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agomez |
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#include "recstatistics.h" |
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#include "commentstream.h" |
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#include "readfunc.h" |
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#include "readword.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 "stockprey.h" |
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#include "mathfunc.h" |
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#include "readaggregation.h" |
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#include "gadget.h" |
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#include "global.h" |
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RecStatistics::RecStatistics(CommentStream& infile, const AreaClass* const Area,
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const TimeClass* const TimeInfo, double weight, TagPtrVector Tag, const char* name)
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: Likelihood(RECSTATISTICSLIKELIHOOD, weight, name), aggregator(0), alptr(0) {
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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int i, j, check, numarea = 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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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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if ((strcasecmp(functionname, "lengthcalcvar") == 0) || (strcasecmp(functionname, "lengthcalcstddev") == 0))
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functionnumber = 1;
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else if ((strcasecmp(functionname, "lengthgivenvar") == 0) || (strcasecmp(functionname, "lengthgivenstddev") == 0))
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functionnumber = 2;
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else if ((strcasecmp(functionname, "lengthnovar") == 0) || (strcasecmp(functionname, "lengthnostddev") == 0))
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functionnumber = 3;
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else
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handle.logFileMessage(LOGFAIL, "\nError in recstatistics - unrecognised function", functionname);
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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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//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;
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while (!infile.eof() && (strcasecmp(text, "[component]") != 0)) {
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infile >> ws;
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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;
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}
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if (fleetnames.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in recstatistics - failed to read fleets");
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handle.logMessage(LOGMESSAGE, "Read fleet data - number of fleets", fleetnames.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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readStatisticsData(subdata, TimeInfo, numarea, Tag);
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handle.Close();
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datafile.close();
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datafile.clear();
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for (j = 0; j < tagnames.Size(); j++) {
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check = 0;
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for (i = 0; i < Tag.Size(); i++) {
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if (strcasecmp(tagnames[j], Tag[i]->getName()) == 0) {
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check++;
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tagvec.resize(Tag[i]);
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}
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}
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if (check == 0)
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handle.logMessage(LOGFAIL, "Error in recstatistics - failed to match tag", tagnames[j]);
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}
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}
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void RecStatistics::readStatisticsData(CommentStream& infile,
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const TimeClass* TimeInfo, int numarea, TagPtrVector Tag) {
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double tmpnumber, tmpmean, tmpstddev;
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char tmparea[MaxStrLength], tmptag[MaxStrLength];
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strncpy(tmparea, "", MaxStrLength);
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strncpy(tmptag, "", MaxStrLength);
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int keepdata, needvar, readvar;
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int i, timeid, tagid, areaid, tmpindex;
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int year, step, count, reject;
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char* tagName;
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readvar = 0;
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if (functionnumber == 2)
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readvar = 1;
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needvar = 0;
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if (functionnumber == 1)
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needvar = 1;
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//Check the number of columns in the inputfile
