setting names to const ref in prebuilt models

UofUEpiBio · Jun 21, 2024 · 26d9590 · 26d9590
1 parent f26bffb
commit 26d9590
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Showing 20 changed files with 138 additions and 158 deletions.
diff --git a/epiworld.hpp b/epiworld.hpp
diff --git a/include/epiworld/agent-events-meat.hpp b/include/epiworld/agent-events-meat.hpp
@@ -192,7 +192,7 @@ 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(e->operator[](i)->get_id() == p->get_id())
+                if(static_cast<int>(e->operator[](i)) == p->get_id())
                     throw std::logic_error("An entity cannot be reassigned to an agent.");
         }
         else                                 // Slower search through the entity

diff --git a/include/epiworld/entity-bones.hpp b/include/epiworld/entity-bones.hpp
@@ -24,8 +24,6 @@ class Entity {
     friend void default_add_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
     friend void default_rm_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
 private:
-
-    Model<TSeq> * model;
 
     int id = -1;
     std::vector< size_t > agents;   ///< Vector of agents
@@ -82,7 +80,7 @@ class Entity {
 
     void add_agent(Agent<TSeq> & p, Model<TSeq> * model);
     void add_agent(Agent<TSeq> * p, Model<TSeq> * model);
-    void rm_agent(size_t idx);
+    void rm_agent(size_t idx, Model<TSeq> * model);
     size_t size() const noexcept;
     void set_location(std::vector< epiworld_double > loc);
     std::vector< epiworld_double > & get_location();
@@ -93,7 +91,7 @@ class Entity {
     typename std::vector< Agent<TSeq> * >::const_iterator begin() const;
     typename std::vector< Agent<TSeq> * >::const_iterator end() const;
 
-    Agent<TSeq> * operator[](size_t i);
+    size_t operator[](size_t i);
 
     int get_id() const noexcept;
     const std::string & get_name() const noexcept;
@@ -115,7 +113,7 @@ class Entity {
      * The idea is to have a flexible way of distributing agents among entities.
      
      */
-    void distribute();
+    void distribute(Model<TSeq> * model);
 
     std::vector< size_t > & get_agents();
 

diff --git a/include/epiworld/entity-meat.hpp b/include/epiworld/entity-meat.hpp
@@ -23,7 +23,7 @@ inline void Entity<TSeq>::add_agent(
 }
 
 template<typename TSeq>
-inline void Entity<TSeq>::rm_agent(size_t idx)
+inline void Entity<TSeq>::rm_agent(size_t idx, Model<TSeq> * model)
 {
     if (idx >= n_agents)
         throw std::out_of_range(
@@ -89,15 +89,15 @@ inline typename std::vector< Agent<TSeq> * >::const_iterator Entity<TSeq>::end()
 }
 
 template<typename TSeq>
-inline Agent<TSeq> * Entity<TSeq>::operator[](size_t i)
+size_t Entity<TSeq>::operator[](size_t i)
 {
     if (n_agents <= i)
         throw std::logic_error(
             "There are not that many agents in this entity. " +
             std::to_string(n_agents) + " <= " + std::to_string(i)
             );
 
-    return &model->get_agents()[i];
+    return i;
 }
 
 template<typename TSeq>
@@ -227,7 +227,7 @@ inline bool Entity<TSeq>::operator==(const Entity<TSeq> & other) const
 }
 
 template<typename TSeq>
-inline void Entity<TSeq>::distribute()
+inline void Entity<TSeq>::distribute(Model<TSeq> * model)
 {
 
     if (dist_fun)

diff --git a/include/epiworld/model-meat.hpp b/include/epiworld/model-meat.hpp
@@ -411,13 +411,6 @@ inline Model<TSeq>::Model(const Model<TSeq> & model) :
         for (auto & p : population_backup)
             p.model = this;
 
-    for (auto & e : entities)
-        e.model = this;
-
-    if (entities_backup.size() != 0u)
-        for (auto & e : entities_backup)
-            e.model = this;
-
     // Pointing to the right place. This needs
     // to be done afterwards since the state zero is set as a function
     // of the population.
@@ -776,7 +769,7 @@ inline void Model<TSeq>::dist_entities()
     for (auto & entity: entities)
     {
 
