#include "stomachcontent.h"
#include "areatime.h"
#include "predator.h"
#include "stockpredator.h"
#include "prey.h"
#include "predatoraggregator.h"
#include "readfunc.h"
#include "readword.h"
#include "readaggregation.h"
#include "multinomial.h"
#include "errorhandler.h"
#include "gadget.h"
#include "global.h"
// ********************************************************
// Functions for main likelihood component StomachContent
// ********************************************************
StomachContent::StomachContent(CommentStream& infile,
const AreaClass* const Area, const TimeClass* const TimeInfo,
Keeper* const keeper, double weight, const char* name)
: Likelihood(STOMACHCONTENTLIKELIHOOD, weight, name) {
functionname = new char[MaxStrLength];
strncpy(functionname, "", MaxStrLength);
readWordAndValue(infile, "function", functionname);
char datafilename[MaxStrLength];
strncpy(datafilename, "", MaxStrLength);
readWordAndValue(infile, "datafile", datafilename);
if (strcasecmp(functionname, "scnumbers") == 0) {
StomCont = new SCNumbers(infile, Area, TimeInfo, keeper, datafilename, this->getName());
} else if (strcasecmp(functionname, "scratios") == 0) {
char numfilename[MaxStrLength];
strncpy(numfilename, "", MaxStrLength);
readWordAndValue(infile, "numberfile", numfilename);
StomCont = new SCRatios(infile, Area, TimeInfo, keeper, datafilename, numfilename, this->getName());
} else if (strcasecmp(functionname, "scamounts") == 0) {
char numfilename[MaxStrLength];
strncpy(numfilename, "", MaxStrLength);
readWordAndValue(infile, "numberfile", numfilename);
StomCont = new SCAmounts(infile, Area, TimeInfo, keeper, datafilename, numfilename, this->getName());
} else if (strcasecmp(functionname, "scsimple") == 0) {
StomCont = new SCSimple(infile, Area, TimeInfo, keeper, datafilename, this->getName());
} else {
handle.logFileMessage(LOGFAIL, "\nError in stomachcontent - unrecognised function", functionname);
}
}
StomachContent::~StomachContent() {
delete StomCont;
delete[] functionname;
}
void StomachContent::addLikelihood(const TimeClass* const TimeInfo) {
if (isZero(weight))
return;
likelihood += StomCont->calcLikelihood(TimeInfo);
}
void StomachContent::Reset(const Keeper* const keeper) {
Likelihood::Reset(keeper);
if (isZero(weight))
handle.logMessage(LOGWARN, "Warning in stomachcontent - zero weight for", this->getName());
StomCont->Reset();
}
void StomachContent::Print(ofstream& outfile) const {
outfile << "\nStomach Content " << this->getName() << " - likelihood value " << likelihood
<< "\n\tFunction " << functionname << endl;
StomCont->Print(outfile);
}
// ********************************************************
// Functions for base SC
// ********************************************************
SC::SC(CommentStream& infile, const AreaClass* const Area, const TimeClass* const TimeInfo,
Keeper* const keeper, const char* datafilename, const char* givenname)
: HasName(givenname), aggregator(0), preyLgrpDiv(0), predLgrpDiv(0), dptr(0) {
int i, j;
char text[MaxStrLength];
strncpy(text, "", MaxStrLength);
int numpred = 0;
int numarea = 0;
timeindex = 0;
usepredages = 0;
char aggfilename[MaxStrLength];
strncpy(aggfilename, "", MaxStrLength);
ifstream datafile;
CommentStream subdata(datafile);
//JMB - changed to make the reading of minimum probability optional
infile >> ws;
char c = infile.peek();
if ((c == 'm') || (c == 'M'))
readWordAndVariable(infile, "minimumprobability", epsilon);
else if ((c == 'e') || (c == 'E'))
readWordAndVariable(infile, "epsilon", epsilon);
else
epsilon = 10.0;
if (epsilon < verysmall) {
handle.logFileMessage(LOGWARN, "epsilon should be a positive integer - set to default value 10");
epsilon = 10.0;
}
//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();
//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 predators
i = 0;
infile >> text >> ws;
if ((strcasecmp(text, "predators") != 0) && (strcasecmp(text, "predatornames") != 0))