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infile >> ws;
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if ((readvar) && (countColumns(infile) != 7))
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 7");
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else if ((!readvar) && (countColumns(infile) != 6))
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 6");
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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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if (readvar)
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infile >> tmptag >> year >> step >> tmparea >> tmpnumber >> tmpmean >> tmpstddev >> ws;
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else
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infile >> tmptag >> year >> step >> tmparea >> tmpnumber >> tmpmean >> 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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tagid = -1;
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if ((TimeInfo->isWithinPeriod(year, step)) && (keepdata == 1)) {
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for (i = 0; i < tagvec.Size(); i++)
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if (strcasecmp(tagvec[i]->getName(), tmptag) == 0)
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tagid = i;
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if (tagid == -1) {
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tmpindex = -1;
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for (i = 0; i < Tag.Size(); i++)
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if (strcasecmp(Tag[i]->getName(), tmptag) == 0)
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tmpindex = i;
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if (tmpindex == -1) {
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keepdata = 0;
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} else {
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tagName = new char[strlen(tmptag) + 1];
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strcpy(tagName, tmptag);
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tagnames.resize(tagName);
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tagid = tagnames.Size() - 1;
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Years.AddRows(1, 1, year);
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Steps.AddRows(1, 1, step);
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timeid = 0;
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numbers.resize(new DoubleMatrix(1, numarea, 0.0));
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obsMean.resize(new DoubleMatrix(1, numarea, 0.0));
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modelMean.resize(new DoubleMatrix(1, numarea, 0.0));
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if (needvar)
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modelStdDev.resize(new DoubleMatrix(1, numarea, 0.0));
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if (readvar)
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obsStdDev.resize(new DoubleMatrix(1, numarea, 0.0));
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}
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} else {
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for (i = 0; i < Years.Ncol(tagid); i++)
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if ((Years[tagid][i] == year) && (Steps[tagid][i] == step))
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timeid = i;
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//if this is a new timestep, resize to store the data
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if (timeid == -1) {
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Years[tagid].resize(1, year);
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Steps[tagid].resize(1, step);
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(*numbers[tagid]).AddRows(1, numarea, 0.0);
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(*obsMean[tagid]).AddRows(1, numarea, 0.0);
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if (readvar)
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(*obsStdDev[tagid]).AddRows(1, numarea, 0.0);
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timeid = Years.Ncol(tagid) - 1;
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}
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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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//statistics data is required, so store it
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count++;
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(*numbers[tagid])[timeid][areaid] = tmpnumber;
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(*obsMean[tagid])[timeid][areaid] = tmpmean;
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if (readvar)
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(*obsStdDev[tagid])[timeid][areaid] = tmpstddev;
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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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timeindex.resize(tagvec.Size(), -1);
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if (count == 0)
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handle.logMessage(LOGWARN, "Warning in recstatistics - 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 recstatistics data - number of invalid entries", reject);
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handle.logMessage(LOGMESSAGE, "Read recstatistics data file - number of entries", count);
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}
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RecStatistics::~RecStatistics() {
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int 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 < tagnames.Size(); i++)
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delete[] tagnames[i];
