on all areas");
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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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| 254 : |
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void MigrationProportion::addLikelihood(const TimeClass* const TimeInfo) {
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| 255 : |
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| 256 : |
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if ((!(AAT.atCurrentTime(TimeInfo))) || (isZero(weight)))
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| 257 : |
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return;
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| 258 : |
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| 259 : |
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if (handle.getLogLevel() >= LOGMESSAGE)
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| 260 : |
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handle.logMessage(LOGMESSAGE, "Calculating likelihood score for migrationproportion component", this->getName());
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| 261 : |
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| 262 : |
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int i;
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| 263 : |
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timeindex = -1;
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| 264 : |
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for (i = 0; i < Years.Size(); i++)
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| 265 : |
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if ((Years[i] == TimeInfo->getYear()) && (Steps[i] == TimeInfo->getStep()))
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| 266 : |
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timeindex = i;
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| 267 : |
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if (timeindex == -1)
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| 268 : |
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handle.logMessage(LOGFAIL, "Error in migrationproportion - invalid timestep");
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| 269 : |
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| 270 : |
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double l = 0.0;
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| 271 : |
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switch (functionnumber) {
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| 272 : |
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case 1:
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| 273 : |
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l = calcLikSumSquares(TimeInfo);
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| 274 : |
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break;
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| 275 : |
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default:
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| 276 : |
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handle.logMessage(LOGWARN, "Warning in migrationproportion - unrecognised function", functionname);
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| 277 : |
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break;
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| 278 : |
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}
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| 279 : |
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| 280 : |
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likelihood += l;
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| 281 : |
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if (handle.getLogLevel() >= LOGMESSAGE)
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| 282 : |
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handle.logMessage(LOGMESSAGE, "The likelihood score for this component on this timestep is", l);
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| 283 : |
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}
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| 284 : |
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| 285 : |
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double MigrationProportion::calcLikSumSquares(const TimeClass* const TimeInfo) {
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| 286 : |
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| 287 : |
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double temp, totalmodel, totaldata;
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| 288 : |
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int a, r, s;
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| 289 : |
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| 290 : |
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if (biomass) {
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| 291 : |
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for (a = 0; a < areas.Nrow(); a++)
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| 292 : |
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for (r = 0; r < areas.Ncol(a); r++)
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| 293 : |
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for (s = 0; s < stocks.Size(); s++)
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| 294 : |
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modelDistribution[timeindex][a] += stocks[s]->getTotalStockBiomass(areas[a][r]);
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| 295 : |
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} else {
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| 296 : |
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for (a = 0; a < areas.Nrow(); a++)
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| 297 : |
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for (r = 0; r < areas.Ncol(a); r++)
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| 298 : |
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for (s = 0; s < stocks.Size(); s++)
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| 299 : |
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modelDistribution[timeindex][a] += stocks[s]->getTotalStockNumber(areas[a][r]);
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| 300 : |
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}
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| 301 : |
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| 302 : |
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totalmodel = 0.0;
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| 303 : |
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totaldata = 0.0;
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| 304 : |
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for (a = 0; a < areas.Nrow(); a++) {
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| 305 : |
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totalmodel += modelDistribution[timeindex][a];
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| 306 : |
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totaldata += obsDistribution[timeindex][a];
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| 307 : |
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}
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| 308 : |
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if (!(isZero(totalmodel)))
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| 309 : |
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totalmodel = 1.0 / totalmodel;
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| 310 : |
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if (!(isZero(totaldata)))
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| 311 : |
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totaldata = 1.0 / totaldata;
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| 312 : |
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| 313 : |
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likelihoodValues[timeindex] = 0.0;
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| 314 : |
|
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for (a = 0; a < areas.Nrow(); a++) {
|
| 315 : |
|
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temp = ((obsDistribution[timeindex][a] * totaldata)
|
| 316 : |
|
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- (modelDistribution[timeindex][a] * totalmodel));
|
| 317 : |
|
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likelihoodValues[timeindex] += (temp * temp);
|
| 318 : |
|
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}
|
| 319 : |
|
|
|
| 320 : |
|
|
return likelihoodValues[timeindex];
|
| 321 : |
|
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}
|
| 322 : |
|
|
|
| 323 : |
|
|
void MigrationProportion::printSummary(ofstream& outfile) {
|
| 324 : |
|
|
int year;
|
| 325 : |
|
|
|
| 326 : |
|
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for (year = 0; year < likelihoodValues.Size(); year++) {
|
| 327 : |
|
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outfile << setw(lowwidth) << Years[year] << sep << setw(lowwidth) << Steps[year] << " all "
|
| 328 : |
|
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<< setw(largewidth) << this->getName() << sep << setprecision(smallprecision)
|
| 329 : |
|
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<< setw(smallwidth) << weight << sep << setprecision(largeprecision)
|
| 330 : |
|
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<< setw(largewidth) << likelihoodValues[year] << endl;
|
| 331 : |
|
|
}
|
| 332 : |
|
|
outfile.flush();
|
| 333 : |
|
|
}
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