more warnings and messages fixes

Community.cpp

@@ -64,7 +64,7 @@ void Community::initialise(Species* pSpecies, int year)
 	int nsubcomms, npatches, ndistcells, spratio, patchnum, rr = 0;
 	locn distloc;
 	patchData pch;
-	patchLimits limits;
+	patchLimits limits = patchLimits();
 	intptr ppatch, subcomm;
 	std::vector <intptr> subcomms;
 	std::vector <bool> selected;
@@ -257,7 +257,8 @@ void Community::initialise(Species* pSpecies, int year)
 			indIx = 0; // reset index for initial individuals
 		}
 		else { // add any initial individuals for the current year
-			initInd iind; iind.year = 0;
+			initInd iind = initInd(); 
+			iind.year = 0;
 			int ninds = paramsInit->numInitInds();
 			while (indIx < ninds && iind.year <= year) {
 				iind = paramsInit->getInitInd(indIx);
@@ -505,7 +506,7 @@ void Community::dispersal(short landIx)
 #endif // SEASONAL || RS_RCPP
 {
 #if RSDEBUG
-	int t0, t1, t2;
+	time_t t0, t1, t2;
 	t0 = time(0);
 #endif
 
@@ -631,7 +632,7 @@ void Community::deleteOccupancy(int nrows) {
 // Determine range margins
 commStats Community::getStats(void)
 {
-	commStats s;
+	commStats s = commStats();
 	landParams ppLand = pLandscape->getLandParams();
 	s.ninds = s.nnonjuvs = s.suitable = s.occupied = 0;
 	s.minX = ppLand.maxX; s.minY = ppLand.maxY; s.maxX = s.maxY = 0;
@@ -883,9 +884,9 @@ void Community::outRange(Species* pSpecies, int rep, int yr, int gen)
 		outrange << "\t0\t0\t0\t0";
 
 	if (emig.indVar || trfr.indVar || sett.indVar) { // output trait means
-		traitsums ts;
+		traitsums ts = traitsums();
 		traitsums scts; // sub-community traits
-		traitCanvas tcanv;
+		traitCanvas tcanv = traitCanvas();
 		int ngenes, popsize;
 
 		tcanv.pcanvas[0] = NULL;
@@ -1889,8 +1890,8 @@ void Community::writeWCPerLocusFstatFile(Species* pSpecies, const int yr, const
 			const auto pPop = (Population*)patch->getPopn((intptr)pSpecies);
 			int popSize = pPop->sampleSize();
 			int het = 0;
-			for (unsigned int a = 0; a < nAlleles; ++a) {
-				het += pPop->getHetero(thisLocus, a);
+			for (int a = 0; a < nAlleles; ++a) {
+				het += static_cast<int>(pPop->getHetero(thisLocus, a)); // not sure why this returns a double
 			}
 			outperlocusfstat << "\t" << het / (2.0 * popSize);
 		}

GeneticLoad.cpp

@@ -211,27 +211,27 @@ float GeneticLoad::drawDominance(float selCoef) {
 	{
 		const float mean = dominanceParameters.find(MEAN)->second;
 		const float sd = dominanceParameters.find(SDEV)->second;
-		h = pRandom->Normal(mean, sd);
+		h = static_cast<float>(pRandom->Normal(mean, sd));
 		break;
 	}
 	case GAMMA:
 	{
 		const float shape = dominanceParameters.find(SHAPE)->second;
 		const float scale = dominanceParameters.find(SCALE)->second;
-		h = pRandom->Gamma(shape, scale);
+		h = static_cast<float>(pRandom->Gamma(shape, scale));
 		break;
 	}
 	case NEGEXP:
 	{
 		const float mean = dominanceParameters.find(MEAN)->second;
-		h = pRandom->NegExp(mean);
+		h = static_cast<float>(pRandom->NegExp(mean));
 		break;
 	}
 	case SCALED:
 	{
 		const float min = 0;
-		const float max = exp((-log(2 * 0.36) / 0.05) * selCoef);
-		h = pRandom->FRandom(min, max);
+		const float max = static_cast<float>(exp((-log(2 * 0.36) / 0.05) * selCoef));
+		h = static_cast<float>(pRandom->FRandom(min, max));
 		break;
 	}
 