handle.logFileUnexpected(LOGFAIL, "predatornames", text);
infile >> text >> ws;
while (!infile.eof() && ((strcasecmp(text, "predatorlengths") != 0)
&& (strcasecmp(text, "predatorages") != 0))) {
predatornames.resize(new char[strlen(text) + 1]);
strcpy(predatornames[i++], text);
infile >> text >> ws;
}
if (predatornames.Size() == 0)
handle.logFileMessage(LOGFAIL, "\nError in stomachcontent - failed to read predators");
handle.logMessage(LOGMESSAGE, "Read predator data - number of predators", predatornames.Size());
if (strcasecmp(text, "predatorlengths") == 0) { //read predator lengths
usepredages = 0; //predator is length structured
readWordAndValue(infile, "lenaggfile", aggfilename);
datafile.open(aggfilename, ios::in);
handle.checkIfFailure(datafile, aggfilename);
handle.Open(aggfilename);
numpred = readLengthAggregation(subdata, predatorlengths, predindex);
handle.Close();
datafile.close();
datafile.clear();
} else if (strcasecmp(text, "predatorages") == 0) { //read predator ages
usepredages = 1; //predator is age structured
readWordAndValue(infile, "ageaggfile", aggfilename);
datafile.open(aggfilename, ios::in);
handle.checkIfFailure(datafile, aggfilename);
handle.Open(aggfilename);
numpred = readAggregation(subdata, predatorages, predindex);
handle.Close();
datafile.close();
datafile.clear();
} else
handle.logFileUnexpected(LOGFAIL, "predatorlengths", text);
//read in the preys
readWordAndValue(infile, "preyaggfile", aggfilename);
datafile.open(aggfilename, ios::in);
handle.checkIfFailure(datafile, aggfilename);
handle.Open(aggfilename);
i = readPreyAggregation(subdata, preynames, preylengths, digestioncoeff, preyindex, keeper);
handle.Close();
datafile.close();
datafile.clear();
//prepare for next likelihood component
infile >> ws;
if (!infile.eof()) {
infile >> text >> ws;
if (strcasecmp(text, "[component]") != 0)
handle.logFileUnexpected(LOGFAIL, "[component]", text);
}
}
void SC::aggregate(int i) {
aggregator[i]->Sum();
}
double SC::calcLikelihood(const TimeClass* const TimeInfo) {
if (!(AAT.atCurrentTime(TimeInfo)))
return 0.0;
int i, a, k, p;
if (handle.getLogLevel() >= LOGMESSAGE)
handle.logMessage(LOGMESSAGE, "Calculating likelihood score for stomachcontent component", this->getName());
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 stomachcontent - invalid timestep");
//Get the consumption from aggregator, indexed the same way as in obsConsumption
int numprey = 0;
for (i = 0; i < preyindex.Size(); i++) {
this->aggregate(i);
for (a = 0; a < areas.Nrow(); a++) {
dptr = aggregator[i]->getSum()[a];
for (k = 0; k < dptr->Nrow(); k++)
for (p = 0; p < dptr->Ncol(k); p++)
(*modelConsumption[timeindex][a])[k][numprey + p] = (*dptr)[k][p] * digestion[i][p];
}
numprey += preylengths[i].Size() - 1;
}
//Now calculate likelihood score
double l = calcLikelihood();
if (handle.getLogLevel() >= LOGMESSAGE)
handle.logMessage(LOGMESSAGE, "The likelihood score for this component on this timestep is", l);
return l;
}
void SC::Reset() {
//JMB - calculate the digestion coefficiant matrix
int i, j;
if (digestion.Nrow() != digestioncoeff.Nrow())
handle.logMessage(LOGFAIL, "Error in stomachcontent - missing digestion coefficient data");
for (i = 0; i < digestion.Nrow(); i++)
for (j = 0; j < digestion.Ncol(i); j++)
digestion[i][j] = digestioncoeff[i][0] + digestioncoeff[i][1] *
pow(preyLgrpDiv[i]->meanLength(j), digestioncoeff[i][2]);
for (i = 0; i < modelConsumption.Nrow(); i++)
for (j = 0; j < modelConsumption.Ncol(i); j++)
(*modelConsumption[i][j]).setToZero();
if (handle.getLogLevel() >= LOGMESSAGE)
handle.logMessage(LOGMESSAGE, "Reset stomachcontent component", this->getName());
}
void SC::printSummary(ofstream& outfile, double weight) {
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();
}
void SC::printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo) {
if (!AAT.atCurrentTime(TimeInfo))
return;
int i, area, pred, prey;
