fix merge conflict with develop

Cell.cpp

@@ -37,12 +37,6 @@ pPatch = patch;
 envVal = 1.0; // default - no effect of any gradient
 envDev = eps = 0.0;
 habIxx.push_back(hab);
-#if RSDEBUG
-//DebugGUI(("Cell::Cell(): this=" + Int2Str((int)this)
-//	+ " x=" + Int2Str(x) + " y=" + Int2Str(y)
-//	+ " habIndex=" + Int2Str(habIndex)
-//).c_str());
-#endif
 visits = 0;
 smsData = 0;
 }
@@ -74,12 +68,6 @@ if (smsData != 0) {
 }
 
 void Cell::setHabIndex(short hx) {
-#if RSDEBUG
-//DebugGUI(("Cell::setHabIndex(): this=" + Int2Str((int)this)
-//	+ " x=" + Int2Str(x) + " y=" + Int2Str(y)
-//	+ " habIx=" + Int2Str(habIx)
-//).c_str());
-#endif
 if (hx < 0) habIxx.push_back(0);
 else habIxx.push_back(hx);
 }
@@ -118,12 +106,6 @@ pPatch = p;
 }
 intptr Cell::getPatch(void)
 {
-#if RSDEBUG
-//DebugGUI(("Cell::getPatch(): this=" + Int2Str((int)this)
-//	+ " x=" + Int2Str(x) + " y=" + Int2Str(y)
-//	+ " habIxx[0]=" + Int2Str(habIxx[0]) + " pPatch=" + Int2Str(pPatch)
-//).c_str());
-#endif
 return pPatch;
 }
 

Cell.h

@@ -165,10 +165,6 @@ class DistCell{
 
 };
 
-#if RSDEBUG
-extern void DebugGUI(string);
-#endif
-
 //---------------------------------------------------------------------------
 
 #endif

Community.cpp

@@ -860,11 +860,8 @@ void Community::outRange(Species* pSpecies, int rep, int yr, int gen)
 	if (emig.indVar || trfr.indVar || sett.indVar) { // output trait means
 		traitsums ts;
 		traitsums scts; // sub-community traits
-		traitCanvas tcanv;
 		int ngenes, popsize;
 
-		tcanv.pcanvas[0] = NULL;
-
 		for (int i = 0; i < NSEXES; i++) {
 			ts.ninds[i] = 0;
 			ts.sumD0[i] = ts.ssqD0[i] = 0.0;
@@ -882,7 +879,7 @@ void Community::outRange(Species* pSpecies, int rep, int yr, int gen)
 
 		int nsubcomms = (int)subComms.size();
 		for (int i = 0; i < nsubcomms; i++) { // all sub-communities (incl. matrix)
-			scts = subComms[i]->outTraits(tcanv, pLandscape, rep, yr, gen, true);
+			scts = subComms[i]->outTraits(pLandscape, rep, yr, gen, true);
 			for (int j = 0; j < NSEXES; j++) {
 				ts.ninds[j] += scts.ninds[j];
 				ts.sumD0[j] += scts.sumD0[j];     ts.ssqD0[j] += scts.ssqD0[j];
@@ -1196,7 +1193,6 @@ void Community::outOccSuit(bool view) {
 		else sd = 0.0;
 		se = sd / sqrt((double)(sim.reps));
 		outsuit << i * sim.outIntOcc << "\t" << mean << "\t" << se << endl;
-		if (view) viewOccSuit(i * sim.outIntOcc, mean, se);
 	}
 
