Panmictic model now working.

include/Makefile

@@ -180,6 +180,7 @@ endif
 # do it this way to help Makefile dependencies work
 ECOLIBS=$(ECOLAB_HOME)/lib/libecolab$(ECOLIBS_EXT).a
 
+# why is boost_thread required here?
 LIBS+=-L$(ECOLAB_HOME)/lib -lecolab$(ECOLIBS_EXT) -lboost_thread
 FLAGS+=-I. -I$(ECOLAB_HOME)/include -DHASH_TCL_hash
 

models/ecolab_model.cc

@@ -102,7 +102,7 @@ void EcolabPoint::condense(const array<bool>& mask, size_t mask_true)
 void ModelData::condense(const array<bool>& mask, size_t mask_true)   /* remove extinct species */
 {
   auto map = enumerate( mask );
-  auto mask_off = mask[ interaction.row ] && mask[ interaction.col ];
+  array<bool> mask_off = mask[ interaction.row ] && mask[ interaction.col ];
 
   create = pack(create, mask, mask_true); 
   species = pack(species, mask, mask_true); 
@@ -124,9 +124,9 @@ void PanmicticModel::condense()
 {
   auto mask=density != 0;
   size_t mask_true=sum(mask);
-  if (species.size()==mask_true) return; /* no change ! */
-  EcolabPoint::condense(mask, mask_true);
+  if (mask.size()==mask_true) return; /* no change ! */
   ModelData::condense(mask,mask_true);
+  EcolabPoint::condense(mask, mask_true);
 }
 
 

models/ecolab_model.h

@@ -16,10 +16,8 @@ using classdesc::Object;
 
 struct ConnectionPlot: public Object<ConnectionPlot, CairoSurface>
 {
-  const array<int>& density;
-  const sparse_mat& connections;
-  ConnectionPlot(const array<int>& density, const sparse_mat& connections):
-    density(density), connections(connections) {}
+  array<int> density;
+  sparse_mat connections;
   bool redraw(int x0, int y0, int width, int height) override;
   void requestRedraw() const {if (surface) surface->requestRedraw();}
 };
@@ -31,7 +29,7 @@ struct ModelData
   array<double> repro_rate, mutation, migration;
   sparse_mat interaction;
   sparse_mat_graph foodweb;
-  unsigned long long tstep=1, last_mut_tstep=0, last_mig_tstep=0;
+  unsigned long long tstep=0, last_mut_tstep=0, last_mig_tstep=0;
   //mutation parameters
   float sp_sep=0.1, mut_max=0, repro_min=0, repro_max=1, odiag_min=0, odiag_max=1;
 
@@ -41,7 +39,7 @@ struct ModelData
         species=pcoord(nsp);
 
       // bugger you, g++!
-      if (!/*model_data::*/create.size()) /*model_data::*/create.resize(species.size(),0);
+      if (!/*ModelData::*/create.size()) /*ModelData::*/create.resize(species.size(),0);
       if (!mutation.size()) mutation.resize(species.size(),0);
       if (!migration.size()) migration.resize(species.size(),0);
     }
@@ -66,7 +64,12 @@ struct EcolabPoint
 
 struct PanmicticModel: public ModelData, public EcolabPoint
 {
-  ConnectionPlot connectionPlot{density,interaction};
+  ConnectionPlot connectionPlot;
+  void updateConnectionPlot() {
+    connectionPlot.density=density;
+    connectionPlot.connections=interaction;
+    connectionPlot.requestRedraw();
+  }
   void makeConsistent() {ModelData::makeConsistent(density.size());}
   void generate(unsigned niter);
   void generate() {generate(1);}

models/default_ecolab_model.py → models/panmictic_ecolab.py

@@ -1,4 +1,4 @@
-from ecolab_model import ecolab
+from ecolab_model import panmictic_ecolab as ecolab
 from random import random
 # initial number of species
 nsp=100
@@ -33,19 +33,20 @@ def randomList(num, min, max):
 from ecolab import ecolabHome
 connectionPlot=Tk()
 connectionPlot.eval('load '+ecolabHome()+'/lib/ecolab.so')
-connectionPlot.eval('image create cairoSurface connectionCanvas -surface ecolab_model ecolab.connectionPlot')
+connectionPlot.eval('image create cairoSurface connectionCanvas -surface ecolab_model panmictic_ecolab.connectionPlot')
 ttk.Label(connectionPlot, image='connectionCanvas').pack()
 windows.append(ref(connectionPlot))
+ecolab.updateConnectionPlot()
 
 def step():
     ecolab.generate()
     ecolab.mutate()
+    ecolab.updateConnectionPlot()
     ecolab.condense()
     nsp=len(ecolab.species)
     statusBar.configure(text=f't={ecolab.tstep()} nsp:{nsp}')
     plot('No. species',ecolab.tstep(),nsp)
     penPlot('Density',ecolab.tstep(),ecolab.density()._properties, ecolab.species()._properties)
-    ecolab.connectionPlot.requestRedraw()
 
 gui(step)
 

models/pred-prey.py

@@ -1,4 +1,4 @@
-from ecolab_model import ecolab
+from ecolab_model import panmictic_ecolab as ecolab
 ecolab.species([1,2])
 ecolab.density([100,100]) 
 ecolab.create([0,0])