Reset entities properly

include/epiworld/agent-bones.hpp

@@ -264,6 +264,8 @@ class Agent {
     bool has_virus(epiworld_fast_uint t) const;
     bool has_virus(std::string name) const;
     bool has_virus(const Virus<TSeq> & v) const;
+    bool has_entity(epiworld_fast_uint t) const;
+    bool has_entity(std::string name) const;
 
     void print(Model<TSeq> * model, bool compressed = false) const;
 

include/epiworld/agent-meat.hpp

@@ -635,6 +635,10 @@ inline void Agent<TSeq>::reset()
     this->tools.clear();
     n_tools = 0u;
 
+    this->entities.clear();
+    this->entities_locations.clear();
+    this->n_entities = 0u;
+
     this->state = 0u;
     this->state_prev = 0u;
 
@@ -702,6 +706,30 @@ inline bool Agent<TSeq>::has_virus(const Virus<TSeq> & virus) const
 
 }
 
+template<typename TSeq>
+inline bool Agent<TSeq>::has_entity(epiworld_fast_uint t) const
+{
+
+    for (auto & entity : entities)
+        if (entity == t)
+            return true;
+
+    return false;
+
+}
+
+template<typename TSeq>
+inline bool Agent<TSeq>::has_entity(std::string name) const
+{
+
+    for (auto & entity : entities)
+        if (model->get_entity(entity).get_name() == name)
+            return true;
+
+    return false;
+
+}
+
 template<typename TSeq>
 inline void Agent<TSeq>::print(
     Model<TSeq> * model,
@@ -813,6 +841,9 @@ inline const Entities_const<TSeq> Agent<TSeq>::get_entities() const
 template<typename TSeq>
 inline const Entity<TSeq> & Agent<TSeq>::get_entity(size_t i) const
 {
+    if (n_entities == 0)
+        throw std::range_error("Agent id " + std::to_string(id) + " has no entities.");
+
     if (i >= n_entities)
         throw std::range_error("Trying to get to an agent's entity outside of the range.");
 
@@ -822,6 +853,9 @@ inline const Entity<TSeq> & Agent<TSeq>::get_entity(size_t i) const
 template<typename TSeq>
 inline Entity<TSeq> & Agent<TSeq>::get_entity(size_t i)
 {
+    if (n_entities == 0)
+        throw std::range_error("Agent id " + std::to_string(id) + " has no entities.");
+
     if (i >= n_entities)
         throw std::range_error("Trying to get to an agent's entity outside of the range.");
 

include/epiworld/config.hpp

@@ -91,7 +91,7 @@ template<typename TSeq>
 struct Event;
 
 template<typename TSeq>
-using ActionFun = std::function<void(Event<TSeq>&,Model<TSeq>*)>;
+using EventFun = std::function<void(Event<TSeq>&,Model<TSeq>*)>;
 
 /**
  * @brief Decides how to distribute viruses at initialization
@@ -124,7 +124,7 @@ struct Event {
     Entity<TSeq> * entity;
     epiworld_fast_int new_state;
     epiworld_fast_int queue;
-    ActionFun<TSeq> call;
+    EventFun<TSeq> call;
     int idx_agent;
     int idx_object;
 public:
@@ -151,7 +151,7 @@ struct Event {
         Entity<TSeq> * entity_,
         epiworld_fast_int new_state_,
         epiworld_fast_int queue_,
-        ActionFun<TSeq> call_,
+        EventFun<TSeq> call_,
         int idx_agent_,
         int idx_object_
     ) : agent(agent_), virus(virus_), tool(tool_), entity(entity_),

include/epiworld/entity-meat.hpp

@@ -266,9 +266,9 @@ inline void Entity<TSeq>::reset()
     sampled_agents_left.clear();
     sampled_agents_left_n = 0u;
 
-    // Removing agents from entities
-    for (size_t i = 0u; i < n_agents; ++i)
-        this->rm_agent(i);
+    this->agents.clear();
+    this->n_agents = 0u;
+    this->agents_location.clear();
 
     return;
 
