#include "catchstatistics.h"
#include "readfunc.h"
#include "readword.h"
#include "errorhandler.h"
#include "areatime.h"
#include "fleet.h"
#include "stock.h"
#include "stockprey.h"
#include "mathfunc.h"
#include "readaggregation.h"
#include "gadget.h"
#include "global.h"
CatchStatistics::CatchStatistics(CommentStream& infile, const AreaClass* const Area,
const TimeClass* const TimeInfo, double weight, const char* name)
: Likelihood(CATCHSTATISTICSLIKELIHOOD, weight, name), alptr(0) {
char text[MaxStrLength];
strncpy(text, "", MaxStrLength);
int i, j;
int numarea = 0, numage = 0;
char datafilename[MaxStrLength];
char aggfilename[MaxStrLength];
strncpy(datafilename, "", MaxStrLength);
strncpy(aggfilename, "", MaxStrLength);
ifstream datafile;
CommentStream subdata(datafile);
timeindex = 0;
functionname = new char[MaxStrLength];
strncpy(functionname, "", MaxStrLength);
readWordAndValue(infile, "datafile", datafilename);
readWordAndValue(infile, "function", functionname);
//JMB - changed to make the reading of overconsumption optional
infile >> ws;
char c = infile.peek();
if ((c == 'o') || (c == 'O'))
readWordAndVariable(infile, "overconsumption", overconsumption);
else
overconsumption = 0;
if (overconsumption != 0 && overconsumption != 1)
handle.logFileMessage(LOGFAIL, "\nError in catchstatistics - overconsumption must be 0 or 1");
if ((strcasecmp(functionname, "lengthcalcvar") == 0) || (strcasecmp(functionname, "lengthcalcstddev") == 0))
functionnumber = 1;
else if ((strcasecmp(functionname, "lengthgivenvar") == 0) || (strcasecmp(functionname, "lengthgivenstddev") == 0))
functionnumber = 2;
else if ((strcasecmp(functionname, "weightgivenvar") == 0) || (strcasecmp(functionname, "weightgivenstddev") == 0))
functionnumber = 3;
else if ((strcasecmp(functionname, "weightnovar") == 0) || (strcasecmp(functionname, "weightnostddev") == 0))
functionnumber = 4;
else if ((strcasecmp(functionname, "lengthnovar") == 0) || (strcasecmp(functionname, "lengthnostddev") == 0))
functionnumber = 5;
else
handle.logFileMessage(LOGFAIL, "\nError in catchstatistics - unrecognised function", functionname);
//read in area aggregation from file
readWordAndValue(infile, "areaaggfile", aggfilename);
datafile.open(aggfilename, ios::in);
handle.checkIfFailure(datafile, aggfilename);
handle.Open(aggfilename);
numarea = readAggregation(subdata, areas, areaindex);
handle.Close();
datafile.close();
datafile.clear();
//read in age aggregation from file
readWordAndValue(infile, "ageaggfile", aggfilename);
datafile.open(aggfilename, ios::in);
handle.checkIfFailure(datafile, aggfilename);
handle.Open(aggfilename);
numage = readAggregation(subdata, ages, ageindex);
handle.Close();
datafile.close();
datafile.clear();
//Must change from outer areas to inner areas.
