Draft of entities model

epiworld.hpp

@@ -6082,9 +6082,9 @@ class Model {
      * AgentsSample<TSeq>::AgentsSample(Model<TSeq>) these vectors are allocated.
      */
     ///@{
-    std::vector< Agent<TSeq> * > sampled_population;
+    std::shared_ptr< std::vector< Agent<TSeq> * > > sampled_population;
     size_t sampled_population_n = 0u;
-    std::vector< size_t > population_left;
+    std::shared_ptr< std::vector< size_t > > population_left;
     size_t population_left_n = 0u;
     ///@}
 
@@ -14621,10 +14621,10 @@ class AgentsSample {
 
     size_t sample_size = 0u;
 
-    std::vector< Agent<TSeq>* > * agents = nullptr; ///< Pointer to sample of agents
+    std::shared_ptr<std::vector< Agent<TSeq>* > > agents = nullptr; ///< Pointer to sample of agents
     size_t * agents_n = nullptr;                    ///< Size of sample of agents
 
-    std::vector< size_t > * agents_left = nullptr;  ///< Pointer to agents left (iota)
+    std::shared_ptr<std::vector< size_t > > agents_left = nullptr;  ///< Pointer to agents left (iota)
     size_t * agents_left_n = nullptr;               ///< Size of agents left
 
     Model<TSeq> * model   = nullptr;   ///< Extracts runif() and (if the case) population.
@@ -14651,13 +14651,17 @@ class AgentsSample {
         );
 
     AgentsSample(
-        Model<TSeq> * model, Entity<TSeq> & entity_, size_t n,
+        Model<TSeq> * model,
+        Entity<TSeq> & entity_,
+        size_t n,
         std::vector< size_t > states_ = {},
         bool truncate = false
         );
 
     AgentsSample(
-        Model<TSeq> * model, Agent<TSeq> & agent_, size_t n,
+        Model<TSeq> * model,
+        Agent<TSeq> & agent_,
+        size_t n,
         std::vector< size_t > states_ = {},
         bool truncate = false
         );

examples/11-entities/Makefile

@@ -0,0 +1,2 @@
+main.o: main.cpp
+	g++ -std=c++17 -g main.cpp -o main.o

examples/11-entities/main.cpp

@@ -0,0 +1,26 @@
+#define EPI_DEBUG
+#include "../../include/epiworld/epiworld.hpp"
+
+using namespace epiworld;
+
+int main() {
+
+    epimodels::ModelSEIREntitiesConn model(
+        "Flu", // std::string vname,
+        10000, // epiworld_fast_uint n,
+        0.01,// epiworld_double prevalence,
+        4.0,// epiworld_double contact_rate,
+        0.1,// epiworld_double transmission_rate,
+        4.0,// epiworld_double avg_incubation_days,
+        1.0/7.0,// epiworld_double recovery_rate,
+        {.1, .1, .8},// std::vector< epiworld_double > entities,
+        {"A", "B", "C"}// std::vector< std::string > entities_names
+    );
+
+    // Running and checking the results
+    model.run(50, 123);
+    model.print();
+
+    return 0;
+
+}

include/epiworld/agent-bones.hpp

@@ -102,9 +102,9 @@ class Agent {
     std::vector< ToolPtr<TSeq> > tools;
     epiworld_fast_uint n_tools = 0u;
 
-    std::vector< Agent<TSeq> * > sampled_agents;
+    std::vector< Agent<TSeq> * > sampled_agents = {};
     size_t sampled_agents_n      = 0u;
-    std::vector< size_t > sampled_agents_left;
+    std::vector< size_t > sampled_agents_left = {};
     size_t sampled_agents_left_n = 0u;
     int date_last_build_sample   = -99;
 

include/epiworld/agentssample-bones.hpp

@@ -30,10 +30,10 @@ class AgentsSample {
 
     size_t sample_size = 0u;
 
-    std::vector< Agent<TSeq>* > * agents = nullptr; ///< Pointer to sample of agents
+    std::vector< Agent<TSeq>* >* agents = nullptr; ///< Pointer to sample of agents
     size_t * agents_n = nullptr;                    ///< Size of sample of agents
 
-    std::vector< size_t > * agents_left = nullptr;  ///< Pointer to agents left (iota)
+    std::vector< size_t >* agents_left = nullptr;  ///< Pointer to agents left (iota)
     size_t * agents_left_n = nullptr;               ///< Size of agents left
 
     Model<TSeq> * model   = nullptr;   ///< Extracts runif() and (if the case) population.
@@ -49,7 +49,7 @@ class AgentsSample {
 public:
 
     // Not available (for now)
-    AgentsSample() = delete;                       ///< Default constructor
+    AgentsSample() = delete;                             ///< Default constructor
     AgentsSample(const AgentsSample<TSeq> & a) = delete; ///< Copy constructor
     AgentsSample(AgentsSample<TSeq> && a) = delete;      ///< Move constructor
 
@@ -60,13 +60,17 @@ class AgentsSample {
         );
 
     AgentsSample(
-        Model<TSeq> * model, Entity<TSeq> & entity_, size_t n,
+        Model<TSeq> * model,
+        Entity<TSeq> & entity_,
+        size_t n,
         std::vector< size_t > states_ = {},
         bool truncate = false
         );
 
     AgentsSample(
-        Model<TSeq> * model, Agent<TSeq> & agent_, size_t n,
+        Model<TSeq> * model,
+        Agent<TSeq> & agent_,
+        size_t n,
         std::vector< size_t > states_ = {},
         bool truncate = false
         );
@@ -228,19 +232,22 @@ inline AgentsSample<TSeq>::AgentsSample(
         agents->resize(n);
 
     size_t i_obs = 0u;
-    for (size_t i = 0u; i < agents_in_entities; ++i)
+    for (size_t i = 0u; i < sample_size; ++i)
     {
+
+        // Sampling a single agent from the set of entities
         int jth = std::floor(model->runif() * agents_in_entities);
         for (size_t e = 0u; e < cum_agents_count.size(); ++e)
         {
+
             // Are we in the limit?
             if (jth <= cum_agents_count[e])
             {
                 size_t agent_idx = 0u;
                 if (e == 0) // From the first group
-                    agent_idx = entities_a[e][jth];
+                    agent_idx = entities_a[e][jth]->get_id();
                 else
-                    agent_idx = entities_a[e][jth - cum_agents_count[e - 1]];
+                    agent_idx = entities_a[e][jth - cum_agents_count[e - 1]]->get_id();
 
                 // Getting the state
                 size_t state = model->population[agent_idx].get_state();
@@ -252,7 +259,7 @@ inline AgentsSample<TSeq>::AgentsSample(
                         continue;
                 }
 
-                agents->operator[](i_obs++) = agent_idx;
+                agents->operator[](i_obs++) = &(model->population[agent_idx]);
 
                 break;
             }

include/epiworld/model-meat.hpp

@@ -2115,6 +2115,7 @@ inline void Model<TSeq>::reset() {
     // Re distributing tools and virus
     dist_virus();
     dist_tools();
+    dist_entities();
 
     // Distributing initial state, if specified
     initial_states_fun(this);

include/epiworld/models/models.hpp

@@ -19,6 +19,7 @@ namespace epimodels {
     #include "seirdconnected.hpp"
     #include "sirlogit.hpp"
     #include "diffnet.hpp"
+    #include "seirentitiesconnected.hpp"
 
 
 }