-        entity.distribute();
+        entity.distribute(this);
 
         // Apply the events
         events_run();
@@ -960,7 +953,6 @@ template<typename TSeq>
 inline void Model<TSeq>::add_entity(Entity<TSeq> e)
 {
 
-    e.model = this;
     e.id = entities.size();
     entities.push_back(e);
 

diff --git a/include/epiworld/models/diffnet.hpp b/include/epiworld/models/diffnet.hpp
@@ -20,7 +20,7 @@ class ModelDiffNet : public epiworld::Model<TSeq>
 
     ModelDiffNet(
         ModelDiffNet<TSeq> & model,
-        std::string innovation_name,
+        const std::string & innovation_name,
         epiworld_double prevalence,
         epiworld_double prob_adopt,
         bool normalize_exposure = true,
@@ -31,7 +31,7 @@ class ModelDiffNet : public epiworld::Model<TSeq>
     );
 
     ModelDiffNet(
-        std::string innovation_name,
+        const std::string & innovation_name,
         epiworld_double prevalence,
         epiworld_double prob_adopt,
         bool normalize_exposure = true,
@@ -52,7 +52,7 @@ class ModelDiffNet : public epiworld::Model<TSeq>
 template<typename TSeq>
 inline ModelDiffNet<TSeq>::ModelDiffNet(
     ModelDiffNet<TSeq> & model,
-    std::string innovation_name,
+    const std::string & innovation_name,
     epiworld_double prevalence,
     epiworld_double prob_adopt,
     bool normalize_exposure,
@@ -180,7 +180,7 @@ inline ModelDiffNet<TSeq>::ModelDiffNet(
 
 template<typename TSeq>
 inline ModelDiffNet<TSeq>::ModelDiffNet(
-    std::string innovation_name,
+    const std::string & innovation_name,
     epiworld_double prevalence,
     epiworld_double prob_adopt,
     bool normalize_exposure,

diff --git a/include/epiworld/models/seir.hpp b/include/epiworld/models/seir.hpp
@@ -25,15 +25,15 @@ class ModelSEIR : public epiworld::Model<TSeq>
 
     ModelSEIR(
         ModelSEIR<TSeq> & model,
-        std::string vname,
+        const std::string & vname,
         epiworld_double prevalence,
         epiworld_double transmission_rate,
         epiworld_double avg_incubation_days,
         epiworld_double recovery_rate
     );
 
     ModelSEIR(
-        std::string vname,
+        const std::string & vname,
         epiworld_double prevalence,
         epiworld_double transmission_rate,
         epiworld_double avg_incubation_days,
@@ -84,7 +84,7 @@ class ModelSEIR : public epiworld::Model<TSeq>
 template<typename TSeq>
 inline ModelSEIR<TSeq>::ModelSEIR(
     ModelSEIR<TSeq> & model,
-    std::string vname,
+    const std::string & vname,
     epiworld_double prevalence,
     epiworld_double transmission_rate,
     epiworld_double avg_incubation_days,
@@ -122,7 +122,7 @@ inline ModelSEIR<TSeq>::ModelSEIR(
 
 template<typename TSeq>
 inline ModelSEIR<TSeq>::ModelSEIR(
-    std::string vname,
+    const std::string & vname,
     epiworld_double prevalence,
     epiworld_double transmission_rate,
     epiworld_double avg_incubation_days,

diff --git a/include/epiworld/models/seirconnected.hpp b/include/epiworld/models/seirconnected.hpp
@@ -20,7 +20,7 @@ class ModelSEIRCONN : public epiworld::Model<TSeq>
 
     ModelSEIRCONN(
         ModelSEIRCONN<TSeq> & model,
-        std::string vname,
+        const std::string & vname,
         epiworld_fast_uint n,
         epiworld_double prevalence,
         epiworld_double contact_rate,
@@ -30,7 +30,7 @@ class ModelSEIRCONN : public epiworld::Model<TSeq>
     );
 