for (i = 0; i < areas.Nrow(); i++)
for (j = 0; j < areas.Ncol(i); j++)
areas[i][j] = Area->getInnerArea(areas[i][j]);
//read in the fleetnames
i = 0;
infile >> text >> ws;
if (strcasecmp(text, "fleetnames") != 0)
handle.logFileUnexpected(LOGFAIL, "fleetnames", text);
infile >> text >> ws;
while (!infile.eof() && (strcasecmp(text, "stocknames") != 0)) {
fleetnames.resize(new char[strlen(text) + 1]);
strcpy(fleetnames[i++], text);
infile >> text >> ws;
}
if (fleetnames.Size() == 0)
handle.logFileMessage(LOGFAIL, "\nError in catchstatistics - failed to read fleets");
handle.logMessage(LOGMESSAGE, "Read fleet data - number of fleets", fleetnames.Size());
//read in the stocknames
i = 0;
if (strcasecmp(text, "stocknames") != 0)
handle.logFileUnexpected(LOGFAIL, "stocknames", text);
infile >> text;
while (!infile.eof() && (strcasecmp(text, "[component]") != 0)) {
infile >> ws;
stocknames.resize(new char[strlen(text) + 1]);
strcpy(stocknames[i++], text);
infile >> text;
}
if (stocknames.Size() == 0)
handle.logFileMessage(LOGFAIL, "\nError in catchstatistics - failed to read stocks");
handle.logMessage(LOGMESSAGE, "Read stock data - number of stocks", stocknames.Size());
//We have now read in all the data from the main likelihood file
//But we have to read in the statistics data from datafilename
datafile.open(datafilename, ios::in);
handle.checkIfFailure(datafile, datafilename);
handle.Open(datafilename);
readStatisticsData(subdata, TimeInfo, numarea, numage);
handle.Close();
datafile.close();
datafile.clear();
}
void CatchStatistics::readStatisticsData(CommentStream& infile,
const TimeClass* TimeInfo, int numarea, int numage) {
int i, year, step;
double tmpnumber, tmpmean, tmpstddev;
char tmparea[MaxStrLength], tmpage[MaxStrLength];
strncpy(tmparea, "", MaxStrLength);
strncpy(tmpage, "", MaxStrLength);
int keepdata, needvar, readvar;
int timeid, ageid, areaid, count, reject;
readvar = 0;
needvar = 0;
switch (functionnumber) {
case 1:
readvar = 0;
needvar = 1;
break;
case 2:
case 3:
readvar = 1;
needvar = 1;
break;
case 4:
case 5:
break;
default:
handle.logMessage(LOGWARN, "Warning in catchstatistics - unrecognised function", functionname);
break;
}
//Check the number of columns in the inputfile
infile >> ws;
if ((readvar) && (countColumns(infile) != 7))
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 7");
else if ((!readvar) && (countColumns(infile) != 6))
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 6");
year = step = count = reject = 0;
while (!infile.eof()) {
keepdata = 1;
if (readvar)
infile >> year >> step >> tmparea >> tmpage >> tmpnumber >> tmpmean >> tmpstddev >> ws;
else
infile >> year >> step >> tmparea >> tmpage >> tmpnumber >> tmpmean >> ws;
//crude check to see if something has gone wrong and avoid infinite loops
if (strlen(tmparea) == 0)
handle.logFileMessage(LOGFAIL, "failed to read data from file");
//if tmparea is in areaindex find areaid, else dont keep the data
areaid = -1;
for (i = 0; i < areaindex.Size(); i++)
if (strcasecmp(areaindex[i], tmparea) == 0)
areaid = i;
if (areaid == -1)
keepdata = 0;
//if tmpage is in ageindex find ageid, else dont keep the data
ageid = -1;
for (i = 0; i < ageindex.Size(); i++)
if (strcasecmp(ageindex[i], tmpage) == 0)
ageid = i;
if (ageid == -1)
keepdata = 0;
//check if the year and step are in the simulation
timeid = -1;
if ((TimeInfo->isWithinPeriod(year, step)) && (keepdata == 1)) {
//if this is a new timestep, resize to store the data
for (i = 0; i < Years.Size(); i++)
if ((Years[i] == year) && (Steps[i] == step))
