Fixing bug in mixing models and implements new entity-related methods (…

…#18)

* Fixing bug in mixing models and implements method for reading entity-agent ties from pointers

* Agents getter

* Adding print method for entity

* Updating single-header

epiworld.hpp

@@ -6351,6 +6351,12 @@ class Model {
         const std::vector<int> & entities_ids
         );
 
+    void load_agents_entities_ties(
+        const int * agents_id,
+        const int * entities_id,
+        size_t n
+        );
+
     /**
      * @name Accessing population of the model
      * 
@@ -7955,7 +7961,7 @@ inline void Model<TSeq>::rm_entity(size_t entity_id)
     entity.reset();
 
     // How should
-    if (entity_pos != (entities.size() - 1))
+    if (entity_pos != (static_cast<int>(entities.size()) - 1))
         std::swap(entities[entity_pos], entities[entities.size() - 1]);
 
     entities.pop_back();
@@ -8101,46 +8107,87 @@ inline void Model<TSeq>::load_agents_entities_ties(
     const std::vector< int > & entities_ids
 ) {
 
+    // Checking the size
     if (agents_ids.size() != entities_ids.size())
         throw std::length_error(
-            std::string("agents_ids (") +
+            std::string("The size of agents_ids (") +
             std::to_string(agents_ids.size()) +
             std::string(") and entities_ids (") +
             std::to_string(entities_ids.size()) +
-            std::string(") should match.")
+            std::string(") must be the same.")
             );
 
+    return this->load_agents_entities_ties(
+        agents_ids.data(),
+        entities_ids.data(),
+        agents_ids.size()
+    );
+
+}
+
+template<typename TSeq>
+inline void Model<TSeq>::load_agents_entities_ties(
+    const int * agents_ids,
+    const int * entities_ids,
+    size_t n
+) {
+
+    auto get_agent = [agents_ids](int i) -> int {
+        return *(agents_ids + i);
+        };
 
-    size_t n_entries = agents_ids.size();
-    for (size_t i = 0u; i < n_entries; ++i)
+    auto get_entity = [entities_ids](int i) -> int {
+        return *(entities_ids + i);
+        };
+
+    for (size_t i = 0u; i < n; ++i)
     {
 
-        if (agents_ids[i] >= this->population.size())
+        if (get_agent(i) < 0)
+            throw std::length_error(
+                std::string("agents_ids[") +
+                std::to_string(i) +
+                std::string("] = ") +
+                std::to_string(get_agent(i)) +
+                std::string(" is negative.")
+                );
+
+        if (get_entity(i) < 0)
+            throw std::length_error(
+                std::string("entities_ids[") +
+                std::to_string(i) +
+                std::string("] = ") +
+                std::to_string(get_entity(i)) +
+                std::string(" is negative.")
+                );
+
+        int pop_size = static_cast<int>(this->population.size());
+        if (get_agent(i) >= pop_size)
             throw std::length_error(
                 std::string("agents_ids[") +
                 std::to_string(i) +
                 std::string("] = ") +
-                std::to_string(agents_ids[i]) +
+                std::to_string(get_agent(i)) +
                 std::string(" is out of range (population size: ") +
-                std::to_string(this->population.size()) +
+                std::to_string(pop_size) +
                 std::string(").")
                 );
 
-
-        if (entities_ids[i] >= this->entities.size())
+        int ent_size = static_cast<int>(this->entities.size());
+        if (get_entity(i) >= ent_size)
             throw std::length_error(
                 std::string("entities_ids[") +
                 std::to_string(i) +
                 std::string("] = ") +
-                std::to_string(entities_ids[i]) +
+                std::to_string(get_entity(i)) +
                 std::string(" is out of range (entities size: ") +
-                std::to_string(this->entities.size()) +
+                std::to_string(ent_size) +
                 std::string(").")
                 );
 
         // Adding the entity to the agent
-        this->population[agents_ids[i]].add_entity(
-            this->entities[entities_ids[i]],
+        this->population[get_agent(i)].add_entity(
+            this->entities[get_entity(i)],
             nullptr /* Immediately add it to the agent */
         );
 
@@ -12088,6 +12135,10 @@ class Entity {
 
     void distribute();
 
+    std::vector< size_t > & get_agents();
+
+    void print() const;
+
 };
 
 
@@ -12392,6 +12443,24 @@ inline void Entity<TSeq>::distribute()
 
 }
 
+template<typename TSeq>
+inline std::vector< size_t > & Entity<TSeq>::get_agents()
+{
+    return agents;
+}
+
+template<typename TSeq>
+inline void Entity<TSeq>::print() const
+{
+
+    printf_epiworld(
+        "Entity '%s' (id %i) with %i agents.\n",
+        this->entity_name.c_str(),
+        static_cast<int>(id),
+        static_cast<int>(n_agents)
+    );
+}
+
 #endif
 /*//////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -19657,7 +19726,10 @@ inline void ModelSEIRMixing<TSeq>::update_infected()
     {
 
         if (a.get_state() == ModelSEIRMixing<TSeq>::INFECTED)
-            infected[a.get_entity(0u).get_id()].push_back(&a);
+        {
+            if (a.get_n_entities() > 0u)
+                infected[a.get_entity(0u).get_id()].push_back(&a);
+        }
 
     }
 
@@ -20190,7 +20262,10 @@ inline void ModelSIRMixing<TSeq>::update_infected_list()
     {
 
         if (a.get_state() == ModelSIRMixing<TSeq>::INFECTED)
-            infected[a.get_entity(0u).get_id()].push_back(&a);
+        {
+            if (a.get_n_entities() > 0u)
+                infected[a.get_entity(0u).get_id()].push_back(&a);
+        }
 