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 stomachcontent - invalid timestep");
for (area = 0; area < modelConsumption.Ncol(timeindex); area++) {
for (pred = 0; pred < modelConsumption[timeindex][area]->Nrow(); pred++) {
for (prey = 0; prey < modelConsumption[timeindex][area]->Ncol(pred); prey++) {
outfile << setw(lowwidth) << Years[timeindex] << sep << setw(lowwidth)
<< Steps[timeindex] << sep << setw(printwidth) << areaindex[area] << sep
<< setw(printwidth) << predindex[pred] << sep << setw(printwidth)
<< preyindex[prey] << sep << setprecision(largeprecision) << setw(largewidth);
//JMB crude filter to remove the 'silly' values from the output
if ((*modelConsumption[timeindex][area])[pred][prey] < rathersmall)
outfile << 0 << endl;
else
outfile << (*modelConsumption[timeindex][area])[pred][prey] << endl;
}
}
}
}
SC::~SC() {
int i, j;
for (i = 0; i < obsConsumption.Nrow(); i++) {
for (j = 0; j < obsConsumption[i].Size(); j++) {
delete obsConsumption[i][j];
delete modelConsumption[i][j];
}
}
for (i = 0; i < preyindex.Size(); i++) {
delete aggregator[i];
delete preyLgrpDiv[i];
for (j = 0; j < preynames[i].Size(); j++)
delete[] preynames[i][j];
}
if (aggregator != 0) {
delete[] aggregator;
aggregator = 0;
}
if (preyLgrpDiv != 0) {
delete[] preyLgrpDiv;
preyLgrpDiv = 0;
}
if (!usepredages)
delete predLgrpDiv;
for (i = 0; i < predatornames.Size(); i++)
delete[] predatornames[i];
for (i = 0; i < areaindex.Size(); i++)
delete[] areaindex[i];
for (i = 0; i < predindex.Size(); i++)
delete[] predindex[i];
for (i = 0; i < preyindex.Size(); i++)
delete[] preyindex[i];
}
void SC::setPredatorsAndPreys(PredatorPtrVector& Predators, PreyPtrVector& Preys) {
int i, j, k, l, found;
int minage, maxage;
PredatorPtrVector predators;
aggregator = new PredatorAggregator*[preyindex.Size()];
for (i = 0; i < predatornames.Size(); i++) {
found = 0;
for (j = 0; j < Predators.Size(); j++)
if (strcasecmp(predatornames[i], Predators[j]->getName()) == 0) {
found++;
predators.resize(Predators[j]);
}
if (found == 0)
handle.logMessage(LOGFAIL, "Error in stomachcontent - failed to match predator", predatornames[i]);
}
//check predator areas
if (handle.getLogLevel() >= LOGWARN) {
for (j = 0; j < areas.Nrow(); j++) {
found = 0;
for (i = 0; i < predators.Size(); i++)
for (k = 0; k < areas.Ncol(j); k++)
if (predators[i]->isInArea(areas[j][k]))
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontent - predator not defined on all areas");
}
}
//check that the predators are stocks and not fleets
for (i = 0; i < predators.Size(); i++)
if (predators[i]->getType() != STOCKPREDATOR)
handle.logMessage(LOGFAIL, "Error in stomachcontent - cannot aggregate predator", predators[i]->getName());
preyLgrpDiv = new LengthGroupDivision*[preyindex.Size()];
if (!usepredages) {
predLgrpDiv = new LengthGroupDivision(predatorlengths);
if (predLgrpDiv->Error())
handle.logFileMessage(LOGFAIL, "\nError in stomachcontent - failed to create length group");
}
if (handle.getLogLevel() >= LOGWARN) {
if (usepredages) {
//check predator ages
minage = 9999;
maxage = -1;
for (j = 0; j < predatorages.Nrow(); j++) {
for (k = 0; k < predatorages.Ncol(j); k++) {
minage = min(predatorages[j][k], minage);
maxage = max(predatorages[j][k], maxage);
}
}
found = 0;
for (j = 0; j < predators.Size(); j++)
if (minage >= ((StockPredator*)predators[j])->minAge())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontent - minimum age less than predator age");
found = 0;
for (j = 0; j < predators.Size(); j++)
if (maxage <= ((StockPredator*)predators[j])->maxAge())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontent - maximum age greater than predator age");
} else {
//check predator lengths
found = 0;
for (j = 0; j < predators.Size(); j++)
if (predLgrpDiv->maxLength(0) > predators[j]->getLengthGroupDiv()->minLength())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontent - minimum length group less than predator length");
