Updating to epiworld 0.12.0 (#166)

* Updating to epiworld 0.12.0

* Fixing issue in how to get agents

* Simplify entity_get_agents function

* Correct way to set the agents id

* Applying suggested fixes by copilot (updates to epiworld C++)

* Bringing last set of changes from epiworld C++

Author: gvegayon

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: epiworldR
 Type: Package
 Title: Fast Agent-Based Epi Models
-Version: 0.11.3.0
+Version: 0.12.0.0
 Depends: R (>= 4.1.0)
 Authors@R: c(
   person(given="George", family="Vega Yon", role=c("aut", "cre"),

Makefile

@@ -11,6 +11,7 @@ help:
 	@echo "  debug               Build and run a debug Docker container"
 	@echo "  docs                Generate documentation with roxygen2"
 	@echo "  local-update        Update epiworld.hpp from local epiworld include folder"
+	@echo "  update              Update epiworld.hpp from the latest version on GitHub"
 	@echo "  local-update-diagrams  Update diagrams from local epiworld docs_src folder"
 	@echo "  website             Build the pkgdown website"
 	@echo "  clean               Clean compiled files and reset DESCRIPTION and NAMESPACE"

NEWS.md

@@ -1,14 +1,20 @@
-# epiworldR 0.11.3.0
+# epiworldR 0.12.0.0
 
-* Updates to `epiworld` version 0.11.3, including a patch to the `ModelSEIRMixingQuarantine` model. It was underestimating the outbreak size. This is a similar issue detected in the collection of the measles models.
+## Bug fixes
+
+* Updates to `epiworld` version 0.12.0, including a patch to the `ModelSEIRMixingQuarantine` model. It was underestimating the outbreak size. This is a similar issue detected in the collection of the measles models.
 
 * The `ModelSEIRMixingQuarantine` gained a couple of extra checks for validating the inputs.
 
+## Internal changes
+
 * Simplified build configuration to comply with CRAN policies: removed custom
   `configure` script, using R's built-in OpenMP settings
   (`$(SHLIB_OPENMP_CXXFLAGS)`) and specifying C++17 via `CXX_STD` in Makevars
   and `SystemRequirements` in DESCRIPTION.
 
+* Changing how `Entities` are managed in the system, moved away from using pointers and instead use `reference_wrapper`.
+
 
 # epiworldR 0.11.2.0
 

inst/include/epiworld/agent-bones.hpp

@@ -70,7 +70,6 @@ class Agent {
     friend class Tools<TSeq>;
     friend class Tools_const<TSeq>;
     friend class Queue<TSeq>;
-    friend class Entities<TSeq>;
     friend class AgentsSample<TSeq>;
     friend void default_add_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
     friend void default_add_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
@@ -87,9 +86,7 @@ class Agent {
     std::vector< size_t > * neighbors_locations = nullptr;
     size_t n_neighbors = 0u;
 
-    std::vector< size_t > entities;
-    std::vector< size_t > entities_locations;
-    size_t n_entities = 0u;
+    std::vector< std::reference_wrapper<Entity<TSeq>> > entities;
 
     unsigned int state = 0u;
     unsigned int state_prev = 0u; ///< For accounting, if need to undo a change.
@@ -102,6 +99,8 @@ class Agent {
     std::vector< ToolPtr<TSeq> > tools;
     unsigned int n_tools = 0u;
 
+    void reset(); ///< Resets the agent to the initial state (no virus, no tools, no entities, state 0.)
+
 public:
 
     Agent();
@@ -247,8 +246,6 @@ class Agent {
 
     const unsigned int & get_state() const;
 
-    void reset();
-
     bool has_tool(epiworld_fast_uint t) const;
     bool has_tool(std::string name) const;
     bool has_tool(const Tool<TSeq> & t) const;
@@ -282,8 +279,8 @@ class Agent {
     double operator[](size_t j) const;
     ///@}
 
-    Entities<TSeq> get_entities();
-    const Entities_const<TSeq> get_entities() const;
+    std::vector< std::reference_wrapper<Entity<TSeq>> > get_entities();
+    const std::vector< std::reference_wrapper<Entity<TSeq>> > get_entities() const;
     const Entity<TSeq> & get_entity(size_t i) const;
     Entity<TSeq> & get_entity(size_t i);
     size_t get_n_entities() const;

inst/include/epiworld/agent-events-meat.hpp

@@ -226,114 +226,59 @@ inline void default_add_entity(Event<TSeq> & a, Model<TSeq> *)
 
         if (p->get_n_entities() > e->size()) // Slower search through the agent
         {
-            for (size_t i = 0u; i < e->size(); ++i)
-                if(static_cast<int>(e->operator[](i)) == p->get_id())
+            for (const Agent<TSeq> & agent: e->get_agents())
+                if(agent.get_id() == p->get_id())
                     throw std::logic_error("An entity cannot be reassigned to an agent.");
         }
         else                                 // Slower search through the entity
         {
-            for (size_t i = 0u; i < p->get_n_entities(); ++i)
-                if(p->get_entity(i).get_id() == e->get_id())
+            for (const Entity<TSeq> & entity: p->get_entities())
+                if(entity.get_id() == e->get_id())
                     throw std::logic_error("An entity cannot be reassigned to an agent.");
         }
 
