species obtained internally rather than passsed

src/RScore/Individual.cpp

@@ -783,7 +783,7 @@ bool Individual::moveKernel(Landscape* pLandscape, const bool absorbing)
 				if (nx < 0.0) newX = -1; else newX = (int)nx;
 				if (ny < 0.0) newY = -1; else newY = (int)ny;
 #ifndef NDEBUG
-				if (path != 0) (path->year)++;
+				if (path != nullptr) (path->year)++;
 #endif
 				loopsteps++;
 			} while (loopsteps < 1000 &&
@@ -796,20 +796,20 @@ bool Individual::moveKernel(Landscape* pLandscape, const bool absorbing)
 				if (newX < land.minX || newX > land.maxX
 					|| newY < land.minY || newY > land.maxY) { // beyond absorbing boundary
 					// this cannot be reached if not absorbing?
-					pCell = 0;
-					patch = 0;
+					pCell = nullptr;
+					patch = nullptr;
 					patchNum = -1;
 				}
 				else {
 					pCell = pLandscape->findCell(newX, newY);
-					if (pCell == 0) { // no-data cell
-						patch = 0;
+					if (pCell == nullptr) { // no-data cell
+						patch = nullptr;
 						patchNum = -1;
 					}
 					else {
 						patch = pCell->getPatch();
-						if (patch == 0) { // matrix
-							pPatch = 0;
+						if (patch == nullptr) { // matrix
+							pPatch = nullptr;
 							patchNum = 0;
 						}
 						else {
@@ -820,16 +820,16 @@ bool Individual::moveKernel(Landscape* pLandscape, const bool absorbing)
 				}
 			}
 			else { // exceeded 1000 attempts
-				patch = 0;
+				patch = nullptr;
 				patchNum = -1;
 			}
 		} while (!absorbing && patchNum < 0 && loopsteps < 1000); 			 // in a no-data region
 	} while (!usefullkernel && pPatch == pNatalPatch && loopsteps < 1000); 	// still in the original (natal) patch
 
 	if (loopsteps < 1000) {
-		if (pCell == 0) { // beyond absorbing boundary or in no-data cell
+		if (pCell == nullptr) { // beyond absorbing boundary or in no-data cell
 			// only if absorbing=true and out of bounddaries
-			pCurrCell = 0;
+			pCurrCell = nullptr;
 			status = diedInTransfer;
 			isDispersing = false;
 		}

src/RScore/Patch.cpp

@@ -32,8 +32,12 @@
 Patch::Patch(int seqnum, int num)
 {
 	pPop = nullptr;
-	patchSeqNum = seqnum; patchNum = num; nCells = 0;
-	xMin = yMin = 999999999; xMax = yMax = 0; x = y = 0;
+	patchSeqNum = seqnum; 
+	patchNum = num; 
+	nCells = 0;
+	xMin = yMin = 999999999; 
+	xMax = yMax = 0; 
+	x = y = 0;
 	localK = 0.0;
 	for (int sex = 0; sex < gMaxNbSexes; sex++) {
 		nTemp[sex] = 0;
@@ -124,9 +128,10 @@ void Patch::addCell(Cell* pCell, int x, int y) {
 
 // Calculate the total carrying capacity (no. of individuals) and
 // centroid co-ordinates of the patch
-void Patch::setCarryingCapacity(Species* pSpecies, patchLimits landlimits,
-	float epsGlobal, short nHab, short rasterType, short landIx, bool gradK) {
+void Patch::setCarryingCapacity(patchLimits landlimits, float epsGlobal,
+	short nHab, short rasterType, short landIx, bool gradK) {
 
+	Species* pSpecies = pPop->getSpecies();
 	envStochParams env = paramsStoch->getStoch();
 	locn loc;
 	int xsum, ysum;
@@ -146,7 +151,7 @@ void Patch::setCarryingCapacity(Species* pSpecies, patchLimits landlimits,
 		return;
 	}
 