found = 0;
for (j = 0; j < predators.Size(); j++)
if (predLgrpDiv->minLength(predLgrpDiv->numLengthGroups()) < predators[j]->getLengthGroupDiv()->maxLength())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontent - maximum length group greater than predator length");
}
}
for (i = 0; i < preynames.Nrow(); i++) {
PreyPtrVector preys;
for (j = 0; j < preynames.Ncol(i); j++) {
found = 0;
for (k = 0; k < Preys.Size(); k++)
if (strcasecmp(preynames[i][j], Preys[k]->getName()) == 0) {
found++;
preys.resize(Preys[k]);
}
if (found == 0)
handle.logMessage(LOGFAIL, "Error in stomachcontent - failed to match prey", preynames[i][j]);
}
//check prey areas
if (handle.getLogLevel() >= LOGWARN) {
for (j = 0; j < areas.Nrow(); j++) {
found = 0;
for (k = 0; k < preys.Size(); k++)
for (l = 0; l < areas.Ncol(j); l++)
if (preys[k]->isInArea(areas[j][l]))
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontent - prey not defined on all areas");
}
}
//resize the digestion matrix
digestion.AddRows(1, preylengths[i].Size(), 0.0);
preyLgrpDiv[i] = new LengthGroupDivision(preylengths[i]);
if (preyLgrpDiv[i]->Error())
handle.logFileMessage(LOGFAIL, "\nError in stomachcontent - failed to create length group");
if (usepredages)
aggregator[i] = new PredatorAggregator(predators, preys, areas, predatorages, preyLgrpDiv[i]);
else
aggregator[i] = new PredatorAggregator(predators, preys, areas, predLgrpDiv, preyLgrpDiv[i]);
}
}
void SC::Print(ofstream& outfile) const {
int i, j;
outfile << "\tPredators:\n\t\t";
for (i = 0; i < predatornames.Size(); i++)
outfile << predatornames[i] << sep;
if (usepredages) {
outfile << "\n\t\tages:";
for (i = 0; i < predatorages.Nrow(); i++) {
outfile << "\n\t\t\t";
for (j = 0; j < predatorages.Ncol(i); j++)
outfile << predatorages[i][j] << sep;
}
outfile << endl;
} else {
outfile << "\n\t\tlengths: ";
for (i = 0; i < predatorlengths.Size(); i++)
outfile << predatorlengths[i] << sep;
outfile << endl;
}
outfile << "\n\tPreys:";
for (i = 0; i < preyindex.Size(); i++) {
outfile << "\n\t\t" << preyindex[i] << "\n\t\t";
for (j = 0; j < preynames[i].Size(); j++)
outfile << preynames[i][j] << sep;
outfile << "\n\t\tlengths: ";
for (j = 0; j < preylengths[i].Size(); j++)
outfile << preylengths[i][j] << sep;
outfile << endl;
aggregator[i]->Print(outfile);
}
outfile.flush();
}
// ********************************************************
// Functions for SCNumbers
// ********************************************************
SCNumbers::SCNumbers(CommentStream& infile, const AreaClass* const Area,
const TimeClass* const TimeInfo, Keeper* const keeper,
const char* datafilename, const char* givenname)
: SC(infile, Area, TimeInfo, keeper, datafilename, givenname) {
ifstream datafile;
CommentStream subdata(datafile);
//read in stomach content from file
datafile.open(datafilename, ios::in);
handle.checkIfFailure(datafile, datafilename);
handle.Open(datafilename);
readStomachNumberContent(subdata, TimeInfo);
handle.Close();
datafile.close();
datafile.clear();
MN = Multinomial();
MN.setValue(epsilon);
mndist.resize(likelihoodValues.Nrow(), 0.0);
mndata.resize(likelihoodValues.Nrow(), 0.0);
}
void SCNumbers::readStomachNumberContent(CommentStream& infile, const TimeClass* const TimeInfo) {
int i, year, step, count, reject;
double tmpnumber;
char tmparea[MaxStrLength], tmppred[MaxStrLength], tmpprey[MaxStrLength];
strncpy(tmparea, "", MaxStrLength);
strncpy(tmppred, "", MaxStrLength);
strncpy(tmpprey, "", MaxStrLength);
int keepdata, timeid, areaid, predid, preyid;
if (usepredages) //age structured predator
handle.logMessage(LOGFAIL, "Error in stomachcontent - age based predators cannot be used with scnumbers");
int numpred = predatorlengths.Size() - 1;
int numarea = areas.Nrow();
int numprey = 0;
for (i = 0; i < preylengths.Nrow(); i++)
numprey += preylengths[i].Size() - 1;
if (numprey == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontents - no prey found for", this->getName());
