Add 'src/RScore/' from commit '3764f7aaaaf9a6624af0037511077a42bbb6ad4e'

git-subtree-dir: src/RScore
git-subtree-mainline: d8d1f6d
git-subtree-split: 3764f7a

src/RScore/.gitignore

@@ -0,0 +1,87 @@
+.gitignore
+#README.md
+
+# CodeLite
+/.build-debug/
+/Debug/
+/Release/
+/RNG_test/
+.codelite/
+compile_commands.json
+Makefile
+.build-release/
+build-Release/
+*.project
+*.workspace
+*.mk
+*.tags
+
+# Hidden source
+/RangeShiftR/src/.*
+
+# Windows files
+/RangeShiftR/src/*.dll
+
+# History files
+.Rhistory
+.Rapp.history
+
+# RStudio files
+.Rproj.user/
+/RangeShiftR/.Rproj.user/
+#/RangeShiftR/RangeShiftR.Rproj
+/RangeShiftR/Read-and-delete-me
+/RangeShiftR/.Rhistory
+#/RangeShiftR/.Rbuildignore
+
+# Session Data files
+.RData
+tags
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+*.tar.gz
+/RangeShiftR/src/*.o
+/RangeShiftR/src/RangeShiftR.so
+
+
+# Windows files
+/RangeShiftR/src/*.dll
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# Output from Rcpp compile.attributes()
+#/RangeShiftR/R/RcppExports.R
+#/RangeShiftR/src/RcppExports.cpp
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+#/RangeShiftR/man/
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# compilation files
+*.o
+
+# Visual Studio
+.vs/
+out/

src/RScore/CMakeLists.txt

@@ -0,0 +1,11 @@
+# Config file for compilation with CMake
+# Only relevant for Batch mode, but this file needs to live in the RScore folder
+
+add_library(RScore Species.cpp Cell.cpp Community.cpp FractalGenerator.cpp Genome.cpp Individual.cpp Landscape.cpp Model.cpp Parameters.cpp Patch.cpp Population.cpp RandomCheck.cpp RSrandom.cpp SubCommunity.cpp)
+
+# pass config definitions to compiler
+if(CMAKE_SYSTEM_NAME STREQUAL "Linux" OR CMAKE_SYSTEM_NAME STREQUAL "Darwin")
+	target_compile_definitions(RScore PRIVATE "RSDEBUG" "RSWIN64" "LINUX_CLUSTER")
+else() # Windows
+	target_compile_definitions(RScore PRIVATE "RSDEBUG" "RSWIN64")
+endif()

