fix merge conflict

CONTRIBUTING.md

@@ -42,7 +42,7 @@ Anyone who whishes to make changes to RangeShifter's code, including regular dev
 
 ![](branches.png)
 
-*Check out the [Git cheatsheet](https://github.com/RangeShifter/RScore/blob/development-guidelines/git_cheatsheet.md) for a reminder on the main git commands*
+*Check out the [Git cheatsheet](https://github.com/RangeShifter/RScore/blob/main/git_cheatsheet.md) for a reminder on the main git commands*
 
 This policy applies to RScore and all three RangeShifter interfaces.
 RangeShifter uses the following branching structure:
@@ -59,12 +59,12 @@ In the meantime, we encourage contributors to work in small and frequent commits
 
 ### Contributing to RangeShifter core code
 
-Any changes regarding the RangeShifter core code should be done in this repository and can afterwards be synced with all interfaces using the git subtree feature (see [Git subtree](https://github.com/RangeShifter/RScore/tree/development-guidelines#usage-git-subtrees) section in the README). 
+Any changes regarding the RangeShifter core code should be done in this repository and can afterwards be synced with all interfaces using the git subtree feature (see [Git subtree](https://github.com/RangeShifter/RScore/tree/main?tab=readme-ov-file#usage-git-subtree) section in the README). 
 
 #### Bugs
 
 To report a bug, please [open an issue](https://github.com/RangeShifter/RangeShiftR-package-dev/issues/new), using the Bug Report template. 
-Please do check if a related issue has already open on one of the other interfaces ([here](https://github.com/RangeShifter/RangeShifter_batch/issues) for the batch interface or [here](https://github.com/RangeShifter/RangeShiftR-package-dev) for the R package interface).
+Please do check if a related issue has already open on one of the other interfaces ([here](https://github.com/RangeShifter/RangeShifter_batch-dev/issues) for the batch interface or [here](https://github.com/RangeShifter/RangeShiftR-package-dev) for the R package interface).
 To propose a bug fix (thank you!!), please create and work on your own branch or fork, from either `main` or `develop` (preferred), and open a pull request when your fix is ready to be merged into the original branch.
 
 Maintainers will review the pull request, possibly request changes, and eventually integrate the bug fix into RScore, and update the subtrees to bring the fix to all interfaces.

Landscape.cpp

@@ -1283,6 +1283,9 @@ 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();
@@ -1294,8 +1297,8 @@ int Landscape::readLandChange(int filenum, bool costs)
 			}
 		}
 	}
-			}
-		}
+			} // for x
+		} // for y
 #if RS_RCPP
 		hfile >> hfloat;
 		if (!hfile.eof()) EOFerrorR("habitatchgfile");
@@ -1421,6 +1424,9 @@ 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();
@@ -1432,8 +1438,8 @@ int Landscape::readLandChange(int filenum, bool costs)
 				}
 			}
 		}
-			}
-		}
+			} // end x
+		} // end y
 #if RS_RCPP
 		hfile >> hfloat;
 		if (!hfile.eof()) EOFerrorR("habitatchgfile");
@@ -1658,7 +1664,7 @@ 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();
 }
@@ -1938,7 +1944,7 @@ 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);
@@ -2288,7 +2294,7 @@ 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;
@@ -2316,17 +2322,26 @@ 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

Main.cpp

@@ -73,7 +73,14 @@ int _tmain(int argc, _TCHAR* argv[])
 	return 1;
 # else
 	assert(0.1 > 0.0); // assert does run correctly
-	run_unit_tests();
+	try
+	{
+		run_unit_tests();
+	}
+	catch (const std::exception& e)
+	{
+		cerr << endl << "Error: " << e.what() << endl;
+	}
 	cout << "All tests have completed." << endl;
 	return 0; // if tests succeed, we are happy
 # endif // NDEBUG

Model.cpp

@@ -737,7 +737,7 @@ int RunModel(Landscape* pLandscape, int seqsim)
 
 }
 
-#if LINUX_CLUSTER || RS_RCPP 
+#if LINUX_CLUSTER || RS_RCPP
 // Check whether a specified directory path exists
 bool is_directory(const char* pathname) {
 	struct stat info;
@@ -1645,23 +1645,40 @@ void OutParameters(Landscape* pLandscape)
 
 	if (trfr.moveModel) {
 		string plusmating = "+ mating requirements";
-		ssteps = pSpecies->getSteps(0, 0);
-
-		outPar << "MIN. No. OF STEPS:\t " << ssteps.minSteps << endl;
-		outPar << "MAX. No. OF STEPS:\t ";
-		if (ssteps.maxSteps == 99999999) outPar << "not applied" << endl;
-		else outPar << ssteps.maxSteps << endl;
 