//Check the number of columns in the inputfile
infile >> ws;
if (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;
infile >> year >> step >> tmparea >> tmppred >> tmpprey >> tmpnumber >> 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 tmppred is in predindex find predid, else dont keep the data
predid = -1;
for (i = 0; i < predindex.Size(); i++)
if (strcasecmp(predindex[i], tmppred) == 0)
predid = i;
if (predid == -1)
keepdata = 0;
//if tmpprey is in preyindex find preyid, else dont keep the data
preyid = -1;
for (i = 0; i < preyindex.Size(); i++)
if (strcasecmp(preyindex[i], tmpprey) == 0)
preyid = i;
if (preyid == -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);
timeid = Years.Size() - 1;
obsConsumption.resize();
modelConsumption.resize();
likelihoodValues.AddRows(1, numarea, 0.0);
for (i = 0; i < numarea; i++) {
obsConsumption[timeid].resize(new DoubleMatrix(numpred, numprey, 0.0));
modelConsumption[timeid].resize(new DoubleMatrix(numpred, numprey, 0.0));
}
}
} else
keepdata = 0;
if (keepdata == 1) {
//stomach content data is required, so store it
count++;
(*obsConsumption[timeid][areaid])[predid][preyid] = tmpnumber;
} else
reject++; //count number of rejected data points read from file
}
AAT.addActions(Years, Steps, TimeInfo);
if (count == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontent - found no data in the data file for", this->getName());
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid stomachcontent data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read stomachcontent data file - number of entries", count);
}
double SCNumbers::calcLikelihood() {
int a, pred, prey;
MN.Reset();
for (a = 0; a < areas.Nrow(); a++) {
likelihoodValues[timeindex][a] = 0.0;
for (prey = 0; prey < obsConsumption[timeindex][a]->Ncol(0); prey++) {
for (pred = 0; pred < mndata.Size(); pred++) {
mndata[pred] = (*obsConsumption[timeindex][a])[pred][prey];
mndist[pred] = (*modelConsumption[timeindex][a])[pred][prey];
}
likelihoodValues[timeindex][a] += MN.calcLogLikelihood(mndata, mndist);
}
}
return MN.getLogLikelihood();
}
void SCNumbers::aggregate(int i) {
aggregator[i]->NumberSum();
}
// ********************************************************
// Functions for SCAmounts
// ********************************************************
SCAmounts::SCAmounts(CommentStream& infile, const AreaClass* const Area,
const TimeClass* const TimeInfo, Keeper* const keeper,
const char* datafilename, const char* numfilename, const char* givenname)
: SC(infile, Area, TimeInfo, keeper, datafilename, givenname) {
ifstream datafile;
CommentStream subdata(datafile);
//read in stomach content amounts from file
datafile.open(datafilename, ios::in);
handle.checkIfFailure(datafile, datafilename);
handle.Open(datafilename);
readStomachAmountContent(subdata, TimeInfo);
handle.Close();
datafile.close();
datafile.clear();
//read in stomach content sample size from file
datafile.open(numfilename, ios::in);
handle.checkIfFailure(datafile, numfilename);
handle.Open(numfilename);
readStomachSampleContent(subdata, TimeInfo);
handle.Close();
datafile.close();
datafile.clear();
}
void SCAmounts::readStomachAmountContent(CommentStream& infile, const TimeClass* const TimeInfo) {
int i, year, step, count, reject;
double tmpnumber, tmpstddev;
char tmparea[MaxStrLength], tmppred[MaxStrLength], tmpprey[MaxStrLength];
strncpy(tmparea, "", MaxStrLength);
strncpy(tmppred, "", MaxStrLength);
strncpy(tmpprey, "", MaxStrLength);
int keepdata, timeid, areaid, predid, preyid;
int numpred = 0;
if (usepredages) //age structured predator
numpred = predatorages.Nrow();
else
numpred = predatorlengths.Size() - 1;
int numarea = areas.Nrow();
int numprey = 0;
for (i = 0; i < preylengths.Nrow(); i++)
numprey += preylengths[i].Size() - 1;
if (numprey == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontents - no prey found for", this->getName());