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for (i = 0; i < areaindex.Size(); i++)
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delete[] areaindex[i];
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for (i = 0; i < numbers.Size(); i++) {
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delete numbers[i];
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delete obsMean[i];
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delete modelMean[i];
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}
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for (i = 0; i < obsStdDev.Size(); i++)
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delete obsStdDev[i];
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for (i = 0; i < modelStdDev.Size(); i++)
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delete modelStdDev[i];
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delete[] functionname;
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if (aggregator != 0) {
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for (i = 0; i < tagvec.Size(); i++)
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| 237 : |
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delete aggregator[i];
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delete[] aggregator;
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| 239 : |
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aggregator = 0;
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| 240 : |
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}
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| 241 : |
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delete LgrpDiv;
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| 242 : |
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}
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void RecStatistics::Reset(const Keeper* const keeper) {
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| 245 : |
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int i;
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| 246 : |
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Likelihood::Reset(keeper);
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| 247 : |
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for (i = 0; i < timeindex.Size(); i++)
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| 248 : |
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timeindex[i] = -1;
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| 249 : |
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for (i = 0; i < modelMean.Size(); i++)
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(*modelMean[i]).setToZero();
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| 251 : |
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if (handle.getLogLevel() >= LOGMESSAGE)
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| 252 : |
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handle.logMessage(LOGMESSAGE, "Reset recstatistics component", this->getName());
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| 253 : |
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}
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| 254 : |
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void RecStatistics::Print(ofstream& outfile) const {
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| 256 : |
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int i;
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| 257 : |
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| 258 : |
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outfile << "\nRecapture Statistics " << this->getName() << " - likelihood value " << likelihood
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| 259 : |
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<< "\n\tFunction " << functionname;
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| 260 : |
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outfile << "\n\tFleet names:";
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| 261 : |
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for (i = 0; i < fleetnames.Size(); i++)
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| 262 : |
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outfile << sep << fleetnames[i];
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| 263 : |
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outfile << endl;
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| 264 : |
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for (i = 0; i < tagnames.Size(); i++) {
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| 265 : |
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outfile << "\tTagging experiment:\t" << tagnames[i] << endl;
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| 266 : |
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aggregator[i]->Print(outfile);
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| 267 : |
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outfile << endl;
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| 268 : |
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}
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| 269 : |
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outfile.flush();
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| 270 : |
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}
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| 271 : |
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| 272 : |
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void RecStatistics::printSummary(ofstream& outfile) {
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| 273 : |
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//JMB to start with just print a summary of all likelihood scores
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| 274 : |