 		if (sett.sexDep) {
 			nsexes = 2;
 			outPar << sexdept << "yes" << endl;
 			if (sett.stgDep) {
 				nstages = sstruct.nStages;
 				outPar << stgdept << "yes" << endl;
+				for (int i = 0; i < nstages; i++) {
+				    if (dem.stageStruct && nstages > 1) outPar << "stage " << i << ": " << endl;
+				    for (int sx = 0; sx < nsexes; sx++) {
+				        if (sx == 0) outPar << "FEMALES:" << endl;
+				        else outPar << "MALES:" << endl;
+				        ssteps = pSpecies->getSteps(i, sx);
+
+				        outPar << "MIN. No. OF STEPS:\t " << ssteps.minSteps << endl;
+				        outPar << "MAX. No. OF STEPS:\t ";
+				        if (ssteps.maxSteps == 99999999) outPar << "not applied" << endl;
+				        else outPar << ssteps.maxSteps << endl;
+				    }
+				}
 			}
 			else { // !sett.stgDep
 				nstages = 1;
 				outPar << stgdept << "no" << endl;
+				for (int sx = 0; sx < nsexes; sx++) {
+				    if (sx == 0) outPar << "FEMALES:" << endl;
+				    else outPar << "MALES:" << endl;
+				    ssteps = pSpecies->getSteps(0, sx);
+
+				    outPar << "MIN. No. OF STEPS:\t " << ssteps.minSteps << endl;
+				    outPar << "MAX. No. OF STEPS:\t ";
+				    if (ssteps.maxSteps == 99999999) outPar << "not applied" << endl;
+				    else outPar << ssteps.maxSteps << endl;
+				}
 			}
 		}
 		else { // !sett.sexDep
@@ -1670,10 +1687,25 @@ void OutParameters(Landscape* pLandscape)
 			if (sett.stgDep) {
 				nstages = sstruct.nStages;
 				outPar << stgdept << "yes" << endl;
+				for (int i = 0; i < nstages; i++) {
+				    if (dem.stageStruct && nstages > 1) outPar << "stage " << i << ": " << endl;
+				    ssteps = pSpecies->getSteps(i, 0);
+
+				    outPar << "MIN. No. OF STEPS:\t " << ssteps.minSteps << endl;
+				    outPar << "MAX. No. OF STEPS:\t ";
+				    if (ssteps.maxSteps == 99999999) outPar << "not applied" << endl;
+				    else outPar << ssteps.maxSteps << endl;
+				}
 			}
 			else { // !sett.stgDep
 				nstages = 1;
 				outPar << stgdept << "no" << endl;
+				ssteps = pSpecies->getSteps(0, 0);
+
+				outPar << "MIN. No. OF STEPS:\t " << ssteps.minSteps << endl;
+				outPar << "MAX. No. OF STEPS:\t ";
+				if (ssteps.maxSteps == 99999999) outPar << "not applied" << endl;
+				else outPar << ssteps.maxSteps << endl;
 			}
 		}
 		for (int sx = 0; sx < nsexes; sx++) {

README.md

@@ -2,7 +2,7 @@
 
 This repo contains the core simulation code for RangeShifter v2.0 and is not meant to be compiled or run on its own.
 
-<img src="https://github.com/RangeShifter/RScore/blob/development-guidelines/RScore_logo.png" align="right" height = 200/>
+<img src="https://github.com/RangeShifter/RScore/blob/main/RScore_logo.png" align="right" height = 200/>
 
 If you are only interested in using RangeShifter, you can ignore this and head to the repo of one of the interfaces:
 
@@ -46,11 +46,15 @@ git subtree pull --prefix RangeShiftR/src/RScore RScore main
 
 ### Pushing new changes to RScore
 
-We haven't yet found a way to push new changes made in a RScore subfolder back into the RScore repo. This is why we ask that contributions are made directly inside the RScore repo.
+```bash
+git subtree push --prefix <path_to_RScore_subfolder> RScore <branch>
+```
 
-If you know how to do this, please drop us a line!
+e.g., from RangeShifter-batch's `main` to RScore's `main`:
 
-Alternatively, if you have already made changes on the subfolder, you could copy its contents into a new branch in RScore, then open a pull request.
+```bash
+git subtree push --prefix src/RScore RScore main
+```
 
 ### Switching the subfolder to a new branch
 

RSrandom.cpp

@@ -1,30 +1,30 @@
 /*----------------------------------------------------------------------------
- *	
- *	Copyright (C) 2020 Greta Bocedi, Stephen C.F. Palmer, Justin M.J. Travis, Anne-Kathleen Malchow, Damaris Zurell 
- *	
+ *
+ *	Copyright (C) 2020 Greta Bocedi, Stephen C.F. Palmer, Justin M.J. Travis, Anne-Kathleen Malchow, Damaris Zurell
+ *
  *	This file is part of RangeShifter.
- *	
+ *
  *	RangeShifter is free software: you can redistribute it and/or modify
  *	it under the terms of the GNU General Public License as published by
  *	the Free Software Foundation, either version 3 of the License, or
  *	(at your option) any later version.
- *	
+ *
  *	RangeShifter is distributed in the hope that it will be useful,
  *	but WITHOUT ANY WARRANTY; without even the implied warranty of
  *	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  *	GNU General Public License for more details.
- *	
+ *
  *	You should have received a copy of the GNU General Public License
  *	along with RangeShifter. If not, see <https://www.gnu.org/licenses/>.
- *	
+ *
  --------------------------------------------------------------------------*/
- 
+
 