src/RScore/Cell.cpp

@@ -0,0 +1,237 @@
+/*----------------------------------------------------------------------------
+ *	
+ *	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 "Cell.h"
+
+//---------------------------------------------------------------------------
+
+//---------------------------------------------------------------------------
+
+// Cell functions
+
+Cell::Cell(int xx,int yy,intptr patch,int hab)
+{
+x = xx; y = yy;
+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;
+}
+
+Cell::Cell(int xx,int yy,intptr patch,float hab)
+{
+x = xx; y = yy;
+pPatch = patch;
+envVal = 1.0; // default - no effect of any gradient
+envDev = eps = 0.0;
+habitats.push_back(hab);
+visits = 0;
+smsData = 0;
+}
+
+Cell::~Cell() {
+#if RSDEBUG
+//DEBUGLOG << "Cell::~Cell(): this = " << this << " smsData = " << smsData << endl;
+#endif
+habIxx.clear();
+habitats.clear();
+if (smsData != 0) {
+	if (smsData->effcosts != 0) delete smsData->effcosts;
+	delete smsData;       
+}
+#if RSDEBUG
+//DEBUGLOG << "Cell::~Cell(): deleted" << endl;
+#endif
+}
+
+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);
+}
+
+void Cell::changeHabIndex(short ix,short hx) {
+if (ix >= 0 && ix < (short)habIxx.size() && hx >= 0) habIxx[ix] = hx;
+else habIxx[ix] = 0;
+}
+
+int Cell::getHabIndex(int ix) {
+if (ix < 0 || ix >= (int)habIxx.size())
+	// nodata cell OR should not occur, but treat as such
+	return -1;
+else return habIxx[ix];
+}
+int Cell::nHabitats(void) {
+int nh = (int)habIxx.size();
+if ((int)habitats.size() > nh) nh = (int)habitats.size();
+return nh;
+}
+
+void Cell::setHabitat(float q) {
+if (q >= 0.0 && q <= 100.0) habitats.push_back(q);
+else habitats.push_back(0.0);
+}
+
+float Cell::getHabitat(int ix) {
+if (ix < 0 || ix >= (int)habitats.size())
+	// nodata cell OR should not occur, but treat as such
+	return -1.0;
+else return habitats[ix];
+}
+
+void Cell::setPatch(intptr p) {
+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;
+}
+
+locn Cell::getLocn(void) { locn q; q.x = x; q.y = y; return q; }
+
+void Cell::setEnvDev(float d) { envDev = d; }
+
+float Cell::getEnvDev(void) { return envDev; }
+
+void Cell::setEnvVal(float e) {
+if (e >= 0.0) envVal = e;
+}
+
+float Cell::getEnvVal(void) { return envVal; }
+
+void Cell::updateEps(float ac,float randpart) {
+eps = eps*ac + randpart;
+}
+
+float Cell::getEps(void) { return eps; }
+
+// Functions to handle costs for SMS
+
+int Cell::getCost(void) {
+int c;
+if (smsData == 0) c = 0; // costs not yet set up
+else c = smsData->cost;
+return c;
+}
+
+void Cell::setCost(int c) {
+if (smsData == 0) {
+	smsData = new smscosts;
+	smsData->effcosts = 0;
+}
+smsData->cost = c;
+}
+
+// Reset the cost and the effective cost of the cell
+void Cell::resetCost(void) {
+if (smsData != 0) { resetEffCosts(); delete smsData; }
+smsData = 0;
+}
+
+array3x3f Cell::getEffCosts(void) {
+array3x3f a;
+if (smsData == 0 || smsData->effcosts == 0) { // effective costs have not been calculated
+	for (int i = 0; i < 3; i++) {
+		for (int j = 0; j < 3; j++) {
+			a.cell[i][j] = -1.0;
+		}
+	}
+}
+else
+	a = *smsData->effcosts;
+return a;
+}
+
+void Cell::setEffCosts(array3x3f a) {     
+if (smsData->effcosts == 0) smsData->effcosts = new array3x3f;
+*smsData->effcosts = a;
+}
+
+// Reset the effective cost, but not the cost, of the cell
+void Cell::resetEffCosts(void) {
+if (smsData != 0) {
+	if (smsData->effcosts != 0) {
+		delete smsData->effcosts;
+		smsData->effcosts = 0;
+	}
+}
+}
+
+void Cell::resetVisits(void) { visits = 0; }
+void Cell::incrVisits(void) { visits++; }
+unsigned long int Cell::getVisits(void) { return visits; }
+
+//---------------------------------------------------------------------------
+
+// Initial species distribution cell functions
+
+DistCell::DistCell(int xx,int yy) {
+x = xx; y = yy; initialise = false;
+}
+
+DistCell::~DistCell() {
+
+}
+
+void DistCell::setCell(bool init) {
+initialise = init;
+}
+
+bool DistCell::toInitialise(locn loc) {
+if (loc.x == x && loc.y == y) return initialise;
+else return false;
+}
+
+bool DistCell::selected(void) { return initialise; }
+
+locn DistCell::getLocn(void) {
+locn loc; loc.x = x; loc.y = y; return loc;
+}
+
+//---------------------------------------------------------------------------
+//---------------------------------------------------------------------------
+//---------------------------------------------------------------------------
+
+
+
+