     ModelSEIRCONN(
-        std::string vname,
+        const std::string & vname,
         epiworld_fast_uint n,
         epiworld_double prevalence,
         epiworld_double contact_rate,
@@ -136,7 +136,7 @@ inline Model<TSeq> * ModelSEIRCONN<TSeq>::clone_ptr()
 template<typename TSeq>
 inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
     ModelSEIRCONN<TSeq> & model,
-    std::string vname,
+    const std::string & vname,
     epiworld_fast_uint n,
     epiworld_double prevalence,
     epiworld_double contact_rate,
@@ -348,7 +348,7 @@ inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
 
 template<typename TSeq>
 inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
-    std::string vname,
+    const std::string & vname,
     epiworld_fast_uint n,
     epiworld_double prevalence,
     epiworld_double contact_rate,

diff --git a/include/epiworld/models/seird.hpp b/include/epiworld/models/seird.hpp
@@ -31,7 +31,7 @@ class ModelSEIRD : public epiworld::Model<TSeq>
    */
   ModelSEIRD(
     ModelSEIRD<TSeq> & model,
-    std::string vname,
+    const std::string & vname,
     epiworld_double prevalence,
     epiworld_double transmission_rate,
     epiworld_double avg_incubation_days,
@@ -50,7 +50,7 @@ class ModelSEIRD : public epiworld::Model<TSeq>
    * @param death_rate Death rate of the disease.
    */
   ModelSEIRD(
-    std::string vname,
+    const std::string & vname,
     epiworld_double prevalence,
     epiworld_double transmission_rate,
     epiworld_double avg_incubation_days,
@@ -145,7 +145,7 @@ class ModelSEIRD : public epiworld::Model<TSeq>
 template<typename TSeq>
 inline ModelSEIRD<TSeq>::ModelSEIRD(
     ModelSEIRD<TSeq> & model,
-    std::string vname,
+    const std::string & vname,
     epiworld_double prevalence,
     epiworld_double transmission_rate,
     epiworld_double avg_incubation_days,
@@ -187,7 +187,7 @@ inline ModelSEIRD<TSeq>::ModelSEIRD(
 
 template<typename TSeq>
 inline ModelSEIRD<TSeq>::ModelSEIRD(
-    std::string vname,
+    const std::string & vname,
     epiworld_double prevalence,
     epiworld_double transmission_rate,
     epiworld_double avg_incubation_days,

diff --git a/include/epiworld/models/seirdconnected.hpp b/include/epiworld/models/seirdconnected.hpp
@@ -20,7 +20,7 @@ class ModelSEIRDCONN : public epiworld::Model<TSeq>
 
     ModelSEIRDCONN(
         ModelSEIRDCONN<TSeq> & model,
-        std::string vname,
+        const std::string & vname,
         epiworld_fast_uint n,
         epiworld_double prevalence,
         epiworld_double contact_rate,
@@ -31,7 +31,7 @@ class ModelSEIRDCONN : public epiworld::Model<TSeq>
     );
 
     ModelSEIRDCONN(
-        std::string vname,
+        const std::string & vname,
         epiworld_fast_uint n,
         epiworld_double prevalence,
         epiworld_double contact_rate,
@@ -142,7 +142,7 @@ inline Model<TSeq> * ModelSEIRDCONN<TSeq>::clone_ptr()
 template<typename TSeq>
 inline ModelSEIRDCONN<TSeq>::ModelSEIRDCONN(
     ModelSEIRDCONN<TSeq> & model,
-    std::string vname,
+    const std::string & vname,
     epiworld_fast_uint n,
     epiworld_double prevalence,
     epiworld_double contact_rate,
@@ -367,7 +367,7 @@ inline ModelSEIRDCONN<TSeq>::ModelSEIRDCONN(
 
 template<typename TSeq>
 inline ModelSEIRDCONN<TSeq>::ModelSEIRDCONN(
-    std::string vname,
+    const std::string & vname,
     epiworld_fast_uint n,
     epiworld_double prevalence,
     epiworld_double contact_rate,

