PR for checking conflicts merging spatial_demography into transloc_new_genetics_spatial_demog_merge

RangeShiftR/src/Cell.cpp → Cell.cpp

@@ -1,34 +1,35 @@
 /*----------------------------------------------------------------------------
- *	
- *	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/>.
- *	
+ *
  --------------------------------------------------------------------------*/
- 
- 
+
+
 //---------------------------------------------------------------------------
 #if RS_EMBARCADERO
 #pragma hdrstop
 #endif
 
 #include "Cell.h"
+#include "algorithm"
 
 //---------------------------------------------------------------------------
-#if RS_EMBARCADERO 
+#if RS_EMBARCADERO
 #pragma package(smart_init)
 #endif
 
@@ -78,8 +79,11 @@ habIxx.clear();
 habitats.clear();
 if (smsData != 0) {
 	if (smsData->effcosts != 0) delete smsData->effcosts;
-	delete smsData;       
+	delete smsData;
 }
+#if SPATIALDEMOG
+demoScalings.clear();
+#endif
 #if RSDEBUG
 //DEBUGLOG << "Cell::~Cell(): deleted" << endl;
 #endif
@@ -171,7 +175,7 @@ if (period == 0 || period == 1) m = mort[period];
 return m;
 }
 
-#endif // SPATIALMORT 
+#endif // SPATIALMORT
 
 // Functions to handle costs for SMS
 
@@ -210,7 +214,7 @@ else
 return a;
 }
 
-void Cell::setEffCosts(array3x3f a) {     
+void Cell::setEffCosts(array3x3f a) {
 if (smsData->effcosts == 0) smsData->effcosts = new array3x3f;
 *smsData->effcosts = a;
 }
@@ -236,7 +240,26 @@ unsigned long int Cell::getVisits(void) { return visits; }
 void Cell::setDamage(DamageLocn *pDmg) { pDamage = pDmg; }
 DamageLocn* Cell::getDamage(void) { return pDamage; }
 
-#endif // RS_CONTAIN 
+#endif // RS_CONTAIN
+
+#if SPATIALDEMOG
+
+void Cell::addchgDemoScaling(std::vector<float> ds) {
+	std::for_each(ds.begin(), ds.end(), [](float& perc){ if(perc < 0.0 || perc > 100.0) perc=100; });
+	demoScalings.push_back(ds);
+	return;
+}
+
+std::vector<float> Cell::getDemoScaling(short chgyear) {
+	if (chgyear < 0 || chgyear >= (int)demoScalings.size()) {
+		std::vector<float> ret(1, -1);
+		return ret;
+	}
+	else return demoScalings[chgyear];
+}
+
+#endif // SPATIALDEMOG
+
 
 //---------------------------------------------------------------------------
 

RangeShiftR/src/Cell.h → Cell.h

@@ -45,7 +45,11 @@ Last updated: 14 January 2021 by Steve Palmer
 #ifndef CellH
 #define CellH
 
+#if SPATIALDEMOG
+#include <algorithm>
+#endif
 #include <vector>
+
 using namespace std;
 
 #include "Parameters.h"
@@ -137,7 +141,12 @@ class Cell{
 //	unsigned int getDamage(void);
 	void setDamage(DamageLocn*);
 	DamageLocn* getDamage(void);
-#endif // RS_CONTAIN 
+#endif // RS_CONTAIN
+#if SPATIALDEMOG
+	void addchgDemoScaling(std::vector<float>);
+	void setDemoScaling(std::vector<float>, short);
+	std::vector<float> getDemoScaling(short);
+#endif // SPATIALDEMOG 
 
 private:
 	int x,y;			// cell co-ordinates
@@ -161,6 +170,9 @@ class Cell{
 		// NB initially, habitat codes are loaded, then converted to index nos.
 		//    once landscape is fully loaded
 	vector <float> habitats;	// habitat proportions (rasterType=1) or quality (rasterType=2)
+#if SPATIALDEMOG
+	std::vector<std::vector<float>> demoScalings;	// demographic scaling layers (only if rasterType==2)
+#endif
 };
 
 //---------------------------------------------------------------------------
@@ -193,6 +205,10 @@ class DistCell{
 extern void DebugGUI(string);
 #endif
 
+#if SPATIALDEMOG
+extern short nDSlayer;
+#endif // SPATIALDEMOG
+
 //---------------------------------------------------------------------------
 
 #endif

RangeShiftR/src/Community.cpp → Community.cpp

@@ -2644,7 +2644,7 @@ return fileOK;
 #endif
 
 #if RS_RCPP && !R_CMD
-Rcpp::IntegerMatrix Community::addYearToPopList(int rep, int yr) {  // TODO: define new simparams to control start and interval of output
+Rcpp::IntegerMatrix Community::addYearToPopList(int rep, int yr) {  // TODO: define new simparams to control type as well as start and interval of output
 
 	landParams ppLand = pLandscape->getLandParams();
 	Rcpp::IntegerMatrix pop_map_year(ppLand.dimY,ppLand.dimX);
@@ -2663,19 +2663,22 @@ Rcpp::IntegerMatrix Community::addYearToPopList(int rep, int yr) {  // TODO: def
 				pop_map_year(ppLand.dimY-1-y,x) = NA_INTEGER;
 			} else {
 				patch = pCell->getPatch();
-				if (patch == 0) { // matrix cell
-					pop_map_year(ppLand.dimY-1-y,x) = 0;
-				}
-				else{
+				if (patch != 0) {
 					pPatch = (Patch*)patch;
-					subcomm = pPatch->getSubComm();
-					if (subcomm == 0) { // check if sub-community exists
+					if (pPatch->getSeqNum() == 0) { // cell in matrix patch
 						pop_map_year(ppLand.dimY-1-y,x) = 0;
-					} else {
-						pSubComm = (SubCommunity*)subcomm;
-						pop = pSubComm->getPopStats();
-						//pop_map_year(ppLand.dimY-1-y,x) = pop.nInds; // use indices like this because matrix gets transposed upon casting it into a raster on R-level
-						pop_map_year(ppLand.dimY-1-y,x) = pop.nAdults;
+					}
+					else{
+						pPatch = (Patch*)patch;
+						subcomm = pPatch->getSubComm();
+						if (subcomm == 0) { // check if sub-community exists
+							pop_map_year(ppLand.dimY-1-y,x) = 0;
+						} else {
+							pSubComm = (SubCommunity*)subcomm;
+							pop = pSubComm->getPopStats();
+							pop_map_year(ppLand.dimY-1-y,x) = pop.nInds; // use indices like this because matrix gets transposed upon casting it into a raster on R-level
+							//pop_map_year(ppLand.dimY-1-y,x) = pop.nAdults;
+						}
 					}
 				}
 			}

RangeShiftR/src/Community.h → Community.h

@@ -58,7 +58,7 @@ Last updated: 25 June 2021 by Anne-Kathleen Malchow
 #include <algorithm>
 using namespace std;
 
-#include "Version.h"
+#include "../Version.h"
 #include "SubCommunity.h"
 #include "Landscape.h"
 #include "Patch.h"