timeid = i;
if (timeid == -1) {
Years.resize(1, year);
Steps.resize(1, step);
likelihoodValues.AddRows(1, numarea, 0.0);
numbers.resize(new DoubleMatrix(numarea, numage, 0.0));
obsMean.resize(new DoubleMatrix(numarea, numage, 0.0));
modelMean.resize(new DoubleMatrix(numarea, numage, 0.0));
if (readvar)
obsStdDev.resize(new DoubleMatrix(numarea, numage, 0.0));
if (needvar)
modelStdDev.resize(new DoubleMatrix(numarea, numage, 0.0));
timeid = (Years.Size() - 1);
}
} else
keepdata = 0;
if (keepdata == 1) {
//statistics data is required, so store it
count++;
(*numbers[timeid])[areaid][ageid] = tmpnumber;
(*obsMean[timeid])[areaid][ageid] = tmpmean;
if (readvar)
(*obsStdDev[timeid])[areaid][ageid] = tmpstddev;
} else
reject++; //count number of rejected data points read from file
}
AAT.addActions(Years, Steps, TimeInfo);
if (count == 0)
handle.logMessage(LOGWARN, "Warning in catchstatistics - found no data in the data file for", this->getName());
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid catchstatistics data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read catchstatistics data file - number of entries", count);
}
CatchStatistics::~CatchStatistics() {
int i;
for (i = 0; i < stocknames.Size(); i++)
delete[] stocknames[i];
for (i = 0; i < fleetnames.Size(); i++)
delete[] fleetnames[i];
for (i = 0; i < areaindex.Size(); i++)
delete[] areaindex[i];
for (i = 0; i < ageindex.Size(); i++)
delete[] ageindex[i];
delete aggregator;
for (i = 0; i < numbers.Size(); i++) {
delete numbers[i];
delete obsMean[i];
delete modelMean[i];
}
for (i = 0; i < obsStdDev.Size(); i++)
delete obsStdDev[i];
for (i = 0; i < modelStdDev.Size(); i++)
delete modelStdDev[i];
delete[] functionname;
delete LgrpDiv;
}
void CatchStatistics::Reset(const Keeper* const keeper) {
Likelihood::Reset(keeper);
if (isZero(weight))
handle.logMessage(LOGWARN, "Warning in catchstatistics - zero weight for", this->getName());
int i;
for (i = 0; i < modelMean.Size(); i++)
(*modelMean[i]).setToZero();
if (handle.getLogLevel() >= LOGMESSAGE)
handle.logMessage(LOGMESSAGE, "Reset catchstatistics component", this->getName());
}
void CatchStatistics::Print(ofstream& outfile) const {
int i;
outfile << "\nCatch Statistics " << this->getName() << " - likelihood value " << likelihood
<< "\n\tFunction " << functionname << "\n\tStock names:";
for (i = 0; i < stocknames.Size(); i++)
outfile << sep << stocknames[i];
outfile << "\n\tFleet names:";
for (i = 0; i < fleetnames.Size(); i++)
outfile << sep << fleetnames[i];
outfile << endl;
aggregator->Print(outfile);
outfile.flush();
}
void CatchStatistics::setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks) {
int i, j, k, found, minage, maxage;
FleetPtrVector fleets;
StockPtrVector stocks;
for (i = 0; i < fleetnames.Size(); i++) {
found = 0;
for (j = 0; j < Fleets.Size(); j++) {
if (strcasecmp(fleetnames[i], Fleets[j]->getName()) == 0) {
found++;
fleets.resize(Fleets[j]);
}
}
if (found == 0)
handle.logMessage(LOGFAIL, "Error in catchstatistics - unrecognised fleet", fleetnames[i]);
}
for (i = 0; i < fleets.Size(); i++)
for (j = 0; j < fleets.Size(); j++)
if ((strcasecmp(fleets[i]->getName(), fleets[j]->getName()) == 0) && (i != j))
handle.logMessage(LOGFAIL, "Error in catchstatistics - repeated fleet", fleets[i]->getName());
for (i = 0; i < stocknames.Size(); i++) {
found = 0;
for (j = 0; j < Stocks.Size(); j++) {
if (Stocks[j]->isEaten()) {
if (strcasecmp(stocknames[i], Stocks[j]->getName()) == 0) {
found++;
stocks.resize(Stocks[j]);
}
}
}
if (found == 0)