 }
@@ -1212,8 +1208,7 @@ only, this function relies on the fact that subcommunities are created in the sa
 sequence as patches, which is in asecending order of x nested within descending
 order of y
 */
-void Community::outTraits(traitCanvas tcanv, Species* pSpecies,
-	int rep, int yr, int gen)
+void Community::outTraits(Species* pSpecies, int rep, int yr, int gen)
 {
 	simParams sim = paramsSim->getSim();
 	simView v = paramsSim->getViews();
@@ -1247,7 +1242,7 @@ void Community::outTraits(traitCanvas tcanv, Species* pSpecies,
 		// generate output for each sub-community (patch) in the community
 		int nsubcomms = (int)subComms.size();
 		for (int i = 1; i < nsubcomms; i++) { // // all except matrix sub-community
-			sctraits = subComms[i]->outTraits(tcanv, pLandscape, rep, yr, gen, false);
+			sctraits = subComms[i]->outTraits(pLandscape, rep, yr, gen, false);
 			locn loc = subComms[i]->getLocn();
 			int y = loc.y;
 			if (sim.outTraitsRows && yr >= sim.outStartTraitRow && yr % sim.outIntTraitRow == 0)

Community.h

@@ -165,12 +165,6 @@ class Community {
 	void outOccSuit(
 		bool	// TRUE if occupancy graph is to be viewed on screen
 	);
-	void viewOccSuit( // Update the occupancy graph on the screen
-										// NULL for the batch version
-		int,		// year
-		double,	// mean occupancy
-		double	// standard error of occupancy
-	);
 	bool outTraitsHeaders( // Open traits file and write header record
 		Species*,	// pointer to Species
 		int				// Landscape number (-999 to close the file)
@@ -180,9 +174,6 @@ class Community {
 		int       // Landscape number (-999 to close the file)
 	);
 	void outTraits( // Write records to traits file
-		traitCanvas,// pointers to canvases for drawing variable traits 
-								// see SubCommunity.h
-								// in the batch version, these are replaced by integers set to zero
 		Species*,		// pointer to Species
 		int,				// replicate
 		int,				// year
@@ -196,13 +187,6 @@ class Community {
 		int,			// row number (Y cell co-ordinate)
 		traitsums	// structure holding sums of trait genes for dispersal (see Population.h)
 	);
-	void draw(	// Draw the Community on the landscape map and optionally save the map
-							// NULL for the batch version
-		int,	// replicate
-		int,	// year
-		int,	// generation
-		int		// Landscape number
-	);
 #if RS_RCPP && !R_CMD
     Rcpp::IntegerMatrix addYearToPopList(int,int);
 #endif

FractalGenerator.cpp

@@ -217,17 +217,8 @@ while (iter != patches.end())
 }
 
 if (arena != NULL) {
-#if RSDEBUG
-//DebugGUI(("fractal_landscape(): arena=" + Int2Str((int)arena)
-//	+ " X=" + Int2Str(X) + " Y=" + Int2Str(Y)
-//	).c_str());
-#endif
 	for(ii = 0; ii < X; ii++) {
-#if RSDEBUG
-//DebugGUI(("fractal_landscape(): ii=" + Int2Str(ii)
-//	+ " arena[ii]=" + Int2Str((int)arena[ii])
-//	).c_str());
-#endif
+
 		delete[] arena[ii];
 	}
 	delete[] arena;

FractalGenerator.h

@@ -78,7 +78,6 @@ bool compare(const land&, const land&);
 
 extern RSrandom *pRandom;
 #if RSDEBUG
-extern void DebugGUI(string);
 #endif
 
 //---------------------------------------------------------------------------

Genome.h

@@ -165,7 +165,6 @@ extern RSrandom* pRandom;
 #if RSDEBUG
 extern ofstream DEBUGLOG;
 extern ofstream MUTNLOG;
-extern void DebugGUI(string);
 #endif
 