@@ -270,21 +270,21 @@ float GeneticLoad::drawSelectionCoef() {
 	{
 		const float mean = mutationParameters.find(MEAN)->second;
 		const float sd = mutationParameters.find(SDEV)->second;
-		s = pRandom->Normal(mean, sd);
+		s = static_cast<float>(pRandom->Normal(mean, sd));
 
 		break;
 	}
 	case GAMMA:
 	{
 		const float shape = mutationParameters.find(SHAPE)->second;
 		const float scale = mutationParameters.find(SCALE)->second;
-		s = pRandom->Gamma(shape, scale);
+		s = static_cast<float>(pRandom->Gamma(shape, scale));
 		break;
 	}
 	case NEGEXP:
 	{
 		const float mean = mutationParameters.find(MEAN)->second;
-		s = pRandom->NegExp(mean);
+		s = static_cast<float>(pRandom->NegExp(mean));
 		break;
 	}
 	default:
@@ -315,7 +315,7 @@ void GeneticLoad::inheritDiploid(sex_t whichChromosome, map<int, vector<shared_p
 
 	auto it = recomPositions.lower_bound(parentGenes.begin()->first);
 
-	unsigned int nextBreakpoint = *it;
+	int nextBreakpoint = *it;
 
 	auto distance = std::distance(recomPositions.begin(), it);
 	if (distance % 2 != 0)

Population.cpp

@@ -56,7 +56,7 @@ Population::Population(Species* pSp, Patch* pPch, int ninds, int resol)
 	pSpecies = pSp;
 	pPatch = pPch;
 	// record the new population in the patch
-	patchPopn pp;
+	patchPopn pp = patchPopn();
 	pp.pSp = (intptr)pSpecies; pp.pPop = (intptr)this;
 	pPatch->addPopn(pp);
 #if RSDEBUG
@@ -229,7 +229,7 @@ Population::~Population(void) {
 
 traitsums Population::getTraits(Species* pSpecies) {
 	int g;
-	traitsums ts;
+	traitsums ts = traitsums();
 	for (int i = 0; i < NSEXES; i++) {
 		ts.ninds[i] = 0;
 		ts.sumD0[i] = ts.ssqD0[i] = 0.0;
@@ -456,10 +456,10 @@ double Population::computeHs() {
 
 popStats Population::getStats(void)
 {
-	popStats p;
+	popStats p = popStats();
 	int ninds;
 	float fec;
-	bool breeders[2]; breeders[0] = breeders[1] = false;
+	bool breeders[2] = { false, false };
 	demogrParams dem = pSpecies->getDemogr();
 	p.pSpecies = pSpecies;
 	p.pPatch = pPatch;
@@ -1147,7 +1147,7 @@ void Population::allEmigrate(void) {
 
 // If an Individual has been identified as an emigrant, remove it from the Population
 disperser Population::extractDisperser(int ix) {
-	disperser d;
+	disperser d = disperser();
 	indStats ind = inds[ix]->getStats();
 	if (ind.status == 1) { // emigrant
 		d.pInd = inds[ix]; d.yes = true;
@@ -1190,7 +1190,7 @@ void Population::addSettleTraitsForInd(int ix, settleTraits& avgSettleTraits) {
 // if it is a settler, return its new location and remove it from the current population
 // otherwise, leave it in the matrix population for possible reporting before deletion
 disperser Population::extractSettler(int ix) {
-	disperser d;
+	disperser d = disperser();
 	Cell* pCell;
 //Patch* pPatch;
 
@@ -1232,7 +1232,8 @@ int Population::transfer(Landscape* pLandscape, short landIx)
 	Cell* pCell = 0;
 	indStats ind;
 	Population* pNewPopn = 0;
-	locn newloc, nbrloc;
+	locn newloc = locn();
+	locn nbrloc = locn();
 
 	landData ppLand = pLandscape->getLandData();
 	short reptype = pSpecies->getRepType();
@@ -1716,6 +1717,9 @@ void Population::survival0(float localK, short option0, short option1)
 		if ((ind.stage == 0 && option0 < 2) || (ind.stage > 0 && option0 > 0)) {
 			// condition for processing the stage is met...
 			if (ind.status < 6) { // not already doomed
+				if (ind.sex < sex_t::FEM || ind.sex > sex_t::MAL)
+					// ?? MSVC believes it's important to bound check ind.sex
+					throw runtime_error("Individual sex is out of bounds");
 				double probsurv = surv[ind.stage][ind.sex];
 				// does the individual survive?
 				if (pRandom->Bernoulli(probsurv)) { // survives
@@ -2129,7 +2133,7 @@ void Population::outIndividual(Landscape* pLandscape, int rep, int yr, int gen,
 				outInds << "\t" << ind.status;
 			}
 			pCell = inds[i]->getLocn(1);
-			locn loc;
+			locn loc = locn();
 			if (pCell == 0) loc.x = loc.y = -1; // beyond boundary or in no-data cell
 			else loc = pCell->getLocn();
 			pCell = inds[i]->getLocn(0);

Population.h

@@ -235,7 +235,6 @@ class Population {
 	int countHeterozygoteLoci();
 	vector<double> countLociHeterozyotes();
 	double computeHs();
-	void updateHeteroTable();
 
 private:
 	short nStages;