handle.logMessage(LOGFAIL, "Error in catchstatistics - unrecognised stock", stocknames[i]);
}
for (i = 0; i < stocks.Size(); i++)
for (j = 0; j < stocks.Size(); j++)
if ((strcasecmp(stocks[i]->getName(), stocks[j]->getName()) == 0) && (i != j))
handle.logMessage(LOGFAIL, "Error in catchstatistics - repeated stock", stocks[i]->getName());
LgrpDiv = new LengthGroupDivision(*(stocks[0]->getPrey()->getLengthGroupDiv()));
for (i = 1; i < stocks.Size(); i++)
if (!LgrpDiv->Combine(stocks[i]->getPrey()->getLengthGroupDiv()))
handle.logMessage(LOGFAIL, "Error in catchstatistics - length groups for preys not compatible");
if (LgrpDiv->Error())
handle.logMessage(LOGFAIL, "Error in catchstatistics - failed to create length group");
//check fleet areas and stock areas, ages and lengths
if (handle.getLogLevel() >= LOGWARN) {
for (j = 0; j < areas.Nrow(); j++) {
found = 0;
for (i = 0; i < fleets.Size(); i++)
for (k = 0; k < areas.Ncol(j); k++)
if (fleets[i]->isInArea(areas[j][k]))
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in catchstatistics - fleet not defined on all areas");
}
for (j = 0; j < areas.Nrow(); j++) {
found = 0;
for (i = 0; i < stocks.Size(); i++)
for (k = 0; k < areas.Ncol(j); k++)
if (stocks[i]->isInArea(areas[j][k]))
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in catchstatistics - stock not defined on all areas");
}
minage = 9999;
maxage = 0;
for (i = 0; i < ages.Nrow(); i++) {
for (j = 0; j < ages.Ncol(i); j++) {
minage = min(ages[i][j], minage);
maxage = max(ages[i][j], maxage);
}
}
found = 0;
for (i = 0; i < stocks.Size(); i++)
if (minage >= stocks[i]->minAge())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in catchstatistics - minimum age less than stock age");
found = 0;
for (i = 0; i < stocks.Size(); i++)
if (maxage <= stocks[i]->maxAge())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in catchstatistics - maximum age greater than stock age");
found = 0;
for (i = 0; i < stocks.Size(); i++)
if (LgrpDiv->maxLength(0) > stocks[i]->getLengthGroupDiv()->minLength())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in catchstatistics - minimum length group less than stock length");
found = 0;
for (i = 0; i < stocks.Size(); i++)
if (LgrpDiv->minLength(LgrpDiv->numLengthGroups()) < stocks[i]->getLengthGroupDiv()->maxLength())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in catchstatistics - maximum length group greater than stock length");
}
aggregator = new FleetPreyAggregator(fleets, stocks, LgrpDiv, areas, ages, overconsumption);
}
void CatchStatistics::addLikelihood(const TimeClass* const TimeInfo) {
if ((!(AAT.atCurrentTime(TimeInfo))) || (isZero(weight)))
return;
int i;
timeindex = -1;
for (i = 0; i < Years.Size(); i++)
if ((Years[i] == TimeInfo->getYear()) && (Steps[i] == TimeInfo->getStep()))
timeindex = i;
if (timeindex == -1)
handle.logMessage(LOGFAIL, "Error in catchstatistics - invalid timestep");
double l = 0.0;
if (handle.getLogLevel() >= LOGMESSAGE)
handle.logMessage(LOGMESSAGE, "Calculating likelihood score for catchstatistics component", this->getName());
aggregator->Sum();
if ((handle.getLogLevel() >= LOGWARN) && (aggregator->checkCatchData()))
handle.logMessage(LOGWARN, "Warning in catchstatistics - zero catch found");
l = calcLikSumSquares();
likelihood += l;
if (handle.getLogLevel() >= LOGMESSAGE)
handle.logMessage(LOGMESSAGE, "The likelihood score for this component on this timestep is", l);
}
double CatchStatistics::calcLikSumSquares() {
int area, age;
double lik, total, simvar, simdiff;
lik = total = simvar = simdiff = 0.0;