 //---------------------------------------------------------------------------

Landscape.cpp

@@ -1293,6 +1293,9 @@ int Landscape::readLandChange(int filenum, bool costs)
 		}
 		if (costs) {
 			if (c < 1) { // invalid cost
+#if RS_RCPP
+			    Rcpp::Rcout << "Found invalid cost value of " << c << " in cell x " << x << " and y  " << y << std::endl;
+#endif
 				hfile.close(); hfile.clear();
 				if (pfile.is_open()) {
 					pfile.close(); pfile.clear();
@@ -1304,8 +1307,8 @@ int Landscape::readLandChange(int filenum, bool costs)
 			}
 		}
 	}
-			}
-		}
+			} // for x
+		} // for y
 #if RS_RCPP
 		hfile >> hfloat;
 		if (!hfile.eof()) EOFerrorR("habitatchgfile");
@@ -1431,6 +1434,9 @@ int Landscape::readLandChange(int filenum, bool costs)
 			}
 			if (costs) {
 				if (c < 1) { // invalid cost
+#if RS_RCPP
+				    Rcpp::Rcout << "Found invalid cost value of " << c << "in cell x " << x << " and y  " << y << std::endl;
+#endif
 					hfile.close(); hfile.clear();
 					if (pfile.is_open()) {
 						pfile.close(); pfile.clear();
@@ -1442,8 +1448,8 @@ int Landscape::readLandChange(int filenum, bool costs)
 				}
 			}
 		}
-			}
-		}
+			} // end x
+		} // end y
 #if RS_RCPP
 		hfile >> hfloat;
 		if (!hfile.eof()) EOFerrorR("habitatchgfile");
@@ -1668,7 +1674,7 @@ bool Landscape::inInitialDist(Species* pSpecies, locn loc) {
 void Landscape::deleteDistribution(Species* pSpecies) {
 	// WILL NEED TO SELECT DISTRIBUTION FOR CORRECT SPECIES ...
 	// ... CURRENTLY IT IS THE ONLY ONE ...
-	// ... FOR MULTIPLE SPECIES IT MAY BE BETTER TO USE A DYNAMIC ARRAY FOR 
+	// ... FOR MULTIPLE SPECIES IT MAY BE BETTER TO USE A DYNAMIC ARRAY FOR
 	// SPECIES DISTRIBUTIONS INDEXED BY SPECIES NUMBER, RATHER THAN A VECTOR
 	if (distns[0] != 0) delete distns[0]; distns.clear();
 }
@@ -1948,7 +1954,7 @@ int Landscape::readLandscape(int fileNum, string habfile, string pchfile, string
 						if (existsPatch(p)) {
 							pPatch = findPatch(p);
 							addNewCellToPatch(pPatch, x, y, h);
-							//								addNewCellToPatch(findPatch(p),x,y,h);   
+							//								addNewCellToPatch(findPatch(p),x,y,h);
 						}
 						else {
 							pPatch = newPatch(seq++, p);
@@ -2294,15 +2300,11 @@ int Landscape::readCosts(string fname)
 	costs.close(); costs.clear();
 	return -1;
 }
-double tmpresolCost;		
+double tmpresolCost;
 costs >> maxXcost >> header >> maxYcost >> header >> minLongCost;
 costs >> header >> minLatCost >> header >> tmpresolCost >> header >> NODATACost;
 resolCost = (int) tmpresolCost;
 
-#if !RS_RCPP
-	MemoLine("Loading costs map. Please wait...");
-#endif
-
 	for (int y = maxYcost - 1; y > -1; y--) {
 		for (int x = 0; x < maxXcost; x++) {
 #if RS_RCPP
@@ -2326,17 +2328,26 @@ resolCost = (int) tmpresolCost;
 #endif
 	if (hc < 1 && hc != NODATACost) {
 #if RS_RCPP && !R_CMD
-		Rcpp::Rcout << "Cost map my only contain values of 1 or higher, but found " << fcost << "." << endl;
+		Rcpp::Rcout << "Cost map may only contain values of 1 or higher, but found " << fcost << "." << endl;
 #endif
 		// error - zero / negative cost not allowed
 		costs.close(); costs.clear();
 		return -999;
 	}
 	pCell = findCell(x, y);
 	if (pCell != 0) { // not no-data cell
-		pCell->setCost(hc);
-		if (hc > maxcost) maxcost = hc;
-	}
+	    if (hc > 0){ // only if cost value is  above 0 in a data cell
+	        pCell->setCost(hc);
+		    if (hc > maxcost) maxcost = hc;
+	    } else { // if cost value is below 0
+#if RS_RCPP && !R_CMD
+	    Rcpp::Rcout << "Cost map may only contain values of 1 or higher in habiat cells, but found " << hc << " in cell x: " << x << " y: " << y << "." << endl;
+#endif
+	    // costs.close(); costs.clear(); // not sure if it should stop at this point
+	    // return -999;
+	    }
+
+	} // end not no data vell
 		}
 	}
 #if RS_RCPP
@@ -2347,8 +2358,6 @@ if (costs.eof()) {
 #endif
 }
 else EOFerrorR(fname);
-#else
-MemoLine("Costs map loaded.");
 #endif
 