//Check the number of columns in the inputfile
infile >> ws;
if (countColumns(infile) != 7)
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 7");
year = step = count = reject = 0;
while (!infile.eof()) {
keepdata = 1;
infile >> year >> step >> tmparea >> tmppred >> tmpprey >> tmpnumber >> tmpstddev >> 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 tmppred is in predindex find predid, else dont keep the data
predid = -1;
for (i = 0; i < predindex.Size(); i++)
if (strcasecmp(predindex[i], tmppred) == 0)
predid = i;
if (predid == -1)
keepdata = 0;
//if tmpprey is in preyindex find preyid, else dont keep the data
preyid = -1;
for (i = 0; i < preyindex.Size(); i++)
if (strcasecmp(preyindex[i], tmpprey) == 0)
preyid = i;
if (preyid == -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);
timeid = Years.Size() - 1;
obsConsumption.resize();
modelConsumption.resize();
stddev.resize();
likelihoodValues.AddRows(1, numarea, 0.0);
for (i = 0; i < numarea; i++) {
obsConsumption[timeid].resize(new DoubleMatrix(numpred, numprey, 0.0));
modelConsumption[timeid].resize(new DoubleMatrix(numpred, numprey, 0.0));
stddev[timeid].resize(new DoubleMatrix(numpred, numprey, 0.0));
}
}
} else
keepdata = 0;
if (keepdata == 1) {
//stomach content data is required, so store it
count++;
(*obsConsumption[timeid][areaid])[predid][preyid] = tmpnumber;
(*stddev[timeid][areaid])[predid][preyid] = 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 stomachcontent - found no data in the data file for", this->getName());
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid stomachcontent data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read stomachcontent data file - number of entries", count);
}
void SCAmounts::readStomachSampleContent(CommentStream& infile, const TimeClass* const TimeInfo) {
int i, year, step, count, reject;
double tmpnumber;
int keepdata, timeid, areaid, predid;
char tmparea[MaxStrLength], tmppred[MaxStrLength];
strncpy(tmparea, "", MaxStrLength);
strncpy(tmppred, "", MaxStrLength);
int numpred = 0;
if (usepredages) //age structured predator
numpred = predatorages.Nrow();
else
numpred = predatorlengths.Size() - 1;
//We know the size that numbers[] will be from obsConsumption
int numarea = areas.Nrow();
for (i = 0; i < obsConsumption.Nrow(); i++)
number.resize(new DoubleMatrix(numarea, numpred, 0.0));
//Check the number of columns in the inputfile
infile >> ws;
if (countColumns(infile) != 5)
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 5");
year = step = count = reject = 0;
while (!infile.eof()) {
keepdata = 1;
infile >> year >> step >> tmparea >> tmppred >> tmpnumber >> 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");
//check if the year and step are in the simulation
timeid = -1;
if (TimeInfo->isWithinPeriod(year, step))
//find the timeid from Years and Steps
for (i = 0; i < Years.Size(); i++)
if ((Years[i] == year) && (Steps[i] == step))
timeid = i;
if (timeid == -1)
keepdata = 0;
//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 tmppred is in predindex find predid, else dont keep the data
predid = -1;
for (i = 0; i < predindex.Size(); i++)
if (strcasecmp(predindex[i], tmppred) == 0)
predid = i;
if (predid == -1)
keepdata = 0;
if (keepdata == 1) {
//stomach content data is required, so store it
count++;
(*number[timeid])[areaid][predid] = tmpnumber;
} else
reject++; //count number of rejected data points read from file
}
if (count == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontent - found no data in the data file for", this->getName());
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid stomachcontent data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read stomachcontent data file - number of entries", count);
}
SCAmounts::~SCAmounts() {
int i, j;
for (i = 0; i < stddev.Nrow(); i++) {
delete number[i];
for (j = 0; j < stddev[i].Size(); j++)
delete stddev[i][j];
}
}
//JMB - note this ignores the number of samples ...