alptr = &aggregator->getSum();
for (area = 0; area < areas.Nrow(); area++) {
likelihoodValues[timeindex][area] = 0.0;
for (age = (*alptr)[area].minAge(); age <= (*alptr)[area].maxAge(); age++) {
switch (functionnumber) {
case 1:
ps.calcStatistics((*alptr)[area][age], LgrpDiv, 0);
(*modelMean[timeindex])[area][age] = ps.meanLength();
simvar = ps.sdevLength() * ps.sdevLength();
(*modelStdDev[timeindex])[area][age] = ps.sdevLength();
break;
case 2:
ps.calcStatistics((*alptr)[area][age], LgrpDiv, 0);
(*modelMean[timeindex])[area][age] = ps.meanLength();
simvar = (*obsStdDev[timeindex])[area][age] * (*obsStdDev[timeindex])[area][age];
break;
case 3:
ps.calcStatistics((*alptr)[area][age], LgrpDiv);
(*modelMean[timeindex])[area][age] = ps.meanWeight();
simvar = (*obsStdDev[timeindex])[area][age] * (*obsStdDev[timeindex])[area][age];
break;
case 4:
ps.calcStatistics((*alptr)[area][age], LgrpDiv);
(*modelMean[timeindex])[area][age] = ps.meanWeight();
simvar = 1.0;
break;
case 5:
ps.calcStatistics((*alptr)[area][age], LgrpDiv, 0);
(*modelMean[timeindex])[area][age] = ps.meanLength();
simvar = 1.0;
break;
default:
handle.logMessage(LOGWARN, "Warning in catchstatistics - unrecognised function", functionname);
break;
}
if (!(isZero(simvar))) {
simdiff = (*modelMean[timeindex])[area][age] - (*obsMean[timeindex])[area][age];
lik = simdiff * simdiff * (*numbers[timeindex])[area][age] / simvar;
likelihoodValues[timeindex][area] += lik;
}
}
total += likelihoodValues[timeindex][area];
}
return total;
}
void CatchStatistics::printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo) {
if (!AAT.atCurrentTime(TimeInfo))
return;
int i, area, age;
timeindex = -1;
for (i = 0; i < Years.Size(); i++)
if ((Years[i] == TimeInfo->getYear()) && (Steps[i] == TimeInfo->getStep()))
timeindex = i;
if (timeindex == -1)
handle.logMessage(LOGFAIL, "Error in catchstatistics - invalid timestep");
for (area = 0; area < (*modelMean[timeindex]).Nrow(); area++) {
for (age = 0; age < (*modelMean[timeindex]).Ncol(area); age++) {
outfile << setw(lowwidth) << Years[timeindex] << sep << setw(lowwidth)
<< Steps[timeindex] << sep << setw(printwidth) << areaindex[area] << sep
<< setw(printwidth) << ageindex[age] << sep << setprecision(printprecision)
<< setw(printwidth) << (*numbers[timeindex])[area][age]
<< sep << setprecision(largeprecision) << setw(largewidth);
//JMB crude filter to remove the 'silly' values from the output
if ((*modelMean[timeindex])[area][age] < rathersmall)
outfile << 0;
else
outfile << (*modelMean[timeindex])[area][age];
switch (functionnumber) {
case 1:
outfile << sep << setprecision(printprecision) << setw(printwidth)
<< (*modelStdDev[timeindex])[area][age] << endl;
break;
case 2:
case 3:
outfile << sep << setprecision(printprecision) << setw(printwidth)
<< (*obsStdDev[timeindex])[area][age] << endl;
break;
case 4:
case 5:
outfile << endl;
break;
default:
handle.logMessage(LOGWARN, "Warning in catchstatistics - unrecognised function", functionname);
break;
}
}
}
}
void CatchStatistics::printSummary(ofstream& outfile) {
int year, area;
for (year = 0; year < likelihoodValues.Nrow(); year++)
for (area = 0; area < likelihoodValues.Ncol(year); area++)
outfile << setw(lowwidth) << Years[year] << sep << setw(lowwidth)
<< Steps[year] << sep << setw(printwidth) << areaindex[area] << sep
<< setw(largewidth) << this->getName() << sep << setprecision(smallprecision)
<< setw(smallwidth) << weight << sep << setprecision(largeprecision)
<< setw(largewidth) << likelihoodValues[year][area] << endl;
outfile.flush();
}