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Merging develop into development-guidelines #21

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merged 4 commits into from
Feb 5, 2024
Merged

Merging develop into development-guidelines #21

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d934fda
Merge branch 'develop' into cmake_batch
TheoPannetier Feb 1, 2024
04a1b92
rm all ref to Version.h
TheoPannetier Feb 2, 2024
6792879
Merge branch 'development-guidelines' into develop
JetteReeg Feb 5, 2024
c3b0a4c
fix missing include fields
TheoPannetier Feb 5, 2024
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3 changes: 0 additions & 3 deletions Community.h
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Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,6 @@ Last updated: 25 June 2021 by Anne-Kathleen Malchow
#include <vector>
#include <algorithm>
using namespace std;
#if RS_RCPP
#include "../Version.h"
#endif

#include "SubCommunity.h"
#include "Landscape.h"
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17 changes: 12 additions & 5 deletions Landscape.cpp
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Expand Up @@ -2281,11 +2281,18 @@ int Landscape::readCosts(string fname)
#else
if (header != "ncols" && header != "NCOLS") {
#endif
costs.close(); costs.clear();
return -1;
}
costs >> maxXcost >> header >> maxYcost >> header >> minLongCost;
costs >> header >> minLatCost >> header >> resolCost >> header >> NODATACost;

// MessageDlg("The selected file is not a raster.",
// MessageDlg("Header problem in import_CostsLand()",
// mtError, TMsgDlgButtons() << mbRetry,0);
costs.close(); costs.clear();
return -1;
}
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...");
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8 changes: 0 additions & 8 deletions Model.h
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Expand Up @@ -49,14 +49,6 @@ Last updated: 26 October 2021 by Steve Palmer
#include <sys/types.h>
#include <sys/stat.h>

#if RS_RCPP
#include "../Version.h"
#endif

//#if !RS_RCPP && R_CMD
//#include "../../Batch/Version.h"
//#endif

#include "Parameters.h"
#include "Landscape.h"
#include "Community.h"
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7 changes: 0 additions & 7 deletions Parameters.h
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Expand Up @@ -60,13 +60,6 @@ Last updated: 25 June 2021 by Steve Palmer
#include <stdlib.h>
#include <vector>
using namespace std;
#if RS_RCPP
#include "../Version.h"
#endif

//#if !RS_RCPP && R_CMD
//#include "../../Batch/Version.h"
//#endif

#include "RSrandom.h"

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8 changes: 0 additions & 8 deletions Patch.h
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Expand Up @@ -68,14 +68,6 @@ Last updated: 25 June 2021 by Steve Palmer
#include <vector>
using namespace std;

#if RS_RCPP
#include "../Version.h"
#endif

//#if !RS_RCPP && R_CMD
//#include "../../Batch/Version.h"
//#endif

#include "Parameters.h"
#include "Cell.h"
#include "Species.h"
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13 changes: 0 additions & 13 deletions RSrandom.h
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Expand Up @@ -41,27 +41,14 @@ Last updated: 12 January 2021 by Steve Palmer
#include <cassert>
#include "Utils.h"

#if RS_RCPP
#include "../Version.h"
#endif

//#if !RS_RCPP && R_CMD
//#include "../../Batch/Version.h"
//#endif

using namespace std;

#if RSDEBUG
extern ofstream DEBUGLOG;
#endif



#if !RS_RCPP

//--------------- 2.) New version of RSrandom.cpp


#include <cmath>
#include <random>
#if !LINUX_CLUSTER
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4 changes: 0 additions & 4 deletions RandomCheck.h
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Expand Up @@ -28,10 +28,6 @@
#include <fstream>
using namespace std;

#if RS_RCPP
#include "../Version.h"
#endif

#include "Parameters.h"
#include "RSrandom.h"

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8 changes: 2 additions & 6 deletions Species.h
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Expand Up @@ -31,9 +31,9 @@
The class holds all the demographic and dispersal parameters of the species.

For full details of RangeShifter, please see:
Bocedi G., Palmer S.C.F., Pe’er G., Heikkinen R.K., Matsinos Y.G., Watts K.
Bocedi G., Palmer S.C.F., Pe’er G., Heikkinen R.K., Matsinos Y.G., Watts K.
and Travis J.M.J. (2014). RangeShifter: a platform for modelling spatial
eco-evolutionary dynamics and species’ responses to environmental changes.
eco-evolutionary dynamics and species’ responses to environmental changes.
Methods in Ecology and Evolution, 5, 388-396. doi: 10.1111/2041-210X.12162

Authors: Greta Bocedi & Steve Palmer, University of Aberdeen
Expand All @@ -45,10 +45,6 @@
#ifndef SpeciesH
#define SpeciesH

#if RS_RCPP
#include "../Version.h"
#endif

#include "Parameters.h"

// structures for demographic parameters
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8 changes: 2 additions & 6 deletions SubCommunity.h
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Expand Up @@ -32,9 +32,9 @@ each Species represented in the simulation.
CURRENTLY the number of Populations withn a SubCommunity is LIMITED TO ONE.

For full details of RangeShifter, please see:
Bocedi G., Palmer S.C.F., Pe’er G., Heikkinen R.K., Matsinos Y.G., Watts K.
Bocedi G., Palmer S.C.F., Pe’er G., Heikkinen R.K., Matsinos Y.G., Watts K.
and Travis J.M.J. (2014). RangeShifter: a platform for modelling spatial
eco-evolutionary dynamics and species’ responses to environmental changes.
eco-evolutionary dynamics and species’ responses to environmental changes.
Methods in Ecology and Evolution, 5, 388-396. doi: 10.1111/2041-210X.12162

Authors: Greta Bocedi & Steve Palmer, University of Aberdeen
Expand All @@ -50,10 +50,6 @@ Last updated: 26 October 2021 by Steve Palmer
#include <algorithm>
using namespace std;

#if RS_RCPP
#include "../Version.h"
#endif

#include "Parameters.h"
#include "Landscape.h"
#include "Population.h"
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