void SCAmounts::printLikelihood(ofstream& outfile, const TimeClass* const TimeInfo) {
if (!AAT.atCurrentTime(TimeInfo))
return;
int i, area, pred, prey;
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 stomachcontent - invalid timestep");
for (area = 0; area < modelConsumption.Ncol(timeindex); area++) {
for (pred = 0; pred < modelConsumption[timeindex][area]->Nrow(); pred++) {
for (prey = 0; prey < modelConsumption[timeindex][area]->Ncol(pred); prey++) {
outfile << setw(lowwidth) << Years[timeindex] << sep << setw(lowwidth)
<< Steps[timeindex] << sep << setw(printwidth) << areaindex[area] << sep
<< setw(printwidth) << predindex[pred] << sep << setw(printwidth)
<< preyindex[prey] << sep << setprecision(largeprecision) << setw(largewidth);
//JMB crude filter to remove the 'silly' values from the output
if ((*modelConsumption[timeindex][area])[pred][prey] < rathersmall)
outfile << 0;
else
outfile << (*modelConsumption[timeindex][area])[pred][prey];
outfile << sep << setprecision(largeprecision) << setw(largewidth)
<< (*stddev[timeindex][area])[pred][prey] << endl;
}
}
}
}
double SCAmounts::calcLikelihood() {
int a, pred, prey;
double tmplik, lik = 0.0;
for (a = 0; a < areas.Nrow(); a++) {
likelihoodValues[timeindex][a] = 0.0;
for (pred = 0; pred < obsConsumption[timeindex][a]->Nrow(); pred++) {
if (!(isZero((*number[timeindex])[a][pred]))) {
tmplik = 0.0;
for (prey = 0; prey < obsConsumption[timeindex][a]->Ncol(pred); prey++) {
if (!(isZero((*stddev[timeindex][a])[pred][prey])))
tmplik += ((*modelConsumption[timeindex][a])[pred][prey] -
(*obsConsumption[timeindex][a])[pred][prey]) *
((*modelConsumption[timeindex][a])[pred][prey] -
(*obsConsumption[timeindex][a])[pred][prey]) /
((*stddev[timeindex][a])[pred][prey] * (*stddev[timeindex][a])[pred][prey]);
}
tmplik *= (*number[timeindex])[a][pred];
likelihoodValues[timeindex][a] += tmplik;
}
}
lik += likelihoodValues[timeindex][a];
}
return lik;
}
// ********************************************************
// Functions for SCRatios
// ********************************************************
void SCRatios::setPredatorsAndPreys(PredatorPtrVector& Predators, PreyPtrVector& Preys) {
int i, j, k, l;
double tmpdivide, scale;
SC::setPredatorsAndPreys(Predators, Preys);
//Scale each row such that it sums up to 1
for (i = 0; i < obsConsumption.Nrow(); i++) {
for (j = 0; j < obsConsumption.Ncol(i); j++) {
for (k = 0; k < obsConsumption[i][j]->Nrow(); k++) {
scale = 0.0;
for (l = 0; l < obsConsumption[i][j]->Ncol(k); l++)
scale += (*obsConsumption[i][j])[k][l];
if (!(isZero(scale))) {
tmpdivide = 1.0 / scale;
for (l = 0; l < obsConsumption[i][j]->Ncol(k); l++)
(*obsConsumption[i][j])[k][l] *= tmpdivide;
}
}
}
}
}
double SCRatios::calcLikelihood() {
int a, pred, prey;
double scale, tmplik, tmpdivide;
double lik = 0.0;
for (a = 0; a < areas.Nrow(); a++) {
likelihoodValues[timeindex][a] = 0.0;
for (pred = 0; pred < obsConsumption[timeindex][a]->Nrow(); pred++) {
scale = 0.0;
for (prey = 0; prey < modelConsumption[timeindex][a]->Ncol(pred); prey++)
scale += (*modelConsumption[timeindex][a])[pred][prey];
if (!(isZero(scale))) {
tmpdivide = 1.0 / scale;
for (prey = 0; prey < obsConsumption[timeindex][a]->Ncol(pred); prey++)
(*modelConsumption[timeindex][a])[pred][prey] *= tmpdivide;
if (!(isZero((*number[timeindex])[a][pred]))) {
tmplik = 0.0;
for (prey = 0; prey < obsConsumption[timeindex][a]->Ncol(pred); prey++) {
if (!(isZero((*stddev[timeindex][a])[pred][prey])))
tmplik += ((*modelConsumption[timeindex][a])[pred][prey] -
(*obsConsumption[timeindex][a])[pred][prey]) *
((*modelConsumption[timeindex][a])[pred][prey] -
(*obsConsumption[timeindex][a])[pred][prey]) /
((*stddev[timeindex][a])[pred][prey] * (*stddev[timeindex][a])[pred][prey]);
}
tmplik *= (*number[timeindex])[a][pred];
likelihoodValues[timeindex][a] += tmplik;
}
}
}
lik += likelihoodValues[timeindex][a];
}
return lik;
}
// ********************************************************
// Functions for SCSimple
// ********************************************************
SCSimple::SCSimple(CommentStream& infile, const AreaClass* const Area,
const TimeClass* const TimeInfo, Keeper* const keeper,
const char* datafilename, const char* givenname)
: SC(infile, Area, TimeInfo, keeper, datafilename, givenname) {