@@ -358,7 +358,7 @@ inline void Entity<TSeq>::distribute()
 
         int n_left = n;
         std::iota(idx.begin(), idx.end(), 0);
-        for (int i = 0; i < n_to_assign; ++i)
+        while (n_to_assign > 0)
         {
             int loc = static_cast<epiworld_fast_uint>(
                 floor(model->runif() * n_left--)
@@ -368,10 +368,13 @@ inline void Entity<TSeq>::distribute()
             if ((loc > 0) && (loc >= n_left))
                 loc = n_left - 1;
 
-            model->get_agent(idx[loc]).add_entity(
-                *this, this->model, this->state_init, this->queue_init
-                );
-
+            auto & agent = model->get_agent(idx[loc]);
+
+            if (!agent.has_entity(id))
+                agent.add_entity(
+                    *this, this->model, this->state_init, this->queue_init
+                    );
+
             std::swap(idx[loc], idx[n_left]);
 
         }

include/epiworld/epiworld.hpp

@@ -19,7 +19,7 @@
 /* Versioning */
 #define EPIWORLD_VERSION_MAJOR 0
 #define EPIWORLD_VERSION_MINOR 3
-#define EPIWORLD_VERSION_PATCH 0
+#define EPIWORLD_VERSION_PATCH 1
 
 static const int epiworld_version_major = EPIWORLD_VERSION_MAJOR;
 static const int epiworld_version_minor = EPIWORLD_VERSION_MINOR;

include/epiworld/model-bones.hpp

@@ -220,7 +220,7 @@ class Model {
         Entity<TSeq> * entity_,
         epiworld_fast_int new_state_,
         epiworld_fast_int queue_,
-        ActionFun<TSeq> call_,
+        EventFun<TSeq> call_,
         int idx_agent_,
         int idx_object_
         );

include/epiworld/model-meat.hpp

@@ -157,7 +157,7 @@ inline void Model<TSeq>::events_add(
     Entity<TSeq> * entity_,
     epiworld_fast_int new_state_,
     epiworld_fast_int queue_,
-    ActionFun<TSeq> call_,
+    EventFun<TSeq> call_,
     int idx_agent_,
     int idx_object_
 ) {
@@ -166,7 +166,7 @@ inline void Model<TSeq>::events_add(
 
     #ifdef EPI_DEBUG
     if (nactions == 0)
-        throw std::logic_error("Actions cannot be zero!!");
+        throw std::logic_error("Events cannot be zero!!");
     #endif
 
     if (nactions > events.size())

tests/05-mixing.cpp

@@ -129,22 +129,22 @@ EPIWORLD_TEST_CASE("SEIRMixing", "[SEIR-mixing]") {
     REQUIRE_THAT(totals, Catch::Equals(expected_totals));
     #endif
 
-    // // If entities don't have a dist function, then it should be
-    // // OK
-    // e1.set_dist_fun(nullptr);
-    // e2.set_dist_fun(nullptr);
-    // e3.set_dist_fun(nullptr);
-
-    // model.rm_entity(0);
-    // model.rm_entity(1);
-    // model.rm_entity(2);
-
-    // model.add_entity(e1);
-    // model.add_entity(e2);
-    // model.add_entity(e3);
-
-    // // Running and checking the results
-    // model.run(50, 123);
+    // If entities don't have a dist function, then it should be
+    // OK
+    e1.set_dist_fun(nullptr);
+    e2.set_dist_fun(nullptr);
+    e3.set_dist_fun(nullptr);
+
+    model.rm_entity(0);
+    model.rm_entity(1);
+    model.rm_entity(2);
+
+    model.add_entity(e1);
+    model.add_entity(e2);
+    model.add_entity(e3);
+
+    // Running and checking the results
+    model.run(50, 123);
 
 
     #ifndef CATCH_CONFIG_MAIN