         // It means that agent and entity were not associated.
     }
 
-    // Adding the entity to the agent
-    if (++p->n_entities <= p->entities.size())
-    {
-
-        p->entities[p->n_entities - 1]           = e->get_id();
-        p->entities_locations[p->n_entities - 1] = e->n_agents;
-
-    } else
-    {
-        p->entities.push_back(e->get_id());
-        p->entities_locations.push_back(e->n_agents);
-    }
-
-    // Adding the agent to the entity
-    // Adding the entity to the agent
-    if (++e->n_agents <= e->agents.size())
-    {
-
-        e->agents[e->n_agents - 1]          = p->get_id();
-        // Adjusted by '-1' since the list of entities in the agent just grew.
-        e->agents_location[e->n_agents - 1] = p->n_entities - 1;
-
-    } else
-    {
-        e->agents.push_back(p->get_id());
-        e->agents_location.push_back(p->n_entities - 1);
-    }
-
-    // Today was the last modification
-    // e->date_last_add_or_remove = m->today();
+    // Adding the to agent and the entity
+    p->entities.push_back(std::ref(*e));
+    e->agents.push_back(std::ref(*p));
 
 }
 
 template<typename TSeq>
-inline void default_rm_entity(Event<TSeq> & a, Model<TSeq> * m)
+inline void default_rm_entity(Event<TSeq> & a, Model<TSeq> *)
 {
 
-    Agent<TSeq> *  p = a.agent;    
-    Entity<TSeq> * e = a.entity;
-    size_t idx_agent_in_entity = a.idx_agent;
-    size_t idx_entity_in_agent = a.idx_object;
-
-    if (--p->n_entities > 0)
-    {
-
-        // When we move the end entity to the new location, the 
-        // moved entity needs to reflect the change, i.e., where the
-        // entity will now be located in the agent
-        size_t agent_location_in_last_entity  =
-            p->entities_locations[p->n_entities];
-
-        Entity<TSeq> * last_entity =
-            &m->get_entity(p->entities[p->n_entities]); ///< Last entity of the agent
-
-        // The end entity will be located where the removed was
-        last_entity->agents_location[agent_location_in_last_entity] =
-            idx_entity_in_agent;
-
-        // We now make the swap
-        std::swap(
-            p->entities[p->n_entities],
-            p->entities[idx_entity_in_agent]
-        );
-
-    }
-
-    if (--e->n_agents > 0)
-    {
-
-        // When we move the end agent to the new location, the 
-        // moved agent needs to reflect the change, i.e., where the
-        // agent will now be located in the entity
-        size_t entity_location_in_last_agent = e->agents_location[e->n_agents];
-        
-        Agent<TSeq> * last_agent  =
-            &m->get_agents()[e->agents[e->n_agents]]; ///< Last agent of the entity
-
-        // The end entity will be located where the removed was
-        last_agent->entities_locations[entity_location_in_last_agent] =
-            idx_agent_in_entity;
-
-        // We now make the swap
-        std::swap(
-            e->agents[e->n_agents],
-            e->agents[idx_agent_in_entity]
-        );
-
-    }
+    Agent<TSeq> &  p = *a.agent;    
+    Entity<TSeq> & e = *a.entity;
+    
+    // Remove entity from agent's entity list
+    p.entities.erase(
+        std::remove_if(
+            p.entities.begin(),
+            p.entities.end(),
+            [&e](const std::reference_wrapper<Entity<TSeq>> & entity_ref) {
+                return entity_ref.get().get_id() == e.get_id();
+            }
+        ),
+        p.entities.end()
+    );
 
-    // Setting the date of the last removal
-    // e->date_last_add_or_remove = m->today();
+    // Remove agent from entity's agent list
+    e.agents.erase(
+        std::remove_if(
+            e.agents.begin(),
+            e.agents.end(),
+            [&p](const std::reference_wrapper<Agent<TSeq>> & agent_ref) {
+                return agent_ref.get().get_id() == p.get_id();
+            }
+        ),
+        e.agents.end()
+    );
 
     return;
 
 };
 
-#endif
+#endif