ifstream datafile;
CommentStream subdata(datafile);
//read in stomach content from file
datafile.open(datafilename, ios::in);
handle.checkIfFailure(datafile, datafilename);
handle.Open(datafilename);
readStomachSimpleContent(subdata, TimeInfo);
handle.Close();
datafile.close();
datafile.clear();
}
void SCSimple::readStomachSimpleContent(CommentStream& infile, const TimeClass* const TimeInfo) {
int i, year, step, count, reject;
double tmpnumber;
char tmparea[MaxStrLength], tmppred[MaxStrLength], tmpprey[MaxStrLength];
strncpy(tmparea, "", MaxStrLength);
strncpy(tmppred, "", MaxStrLength);
strncpy(tmpprey, "", MaxStrLength);
int keepdata, timeid, areaid, predid, preyid;
int numpred = 0;
if (usepredages) //age structured predator
numpred = predatorages.Nrow();
else
numpred = predatorlengths.Size() - 1;
int numarea = areas.Nrow();
int numprey = 0;
for (i = 0; i < preylengths.Nrow(); i++)
numprey += preylengths[i].Size() - 1;
if (numprey == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontents - no prey found for", this->getName());
//Check the number of columns in the inputfile
infile >> ws;
if (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;
infile >> year >> step >> tmparea >> tmppred >> tmpprey >> tmpnumber >> 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 tmppred is in predindex find predid, else dont keep the data
predid = -1;
for (i = 0; i < predindex.Size(); i++)
if (strcasecmp(predindex[i], tmppred) == 0)
predid = i;
if (predid == -1)
keepdata = 0;
//if tmpprey is in preyindex find preyid, else dont keep the data
preyid = -1;
for (i = 0; i < preyindex.Size(); i++)
if (strcasecmp(preyindex[i], tmpprey) == 0)
preyid = i;
if (preyid == -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);
timeid = Years.Size() - 1;
obsConsumption.resize();
modelConsumption.resize();
likelihoodValues.AddRows(1, numarea, 0.0);
for (i = 0; i < numarea; i++) {
obsConsumption[timeid].resize(new DoubleMatrix(numpred, numprey, 0.0));
modelConsumption[timeid].resize(new DoubleMatrix(numpred, numprey, 0.0));
}
}
} else
keepdata = 0;
if (keepdata == 1) {
//stomach content data is required, so store it
count++;
(*obsConsumption[timeid][areaid])[predid][preyid] = tmpnumber;
} else
reject++; //count number of rejected data points read from file
}
AAT.addActions(Years, Steps, TimeInfo);
if (count == 0)
handle.logMessage(LOGWARN, "Warning in stomachcontent - found no data in the data file for", this->getName());
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid stomachcontent data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read stomachcontent data file - number of entries", count);
}
void SCSimple::setPredatorsAndPreys(PredatorPtrVector& Predators, PreyPtrVector& Preys) {
int i, j, k, l;
double tmpdivide, scale;
SC::setPredatorsAndPreys(Predators, Preys);
//Scale each row such that it sums up to 1
for (i = 0; i < obsConsumption.Nrow(); i++) {
for (j = 0; j < obsConsumption.Ncol(i); j++) {
for (k = 0; k < obsConsumption[i][j]->Nrow(); k++) {
scale = 0.0;
for (l = 0; l < obsConsumption[i][j]->Ncol(k); l++)
scale += (*obsConsumption[i][j])[k][l];
if (!(isZero(scale))) {
tmpdivide = 1.0 / scale;
for (l = 0; l < obsConsumption[i][j]->Ncol(k); l++)
(*obsConsumption[i][j])[k][l] *= tmpdivide;
}
}
}
}
}
double SCSimple::calcLikelihood() {
int a, pred, prey;
double scale, tmplik, tmpdivide;
double lik = 0.0;
for (a = 0; a < areas.Nrow(); a++) {
likelihoodValues[timeindex][a] = 0.0;
for (pred = 0; pred < obsConsumption[timeindex][a]->Nrow(); pred++) {
scale = 0.0;
for (prey = 0; prey < modelConsumption[timeindex][a]->Ncol(pred); prey++)
scale += (*modelConsumption[timeindex][a])[pred][prey];
if (!(isZero(scale))) {
tmpdivide = 1.0 / scale;
tmplik = 0.0;
for (prey = 0; prey < obsConsumption[timeindex][a]->Ncol(pred); prey++) {
(*modelConsumption[timeindex][a])[pred][prey] *= tmpdivide;
tmplik += ((*modelConsumption[timeindex][a])[pred][prey] -
(*obsConsumption[timeindex][a])[pred][prey]) *
((*modelConsumption[timeindex][a])[pred][prey] -
(*obsConsumption[timeindex][a])[pred][prey]);
}
likelihoodValues[timeindex][a] += tmplik;
}
}
lik += likelihoodValues[timeindex][a];
}
return lik;
}
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