-	int ncells = cells.size();
+	int ncells = static_cast<int>(cells.size());
 	xsum = ysum = 0;
 	for (int i = 0; i < ncells; i++) {
 		if (gradK) // gradient in carrying capacity
@@ -219,14 +224,14 @@ int Patch::getInitNbInds(const bool& isPatchModel, const int& landResol) const {
 	if (localK > 0.0) { // patch is currently suitable for this species
 		switch (init.initDens) {
 		case 0: // at carrying capacity
-			nInds = trunc(localK);
+			nInds = static_cast<int>(localK);
 			break;
 		case 1: // at half carrying capacity
-			nInds = trunc(localK / 2.0);
+			nInds = static_cast<int>(localK / 2.0);
 			break;
 		case 2: // specified no. per cell or density
 			if (isPatchModel) {
-				nInds = trunc(init.indsHa * (float)(nCells * landResol * landResol) / 10000.0);
+				nInds = static_cast<int>(init.indsHa * (float)(nCells * landResol * landResol) / 10000.0);
 			}
 			else {
 				nInds = init.indsCell * nCells;
@@ -336,18 +341,13 @@ void Patch::resetPossSettlers() {
 }
 
 // Record the presence of a potential settler within the Patch
-void Patch::incrPossSettler(Species* pSpecies, int sex) {
-// NOTE: THE FOLLOWING OPERATION WILL NEED TO BE MADE SPECIES-SPECIFIC...
-	if (sex >= 0 && sex < gMaxNbSexes) {
-		nTemp[sex]++;
-	}
+void Patch::incrPossSettler(int sex) {
+	nTemp[sex]++;
 }
 
 // Get number of a potential settlers within the Patch
-int Patch::getPossSettlers(Species* pSpecies, int sex) {
-// NOTE: THE FOLLOWING OPERATION WILL NEED TO BE MADE SPECIES-SPECIFIC...
-	if (sex >= 0 && sex < gMaxNbSexes) return nTemp[sex];
-	else return 0;
+int Patch::getPossSettlers(int sex) {
+	return nTemp[sex];
 }
 
 bool Patch::speciesIsPresent() {

src/RScore/Patch.h

@@ -112,14 +112,14 @@ class Patch {
 	void resetPop();
 
 	// Record the presence of a potential settler within the Patch
-	void incrPossSettler(Species* pSpecies, int sex);
+	void incrPossSettler(int sex);
 	// Get number of a potential settlers within the Patch
-	int getPossSettlers(Species* pSpecies, int sex);
+	int getPossSettlers(int sex);
 	void resetPossSettlers();
 
 	// Calculate total Patch carrying capacity (no. of inds)
-	void setCarryingCapacity(Species* pSpecies, patchLimits landlimits,
-		float epsGlobal, short nHab, short rasterType, short landIx, bool gradK);
+	void setCarryingCapacity(patchLimits landlimits, float epsGlobal, 
+		short nHab, short rasterType, short landIx, bool gradK);
 	float getK();
 
 	int getInitNbInds(const bool& isPatchModel, const int& landResol) const;

src/RScore/Population.cpp

@@ -523,7 +523,7 @@ void Population::reproduction(const float localK, const float envval, const int
 {
 
 	// get population size at start of reproduction
-	int ninds = inds.size();
+	int ninds = static_cast<int>(inds.size());
 	if (ninds == 0) return;
 
 	int nsexes, stage, sex, njuvs, nj, nmales, nfemales;
@@ -944,17 +944,16 @@ disperser Population::extractDisperser(int ix) {
 // 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();
-	Cell* pCell;
-
 	indStats ind = inds[ix]->getStats();
-	pCell = inds[ix]->getLocn(1);
+	Cell* pCell = inds[ix]->getLocn(1);
 	d.pInd = inds[ix];  
 	d.pCell = pCell;
 	d.yes = false;
 	if (ind.status == settled || ind.status == settledNeighbour) {
 		d.yes = true;
-		inds[ix] = 0;
+		inds[ix] = nullptr;
 		nInds[ind.stage][ind.sex]--;
 	}
 	return d;
@@ -1017,7 +1016,7 @@ int Population::transfer(Landscape* pLandscape, short landIx, short nextseason)
 			pCell = inds[i]->getLocn(1);
 			pPatch = pCell->getPatch();
 			if (pPatch != nullptr) { // not no-data area
-				pPatch->incrPossSettler(pSpecies, inds[i]->getSex());
+				pPatch->incrPossSettler(inds[i]->getSex());
 			}
 		}
 	}
@@ -1212,7 +1211,7 @@ bool Population::isMatePresent(Cell* pCell, short othersex)
 					}
 				}
 				// If empty, check for incoming settlers
-				if (pPatch->getPossSettlers(pSpecies, othersex) > 0) 
+				if (pPatch->getPossSettlers(othersex) > 0) 
 					return true;
 		}
 	}