     }
 

include/epiworld/entity-bones.hpp

@@ -103,6 +103,10 @@ class Entity {
 
     void distribute();
 
+    std::vector< size_t > & get_agents();
+
+    void print() const;
+
 };
 
 

include/epiworld/entity-meat.hpp

@@ -280,4 +280,22 @@ inline void Entity<TSeq>::distribute()
 
 }
 
+template<typename TSeq>
+inline std::vector< size_t > & Entity<TSeq>::get_agents()
+{
+    return agents;
+}
+
+template<typename TSeq>
+inline void Entity<TSeq>::print() const
+{
+
+    printf_epiworld(
+        "Entity '%s' (id %i) with %i agents.\n",
+        this->entity_name.c_str(),
+        static_cast<int>(id),
+        static_cast<int>(n_agents)
+    );
+}
+
 #endif

include/epiworld/model-bones.hpp

@@ -372,6 +372,12 @@ class Model {
         const std::vector<int> & entities_ids
         );
 
+    void load_agents_entities_ties(
+        const int * agents_id,
+        const int * entities_id,
+        size_t n
+        );
+
     /**
      * @name Accessing population of the model
      * 

include/epiworld/model-meat.hpp

@@ -1213,7 +1213,7 @@ inline void Model<TSeq>::rm_entity(size_t entity_id)
     entity.reset();
 
     // How should
-    if (entity_pos != (entities.size() - 1))
+    if (entity_pos != (static_cast<int>(entities.size()) - 1))
         std::swap(entities[entity_pos], entities[entities.size() - 1]);
 
     entities.pop_back();
@@ -1359,46 +1359,87 @@ inline void Model<TSeq>::load_agents_entities_ties(
     const std::vector< int > & entities_ids
 ) {
 
+    // Checking the size
     if (agents_ids.size() != entities_ids.size())
         throw std::length_error(
-            std::string("agents_ids (") +
+            std::string("The size of agents_ids (") +
             std::to_string(agents_ids.size()) +
             std::string(") and entities_ids (") +
             std::to_string(entities_ids.size()) +
-            std::string(") should match.")
+            std::string(") must be the same.")
             );
 
+    return this->load_agents_entities_ties(
+        agents_ids.data(),
+        entities_ids.data(),
+        agents_ids.size()
+    );
+
+}
 
-    size_t n_entries = agents_ids.size();
-    for (size_t i = 0u; i < n_entries; ++i)
+template<typename TSeq>
+inline void Model<TSeq>::load_agents_entities_ties(
+    const int * agents_ids,
+    const int * entities_ids,
+    size_t n
+) {
+
+    auto get_agent = [agents_ids](int i) -> int {
+        return *(agents_ids + i);
+        };
+
+    auto get_entity = [entities_ids](int i) -> int {
+        return *(entities_ids + i);
+        };
+
+    for (size_t i = 0u; i < n; ++i)
     {
 
-        if (agents_ids[i] >= this->population.size())
+        if (get_agent(i) < 0)
+            throw std::length_error(
+                std::string("agents_ids[") +
+                std::to_string(i) +
+                std::string("] = ") +
+                std::to_string(get_agent(i)) +
+                std::string(" is negative.")
+                );
+
+        if (get_entity(i) < 0)
+            throw std::length_error(
+                std::string("entities_ids[") +
+                std::to_string(i) +
+                std::string("] = ") +
+                std::to_string(get_entity(i)) +
+                std::string(" is negative.")
+                );
+
+        int pop_size = static_cast<int>(this->population.size());
+        if (get_agent(i) >= pop_size)
             throw std::length_error(
                 std::string("agents_ids[") +
                 std::to_string(i) +
                 std::string("] = ") +
-                std::to_string(agents_ids[i]) +
+                std::to_string(get_agent(i)) +
                 std::string(" is out of range (population size: ") +
-                std::to_string(this->population.size()) +
+                std::to_string(pop_size) +
                 std::string(").")
                 );
 
-
-        if (entities_ids[i] >= this->entities.size())
+        int ent_size = static_cast<int>(this->entities.size());
+        if (get_entity(i) >= ent_size)
             throw std::length_error(
                 std::string("entities_ids[") +
                 std::to_string(i) +
                 std::string("] = ") +
-                std::to_string(entities_ids[i]) +
+                std::to_string(get_entity(i)) +
                 std::string(" is out of range (entities size: ") +
-                std::to_string(this->entities.size()) +
+                std::to_string(ent_size) +
                 std::string(").")
                 );
 
         // Adding the entity to the agent
-        this->population[agents_ids[i]].add_entity(
-            this->entities[entities_ids[i]],
+        this->population[get_agent(i)].add_entity(
+            this->entities[get_entity(i)],
             nullptr /* Immediately add it to the agent */
         );
 

include/epiworld/models/seirmixing.hpp

@@ -164,7 +164,10 @@ inline void ModelSEIRMixing<TSeq>::update_infected()
     {
 
         if (a.get_state() == ModelSEIRMixing<TSeq>::INFECTED)
-            infected[a.get_entity(0u).get_id()].push_back(&a);
+        {
+            if (a.get_n_entities() > 0u)
+                infected[a.get_entity(0u).get_id()].push_back(&a);
+        }
 
     }
 

include/epiworld/models/sirmixing.hpp

@@ -159,7 +159,10 @@ inline void ModelSIRMixing<TSeq>::update_infected_list()
     {
 
         if (a.get_state() == ModelSIRMixing<TSeq>::INFECTED)
-            infected[a.get_entity(0u).get_id()].push_back(&a);
+        {
+            if (a.get_n_entities() > 0u)
+                infected[a.get_entity(0u).get_id()].push_back(&a);
+        }
 
     }