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//This needs to be changed to print something for each timestep and area
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| 275 : |
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//but we need to sort out how to get the information in the same format as other components
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| 276 : |
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if (!(isZero(likelihood))) {
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| 277 : |
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outfile << "all all all" << sep << setw(largewidth) << this->getName() << sep
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| 278 : |
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<< setprecision(smallprecision) << setw(smallwidth) << weight << sep
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| 279 : |
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<< setprecision(largeprecision) << setw(largewidth) << likelihood << endl;
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| 280 : |
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outfile.flush();
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| 281 : |
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}
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| 282 : |
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}
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| 283 : |
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| 284 : |
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void RecStatistics::setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks) {
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| 285 : |
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int i, j, t, found, minage, maxage;
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| 286 : |
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FleetPtrVector fleets;
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| 287 : |
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StockPtrVector stocks;
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| 288 : |
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CharPtrVector stocknames;
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| 289 : |
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| 290 : |
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for (i = 0; i < fleetnames.Size(); i++) {
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| 291 : |
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found = 0;
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| 292 : |
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for (j = 0; j < Fleets.Size(); j++)
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| 293 : |
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if (strcasecmp(fleetnames[i], Fleets[j]->getName()) == 0) {
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| 294 : |
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found++;
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| 295 : |
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fleets.resize(Fleets[j]);
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| 296 : |
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}
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| 297 : |
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| 298 : |
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if (found == 0)
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| 299 : |
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handle.logMessage(LOGFAIL, "Error in recstatistics - unrecognised fleet", fleetnames[i]);
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| 300 : |
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}
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| 301 : |
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| 302 : |
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for (i = 0; i < fleets.Size(); i++)
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| 303 : |
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for (j = 0; j < fleets.Size(); j++)
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| 304 : |
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if ((strcasecmp(fleets[i]->getName(), fleets[j]->getName()) == 0) && (i != j))
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| 305 : |
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handle.logMessage(LOGFAIL, "Error in recstatistics - repeated fleet", fleets[i]->getName());
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| 306 : |
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| 307 : |
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aggregator = new RecAggregator*[tagvec.Size()];
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| 308 : |
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for (t = 0; t < tagvec.Size(); t++) {
|
| 309 : |
|
|
stocks.Reset();
|
| 310 : |
|
|
stocknames = tagvec[t]->getStockNames();
|
| 311 : |
|
|
for (i = 0; i < stocknames.Size(); i++) {
|
| 312 : |
|
|
found = 0;
|
| 313 : |
|
|
for (j = 0; j < Stocks.Size(); j++)
|
| 314 : |
|
|
if (Stocks[j]->isEaten())
|
| 315 : |
|
|
if (strcasecmp(stocknames[i], Stocks[j]->getName()) == 0) {
|
| 316 : |
|
|
found++;
|
| 317 : |
|
|
stocks.resize(Stocks[j]);
|
| 318 : |
|
|
}
|
| 319 : |
|
|
|
| 320 : |
|
|
if (found == 0)
|
| 321 : |
|
|
handle.logMessage(LOGFAIL, "Error in recstatistics - unrecognised stock", stocknames[i]);
|
| 322 : |
|
|
}
|
| 323 : |
|
|
|
| 324 : |
|
|
//Check the stock has been tagged
|
| 325 : |
|
|
for (j = 0; j < stocks.Size(); j++)
|
| 326 : |
|
|
if (!stocks[j]->isTagged())
|
| 327 : |
|
|
handle.logMessage(LOGFAIL, "Error in recstatistics - stocks hasnt been tagged", stocks[j]->getName());
|
| 328 : |
|
|
|
| 329 : |
|
|
LgrpDiv = new LengthGroupDivision(*(stocks[0]->getPrey()->getLengthGroupDiv()));
|
| 330 : |
|
|