 costs.close(); costs.clear();
@@ -2373,40 +2382,22 @@ rasterdata CheckRasterFile(string fname)
 	infile.open(fname.c_str());
 	if (infile.is_open()) {
 		infile >> header >> r.ncols;
-#if RSDEBUG
-		DebugGUI(("CheckRasterFile(): header=" + header + " r.ncols=" + Int2Str(r.ncols)
-			).c_str());
-#endif
+
 		if (header != "ncols" && header != "NCOLS") r.errors++;
 		infile >> header >> r.nrows;
-#if RSDEBUG
-		DebugGUI(("CheckRasterFile(): header=" + header + " r.nrows=" + Int2Str(r.nrows)
-			).c_str());
-#endif
+
 		if (header != "nrows" && header != "NROWS") r.errors++;
 		infile >> header >> r.xllcorner;
-#if RSDEBUG
-		DebugGUI(("CheckRasterFile(): header=" + header + " r.xllcorner=" + Float2Str(r.xllcorner)
-			).c_str());
-#endif
+
 		if (header != "xllcorner" && header != "XLLCORNER") r.errors++;
 		infile >> header >> r.yllcorner;
-#if RSDEBUG
-		DebugGUI(("CheckRasterFile(): header=" + header + " r.yllcorner=" + Float2Str(r.yllcorner)
-			).c_str());
-#endif
+
 		if (header != "yllcorner" && header != "YLLCORNER") r.errors++;
 		infile >> header >> r.cellsize;
-#if RSDEBUG
-		DebugGUI(("CheckRasterFile(): header=" + header + " r.cellsize=" + Int2Str(r.cellsize)
-			).c_str());
-#endif
+
 		if (header != "cellsize" && header != "CELLSIZE") r.errors++;
 		infile >> header >> inint;
-#if RSDEBUG
-		DebugGUI(("CheckRasterFile(): header=" + header + " inint=" + Int2Str(inint)
-			).c_str());
-#endif
+
 		if (header != "NODATA_value" && header != "NODATA_VALUE") r.errors++;
 		infile.close();
 		infile.clear();

Landscape.h

@@ -454,14 +454,6 @@ class Landscape{
 	int readCosts(
 		string	// costs file name
 	);
-	// the following four functions are implemented for the GUI version only
-	// in the batch version, they are defined, but empty
-	void setLandMap(void);
-	void drawLandscape(
-		int,	// replicate no.
-		int,	// landscape index number (always 0 if landscape is not dynamic)
-		int		// landscape no.
-	);
 	void resetVisits(void);
 	void outVisits(int,int);	// save SMS path visits map to raster text file
 
@@ -545,13 +537,9 @@ extern RSrandom *pRandom;
 
 #if RSDEBUG
 extern ofstream DEBUGLOG;
-extern void DebugGUI(string);
-Landscape createLandscapeFromCells(vector<Cell*> cells, const landParams& lp, Species sp);
 void testLandscape();
 #endif
 
-extern void MemoLine(string);
-
 #if RS_RCPP
 extern rasterdata landraster,patchraster,spdistraster,costsraster;
 extern void EOFerrorR(string);