Add individual-based phylogeny

emilydolson · Mar 26, 2024 · 878fce4 · 878fce4
1 parent f0bbd25
commit 878fce4
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Showing 5 changed files with 43 additions and 20 deletions.
diff --git a/avida-core/source/main/cAvidaConfig.h b/avida-core/source/main/cAvidaConfig.h
@@ -286,6 +286,7 @@ class cAvidaConfig {
   CONFIG_ADD_VAR(POP_CAP_ELDEST, int, 0, "Carrying capacity in number of organisms (use 0 for no cap). Will kill oldest organism in population, but still use birth method to place new offspring."); 
   CONFIG_ADD_VAR(FILTER_TIME, int, 10000, "How long does a lineage need to survive to pass the coalesence filter?");
   CONFIG_ADD_VAR(OEE_RES, int, 1000, "How often should we print OEE stats?");
+  CONFIG_ADD_VAR(TRACK_INDIVIDUALS, bool, 0, "Should we track phylogeny based on individuals or genomes (default)?");
   CONFIG_ADD_VAR(PHYLOGENY_SNAPSHOT_RES, int, 1000, "How often should we print phylogeny stats?");
   CONFIG_ADD_VAR(SYSTEMATICS_RES, int, 1000, "How often should we print phylodiversity stats?");
 

diff --git a/avida-core/source/main/cPopulation.cc b/avida-core/source/main/cPopulation.cc
@@ -1377,7 +1377,8 @@ bool cPopulation::ActivateOrganism(cAvidaContext& ctx, cOrganism* in_organism, c
   InstructionSequence* nseq = new InstructionSequence(*seq);
   m_world->curr_genome = in_organism->GetGenome();
   m_world->next_cell_id = target_cell.GetID();
-  m_world->offspring_ready_sig.Trigger(*nseq);
+
+  m_world->offspring_ready_sig.Trigger(*in_organism);
 
   delete nseq;
 

diff --git a/avida-core/source/main/cWorld.cc b/avida-core/source/main/cWorld.cc
@@ -70,10 +70,13 @@ cWorld::cWorld(cAvidaConfig* cfg, const cString& wd)
       return test_info.GetGenotypeFitness();
    };
 
-    eval_fun = [this](emp::Ptr<taxon_t> tax){
+    eval_fun = [this](emp::Ptr<taxon_t> tax, cOrganism & org){
       // std::cout << "evaluating" << tax << std::endl;
 
-       Avida::Genome gen(curr_genome.HardwareType(), curr_genome.Properties(), GeneticRepresentationPtr(new InstructionSequence(tax->GetInfo())));
+      // Avida::GeneticRepresentation rep = *(org.GetGenome().Representation());
+      // GeneticRepresentationPtr(org.GetGenome().Representation())
+      Avida::Genome gen(curr_genome.HardwareType(), curr_genome.Properties(), GeneticRepresentationPtr(new InstructionSequence(tax->GetData().GetPhenotype().genotype)));
+      // Avida::Genome gen(curr_genome.HardwareType(), curr_genome.Properties(), );
       //  cAnalyzeGenotype genotype(this, gen);
       //  genotype.Recalculate(*m_ctx);
       cCPUTestInfo test_info;
@@ -90,6 +93,11 @@ cWorld::cWorld(cAvidaConfig* cfg, const cString& wd)
       for (int i = 0; i < tasks.GetSize(); i++) {
         p.final_task_count.push_back(tasks[i]);
       }
+      ConstInstructionSequencePtr seq;
+      seq.DynamicCastFrom(org.GetGenome().Representation());
+
+      p.genotype = Avida::InstructionSequence(*seq);
+
       tax->GetData().RecordPhenotype(p);
    };
 
@@ -256,20 +264,31 @@ bool cWorld::setup(World* new_world, cUserFeedback* feedback, const Apto::Map<Ap
 
   // std::cout << "Got hardware manager" << std::endl;
   // emp_assert(false);
-  skel_fun = [this, null_inst](const Avida::InstructionSequence & seq){
+  skel_fun = [this, null_inst](emp::Ptr<taxon_t> tax){
     // std::cout << "Skeletonizing" <<std::endl;
+
     std::stringstream ss;
+    Avida::InstructionSequence seq = tax->GetData().GetPhenotype().genotype;
     emp::vector<Avida::Instruction> skel = emp::Skeletonize(seq, null_inst, fit_fun);
     for (auto inst : skel) {
       ss << inst.GetSymbol();
     }
     return ss.str();
   };
   // std::cout << "About to make sys" << std::endl;
-  systematics_manager.New([](const Avida::InstructionSequence & seq){return Avida::InstructionSequence(seq);});
+  if (m_conf->TRACK_INDIVIDUALS.Get()) {
+    systematics_manager.New([](cOrganism & org){return emp::to_string(org.GetID());});
+  } else {
+    systematics_manager.New([](cOrganism & org){
+      ConstInstructionSequencePtr seq;
+      seq.DynamicCastFrom(org.GetGenome().Representation());
+
+      return Avida::InstructionSequence(*seq).AsString().GetCString();
+    });
+  }
   systematics_manager->PrintStatus();
   systematics_manager->AddSnapshotFun([](const taxon_t & tax) {
-      return emp::to_string(tax.GetInfo().AsString().GetCString());
+      return emp::to_string(tax.GetData().GetPhenotype().genotype.AsString().GetCString());
     }, "sequence", "Avida instruction sequence for this taxon.");
 