diff --git a/include/epiworld/models/seirmixing.hpp b/include/epiworld/models/seirmixing.hpp
@@ -48,7 +48,7 @@ class ModelSEIRMixing : public epiworld::Model<TSeq>
      */
     ModelSEIRMixing(
         ModelSEIRMixing<TSeq> & model,
-        std::string vname,
+        const std::string & vname,
         epiworld_fast_uint n,
         epiworld_double prevalence,
         epiworld_double contact_rate,
@@ -71,7 +71,7 @@ class ModelSEIRMixing : public epiworld::Model<TSeq>
      * @param contact_matrix The contact matrix between entities in the model.
      */
     ModelSEIRMixing(
-        std::string vname,
+        const std::string & vname,
         epiworld_fast_uint n,
         epiworld_double prevalence,
         epiworld_double contact_rate,
@@ -281,7 +281,7 @@ inline Model<TSeq> * ModelSEIRMixing<TSeq>::clone_ptr()
 template<typename TSeq>
 inline ModelSEIRMixing<TSeq>::ModelSEIRMixing(
     ModelSEIRMixing<TSeq> & model,
-    std::string vname,
+    const std::string & vname,
     epiworld_fast_uint n,
     epiworld_double prevalence,
     epiworld_double contact_rate,
@@ -477,7 +477,7 @@ inline ModelSEIRMixing<TSeq>::ModelSEIRMixing(
 
 template<typename TSeq>
 inline ModelSEIRMixing<TSeq>::ModelSEIRMixing(
-    std::string vname,
+    const std::string & vname,
     epiworld_fast_uint n,
     epiworld_double prevalence,
     epiworld_double contact_rate,

diff --git a/include/epiworld/models/sir.hpp b/include/epiworld/models/sir.hpp
@@ -19,14 +19,14 @@ class ModelSIR : public epiworld::Model<TSeq>
 
     ModelSIR(
         ModelSIR<TSeq> & model,
-        std::string vname,
+        const std::string & vname,
         epiworld_double prevalence,
         epiworld_double transmission_rate,
         epiworld_double recovery_rate
     );
 
     ModelSIR(
-        std::string vname,
+        const std::string & vname,
         epiworld_double prevalence,
         epiworld_double transmission_rate,
         epiworld_double recovery_rate
@@ -47,7 +47,7 @@ class ModelSIR : public epiworld::Model<TSeq>
 template<typename TSeq>
 inline ModelSIR<TSeq>::ModelSIR(
     ModelSIR<TSeq> & model,
-    std::string vname,
+    const std::string & vname,
     epiworld_double prevalence,
     epiworld_double transmission_rate,
     epiworld_double recovery_rate
@@ -80,7 +80,7 @@ inline ModelSIR<TSeq>::ModelSIR(
 
 template<typename TSeq>
 inline ModelSIR<TSeq>::ModelSIR(
-    std::string vname,
+    const std::string & vname,
     epiworld_double prevalence,
     epiworld_double transmission_rate,
     epiworld_double recovery_rate

diff --git a/include/epiworld/models/sirconnected.hpp b/include/epiworld/models/sirconnected.hpp
@@ -21,7 +21,7 @@ class ModelSIRCONN : public epiworld::Model<TSeq>
 
     ModelSIRCONN(
         ModelSIRCONN<TSeq> & model,
-        std::string vname,
+        const std::string & vname,
         epiworld_fast_uint n,
         epiworld_double prevalence,
         epiworld_double contact_rate,
@@ -30,7 +30,7 @@ class ModelSIRCONN : public epiworld::Model<TSeq>
     );
 
     ModelSIRCONN(
-        std::string vname,
+        const std::string & vname,
         epiworld_fast_uint n,
         epiworld_double prevalence,
         epiworld_double contact_rate,
@@ -143,7 +143,7 @@ inline Model<TSeq> * ModelSIRCONN<TSeq>::clone_ptr()
 template<typename TSeq>
 inline ModelSIRCONN<TSeq>::ModelSIRCONN(
     ModelSIRCONN<TSeq> & model,
-    std::string vname,
+    const std::string & vname,
     epiworld_fast_uint n,
     epiworld_double prevalence,
     epiworld_double contact_rate,
@@ -324,7 +324,7 @@ inline ModelSIRCONN<TSeq>::ModelSIRCONN(
 
 template<typename TSeq>
 inline ModelSIRCONN<TSeq>::ModelSIRCONN(
-    std::string vname,
+    const std::string & vname,
     epiworld_fast_uint n,
     epiworld_double prevalence,
     epiworld_double contact_rate,