for (i = 1; i < stocks.Size(); i++)
|
| 331 : |
|
|
if (!LgrpDiv->Combine(stocks[i]->getPrey()->getLengthGroupDiv()))
|
| 332 : |
|
|
handle.logMessage(LOGFAIL, "Error in recstatistics - length groups not compatible");
|
| 333 : |
|
|
|
| 334 : |
|
|
if (LgrpDiv->Error())
|
| 335 : |
|
|
handle.logMessage(LOGFAIL, "Error in recstatistics - failed to create length group");
|
| 336 : |
|
|
|
| 337 : |
|
|
minage = 999;
|
| 338 : |
|
|
maxage = 0;
|
| 339 : |
|
|
for (i = 0; i < stocks.Size(); i++) {
|
| 340 : |
|
|
minage = min(stocks[i]->minAge(), minage);
|
| 341 : |
|
|
maxage = max(stocks[i]->maxAge(), maxage);
|
| 342 : |
|
|
}
|
| 343 : |
|
|
|
| 344 : |
|
|
IntMatrix ages(1, 0, 0);
|
| 345 : |
|
|
for (i = 0; i <= maxage - minage; i++)
|
| 346 : |
|
|
ages[0].resize(1, minage + i);
|
| 347 : |
|
|
aggregator[t] = new RecAggregator(fleets, stocks, LgrpDiv, areas, ages, tagvec[t]);
|
| 348 : |
|
|
}
|
| 349 : |
|
|
}
|
| 350 : |
|
|
|
| 351 : |
|
|
void RecStatistics::addLikelihood(const TimeClass* const TimeInfo) {
|
| 352 : |
|
|
int t, i, check;
|
| 353 : |
|
|
double l = 0.0;
|
| 354 : |
|
|
|
| 355 : |
|
|
check = 0;
|
| 356 : |
|
|
for (t = 0; t < tagvec.Size(); t++) {
|
| 357 : |
|
|
timeindex[t] = -1;
|
| 358 : |
|
|
if (tagvec[t]->isWithinPeriod(TimeInfo->getYear(), TimeInfo->getStep())) {
|
| 359 : |
|
|
for (i = 0; i < Years.Ncol(t); i++) {
|
| 360 : |
|
|
if (Years[t][i] == TimeInfo->getYear() && Steps[t][i] == TimeInfo->getStep()) {
|
| 361 : |
|
|
if (check == 0)
|
| 362 : |
|
|
if (handle.getLogLevel() >= LOGMESSAGE)
|
| 363 : |
|
|
handle.logMessage(LOGMESSAGE, "Calculating likelihood score for recstatistics component", this->getName());
|
| 364 : |
|
|
timeindex[t] = i;
|
| 365 : |
|
|
aggregator[t]->Sum();
|
| 366 : |
|
|
check++;
|
| 367 : |
|
|
}
|
| 368 : |
|
|
}
|
| 369 : |
|
|
}
|
| 370 : |
|
|
}
|
| 371 : |
|
|
|
| 372 : |
|
|
if (check > 0) {
|
| 373 : |
|
|
l = calcLikSumSquares();
|
| 374 : |
|
|
likelihood += l;
|
| 375 : |
|
|
if (handle.getLogLevel() >= LOGMESSAGE)
|
| 376 : |
|
|
handle.logMessage(LOGMESSAGE, "The likelihood score for this component on this timestep is", l);
|
| 377 : |
|
|
}
|
| 378 : |
|
|
}
|
| 379 : |
|
|
|
| 380 : |
|
|
double RecStatistics::calcLikSumSquares() {
|
| 381 : |
|
|
double lik = 0.0;
|
| 382 : |
|
|
int t, area;
|
| 383 : |
|
|
double simvar, simdiff;
|
| 384 : |
|
|
|
| 385 : |
|
|
for (t = 0; t < tagvec.Size(); t++) {
|
| 386 : |
|
|
if (timeindex[t] > -1) {
|
| 387 : |
|
|
alptr = &aggregator[t]->getSum();
|
| 388 : |
|
|
for (area = 0; area < alptr->Size(); area++) {
|
| 389 : |
|
|
simvar = 0.0;
|
| 390 : |
|
|
ps.calcStatistics((*alptr)[area][0], aggregator[t]->getLengthGroupDiv(), 0);
|
| 391 : |
|
|
(*modelMean[t])[timeindex[t]][area] = ps.meanLength();
|
| 392 : |
|
|
|
| 393 : |
|
|
switch (functionnumber) {
|
| 394 : |
|
|
case 1:
|
| 395 : |
|
|
(*modelStdDev[t])[timeindex[t]][area] = ps.sdevLength();
|
| 396 : |
|
|
simvar = (*modelStdDev[t])[timeindex[t]][area] * (*modelStdDev[t])[timeindex[t]][area];
|
| 397 : |
|
|
break;
|
| 398 : |
|
|
case 2:
|
| 399 : |
|
|
simvar = (*obsStdDev[t])[timeindex[t]][area] * (*obsStdDev[t])[timeindex[t]][area];
|
| 400 : |
|
|
break;
|
| 401 : |
|
|
case 3:
|
| 402 : |
|
|
simvar = 1.0;
|
| 403 : |
|
|
break;
|
| 404 : |
|
|
default:
|
| 405 : |
|
|
handle.logMessage(LOGWARN, "Warning in recstatistics - unrecognised function", functionname);
|
| 406 : |
|
|
break;
|
| 407 : |
|
|
}
|
| 408 : |
|
|
|
| 409 : |
|
|
if (!(isZero(simvar))) {
|
| 410 : |
|
|
simdiff = (*modelMean[t])[timeindex[t]][area] - (*obsMean[t])[timeindex[t]][area];
|
| 411 : |
|
|
lik += simdiff * simdiff * (*numbers[t])[timeindex[t]][area] / simvar;
|
| 412 : |
|
|
}
|
| 413 : |
|
|
}
|
| 414 : |
|
|
}
|
| 415 : |
|
|
}
|
| 416 : |
|
|
return lik;
|
| 417 : |
|
|
}
|
| 418 : |
|
|
|
| 419 : |
|
|
void RecStatistics::printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo) {
|
| 420 : |
|
|
int year = TimeInfo->getYear();
|
| 421 : |
|
|
int step = TimeInfo->getStep();
|
| 422 : |
|
|
int t, ti, timeid, area;
|
| 423 : |
|
|
|
| 424 : |
|
|
for (t = 0; t < tagvec.Size(); t++) {
|
| 425 : |
|
|
if (tagvec[t]->isWithinPeriod(year, step)) {
|
| 426 : |
|
|
timeid = -1;
|
| 427 : |
|
|
for (ti = 0; ti < Years.Ncol(t); ti++)
|
| 428 : |
|
|
if (Years[t][ti] == year && Steps[t][ti] == step)
|
| 429 : |
|
|
timeid = ti;
|
| 430 : |
|
|
|
| 431 : |
|
|
if (timeid > -1) {
|
| 432 : |
|
|
for (area = 0; area < areaindex.Size(); area++) {
|
| 433 : |
|
|
outfile << setw(printwidth) << tagnames[t] << sep << setw(lowwidth)
|
| 434 : |
|
|
<< year << sep << setw(lowwidth) << step << sep << setw(printwidth)
|
| 435 : |
|
|
<< areaindex[area] << sep << setprecision(printprecision)
|
| 436 : |
|
|
<< setw(printwidth) << (*numbers[t])[timeid][area] << sep
|
| 437 : |
|
|
<< setprecision(largeprecision) << setw(largewidth);
|
| 438 : |
|
|
|
| 439 : |
|
|
//JMB crude filter to remove the 'silly' values from the output
|
| 440 : |
|
|
if ((*modelMean[t])[timeid][area] < rathersmall)
|
| 441 : |
|
|
outfile << 0;
|
| 442 : |
|
|
else
|
| 443 : |
|
|
outfile << (*modelMean[t])[timeid][area];
|
| 444 : |
|
|
|
| 445 : |
|
|
switch (functionnumber) {
|
| 446 : |
|
|
case 1:
|
| 447 : |
|
|
outfile << sep << setprecision(printprecision) << setw(printwidth)
|
| 448 : |
|
|
<< (*modelStdDev[t])[timeid][area] << endl;
|
| 449 : |
|
|
break;
|
| 450 : |
|
|
case 2:
|
| 451 : |
|
|
outfile << sep << setprecision(printprecision) << setw(printwidth)
|
| 452 : |
|
|
<< (*obsStdDev[t])[timeid][area] << endl;
|
| 453 : |
|
|
break;
|
| 454 : |
|
|
case 3:
|
| 455 : |
|
|
outfile << endl;
|
| 456 : |
|
|
break;
|
| 457 : |
|
|
default:
|
| 458 : |
|
|
handle.logMessage(LOGWARN, "Warning in recstatistics - unrecognised function", functionname);
|
| 459 : |
|
|
break;
|
| 460 : |
|
|
}
|
| 461 : |
|
|
}
|
| 462 : |
|
|
}
|
| 463 : |
|
|
}
|
| 464 : |
|
|
}
|
| 465 : |
|
|
}
|
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