 #include "RSrandom.h"
 
 //--------------- 2.) New version of RSrandom.cpp
 
-#if !RS_RCPP 
+#if !RS_RCPP
 
 #if RSDEBUG
 #include "Parameters.h"
@@ -113,7 +113,7 @@ int RSrandom::Poisson(double mean)
 //--------------------------------------------------------------------------------------------------
 //--------------------------------------------------------------------------------------------------
 
-#else // if RS_RCPP 
+#else // if RS_RCPP
 
 //--------------- 3.) R package version of RSrandom.cpp
 
@@ -257,11 +257,11 @@ int RSrandom::Poisson(double mean)
 #endif // RS_RCPP
 
 
-#if RSDEBUG
+#if RSDEBUG && !RS_RCPP
 	void testRSrandom() {
 
 		{
-			// Bernoulli distribution 
+			// Bernoulli distribution
 			// Abuse cases
 			assert_error("Bernoulli's p cannot be negative.\n", []{
 				RSrandom rsr;

Species.cpp

@@ -116,11 +116,11 @@ Species::Species(void)
 
 	// initialise settlement parameters
 	stgDepSett = false; sexDepSett = false; indVarSett = false;
-	minSteps = 0; maxSteps = 99999999;
+
 	for (int i = 0; i < NSTAGES; i++) {
 		for (int j = 0; j < NSEXES; j++) {
 			densDepSett[i][j] = false; wait[i][j] = false; go2nbrLocn[i][j] = false; findMate[i][j] = false;
-			maxStepsYr[i][j] = 99999999;
+			maxStepsYr[i][j] = 99999999; 	minSteps[i][j] = 0; maxSteps[i][j] = 99999999;
 			s0[i][j] = 1.0; alphaS[i][j] = 0.0; betaS[i][j] = 1.0;
 		}
 	}
@@ -1262,24 +1262,28 @@ settleRules Species::getSettRules(short stg, short sex) {
 }
 
 void Species::setSteps(const short stg, const short sex, const settleSteps s) {
-	if (stg == 0 && sex == 0) {
-		if (s.minSteps >= 0) minSteps = s.minSteps;
-		else minSteps = 0;
-		if (s.maxSteps >= 1) maxSteps = s.maxSteps;
-		else maxSteps = 99999999;
-	}
 	if (stg >= 0 && stg < NSTAGES && sex >= 0 && sex < NSEXES) {
 		if (s.maxStepsYr >= 1) maxStepsYr[stg][sex] = s.maxStepsYr;
 		else maxStepsYr[stg][sex] = 99999999;
+		if (s.minSteps >= 0) minSteps[stg][sex] = s.minSteps;
+		else minSteps[stg][sex] = 0;
+		if (s.maxSteps >= 1) maxSteps[stg][sex] = s.maxSteps;
+		else maxSteps[stg][sex] = 99999999;
 	}
 }
 
 settleSteps Species::getSteps(short stg, short sex) {
 	settleSteps s;
-	s.minSteps = minSteps;
-	s.maxSteps = maxSteps;
-	if (stg >= 0 && stg < NSTAGES && sex >= 0 && sex < NSEXES) s.maxStepsYr = maxStepsYr[stg][sex];
-	else s.maxStepsYr = 99999999;
+	if (stg >= 0 && stg < NSTAGES && sex >= 0 && sex < NSEXES) {
+	    s.maxStepsYr = maxStepsYr[stg][sex];
+	    s.minSteps = minSteps[stg][sex];
+	    s.maxSteps = maxSteps[stg][sex];
+	}
+	else {
+	    s.maxStepsYr = 99999999;
+	    s.minSteps = 0;
+	    s.maxSteps = 99999999;
+	}
 	return s;
 }
 

Species.h

@@ -701,8 +701,8 @@ class Species {
 	bool wait[NSTAGES][NSEXES];				// wait to continue moving next season (stage-structured model only)
 	bool go2nbrLocn[NSTAGES][NSEXES];	// settle in neighbouring cell/patch if available (ditto)
 	bool findMate[NSTAGES][NSEXES];
-	int minSteps;     								// minimum no. of steps
-	int maxSteps;											// maximum total no. of steps
+	int minSteps[NSTAGES][NSEXES];     								// minimum no. of steps
+	int maxSteps[NSTAGES][NSEXES];											// maximum total no. of steps
 	int maxStepsYr[NSTAGES][NSEXES]; 	// maximum no. of steps in any one dispersal period
 	float	s0[NSTAGES][NSEXES];				// maximum settlement probability
 	float alphaS[NSTAGES][NSEXES];		// slope of the settlement reaction norm to density