   if (m_conf->OEE_RES.Get() != 0) {
@@ -284,18 +303,18 @@ bool cWorld::setup(World* new_world, cUserFeedback* feedback, const Apto::Map<Ap
     //   std::cout << systematics_manager->GetTaxonAt(pos)->GetID();
     // } 
     systematics_manager->SetNextParent(pos);});
-  OnOffspringReady([this](Avida::InstructionSequence seq){ 
+  OnOffspringReady([this](cOrganism & org){ 
     // std::cout << "on ready" << std::endl;
-    systematics_manager->AddOrg(seq, emp::WorldPosition(next_cell_id,0), GetStats().GetUpdate());
+    systematics_manager->AddOrg(org, emp::WorldPosition(next_cell_id,0));
     emp::Ptr<taxon_t> tax = systematics_manager->GetMostRecent();
     if (tax->GetData().GetPhenotype().gestation_time == -1) {
-      eval_fun(tax);
+      eval_fun(tax, org);
     }
     // std::cout << "Done with on ready" << std::endl;
   });
   OnOrgDeath([this](int pos){ 
     // std::cout << "on death " << std::endl; 
-    systematics_manager->RemoveOrgAfterRepro(emp::WorldPosition(pos, 0), GetStats().GetUpdate());});
+    systematics_manager->RemoveOrgAfterRepro(emp::WorldPosition(pos, 0));});
   if (m_conf->OEE_RES.Get() != 0) {
     OnUpdate([this](int ud){
       // std::cout << "On update" << std::endl;

diff --git a/avida-core/source/main/cWorld.h b/avida-core/source/main/cWorld.h
@@ -62,6 +62,7 @@ class cUserFeedback;
 template<class T> class tDataEntry;
 
 struct Phenotype {
+  Avida::InstructionSequence genotype;
   int gestation_time = -1;
   int start_generation = -1;
   emp::vector<int> final_task_count;
@@ -170,8 +171,8 @@ class cWorld
   // Signals triggered by the world.
   emp::SignalControl control;  // Setup the world to control various signals.
   emp::Signal<void(int)> before_repro_sig;       // Trigger: Immediately prior to producing offspring
-  emp::Signal<void(Avida::InstructionSequence)> offspring_ready_sig;  // Trigger: Offspring about to enter population
-  emp::Signal<void(const Avida::InstructionSequence*)> inject_ready_sig;     // Trigger: New org about to be added to population
+  emp::Signal<void(cOrganism &)> offspring_ready_sig;  // Trigger: Offspring about to enter population
+  emp::Signal<void(cOrganism &)> inject_ready_sig;     // Trigger: New org about to be added to population
   emp::Signal<void(int)> org_placement_sig;      // Trigger: Organism has been added to population
   emp::Signal<void(int)> org_death_sig;      // Trigger: Organism has been added to population
   emp::Signal<void(int)> on_update_sig;          // Trigger: New update is starting.
@@ -183,15 +184,18 @@ class cWorld
   emp::DataFile lineage_file;
   emp::DataFile dom_file;
 
-  std::function<double(const Avida::InstructionSequence&)> fit_fun;
-  std::function<std::string(const Avida::InstructionSequence&)> skel_fun;
+  using systematics_t = emp::Systematics<cOrganism, std::string, emp::datastruct::mut_landscape_info<Phenotype>>;
+  using taxon_t = emp::Taxon< std::string, emp::datastruct::mut_landscape_info<Phenotype>>;
+
+  std::function<double(Avida::InstructionSequence&)> fit_fun;
+  std::function<std::string(emp::Ptr<taxon_t>)> skel_fun;
 
   emp::SignalKey OnBeforeRepro(const std::function<void(int)> & fun) { return before_repro_sig.AddAction(fun); }
-  emp::SignalKey OnOffspringReady(const std::function<void(Avida::InstructionSequence)> & fun) { return offspring_ready_sig.AddAction(fun); }
+  emp::SignalKey OnOffspringReady(const std::function<void(cOrganism &)> & fun) { return offspring_ready_sig.AddAction(fun); }
   emp::SignalKey OnOrgPlacement(const std::function<void(int)> & fun) { return org_placement_sig.AddAction(fun); }
   emp::SignalKey OnOrgDeath(const std::function<void(int)> & fun) { return org_death_sig.AddAction(fun); }
   emp::SignalKey OnUpdate(const std::function<void(int)> & fun) { return on_update_sig.AddAction(fun); }
-  emp::SignalKey OnInjectReady(const std::function<void(const Avida::InstructionSequence*)> & fun) { return inject_ready_sig.AddAction(fun); }
+  emp::SignalKey OnInjectReady(const std::function<void(cOrganism &)> & fun) { return inject_ready_sig.AddAction(fun); }
 
   void SetDriver(WorldDriver* driver, bool take_ownership = false);
 
@@ -214,11 +218,9 @@ class cWorld
   bool all_tasks = false;
   int latest_gen = -1; // Force time to go forward
 
-  using systematics_t = emp::Systematics<Avida::InstructionSequence, Avida::InstructionSequence, emp::datastruct::mut_landscape_info<Phenotype>>;
-  using taxon_t = emp::Taxon< Avida::InstructionSequence, emp::datastruct::mut_landscape_info<Phenotype>>;
   emp::Ptr<taxon_t> best_tax;
 
-  std::function<void(emp::Ptr<taxon_t>)> eval_fun;
+  std::function<void(emp::Ptr<taxon_t>, cOrganism&)> eval_fun;
   const emp::vector<std::string> MUTATION_TYPES = {"substitution", "insertion", "deletion"};
 
   using mut_count_t = std::unordered_map<std::string, double>;

diff --git a/libs/Empirical b/libs/Empirical
+2 −3		include/emp/Evolve/OEE.hpp
+5 −5		include/emp/Evolve/Systematics.hpp
+6 −6		include/emp/base/_optional_throw.hpp