Virus now hold info about dist

UofUEpiBio · Jun 6, 2024 · 917d21d · 917d21d
1 parent 5cc1bcd
commit 917d21d
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Showing 35 changed files with 238 additions and 285 deletions.
diff --git a/epiworld.hpp b/epiworld.hpp
diff --git a/examples/00-hello-world/main.cpp b/examples/00-hello-world/main.cpp
@@ -17,11 +17,11 @@ int main()
     model.add_state("Removed");
 
     // Adding the tool and virus
-    epiworld::Virus<int> virus("covid 19");
+    epiworld::Virus<int> virus("covid 19", 50, false);
     virus.set_post_immunity(1.0);
     virus.set_state(1,2,3);
     virus.set_prob_death(.01);
-    model.add_virus_n(virus, 50);
+    model.add_virus(virus);
 
     epiworld::Tool<int> tool("vaccine");
     model.add_tool(tool, .5);

diff --git a/examples/03-simple-sir/main.cpp b/examples/03-simple-sir/main.cpp
@@ -5,7 +5,7 @@ int main()
 {
 
   // Creating a virus
-  epiworld::Virus<> covid19("covid 19");
+  epiworld::Virus<> covid19("covid 19", 0.05, true);
   covid19.set_prob_infecting(0.8);
   covid19.set_state(1,2,2);
 
@@ -21,7 +21,7 @@ int main()
   model.add_state("Removed");
 
   // Adding the tool and virus
-  model.add_virus(covid19, .05);
+  model.add_virus(covid19);
 
   model.add_tool(vax, .5);
 

diff --git a/examples/04-advanced-usage/main.cpp b/examples/04-advanced-usage/main.cpp
@@ -63,7 +63,7 @@ int main() {
     model.add_param(0.01, "virus death");
 
     // Initializing disease ---------------------------------------------------
-    epiworld::Virus<DAT> covid19("COVID19");
+    epiworld::Virus<DAT> covid19("COVID19", 0.01, true);
     covid19.set_sequence(base_seq);
     covid19.set_mutation(covid19_mut);
     covid19.set_post_recovery(post_covid); 
@@ -94,7 +94,7 @@ int main() {
     post_immunity.set_susceptibility_reduction(1.0);
 
     // Adding the virus and the tools to the model ----------------------------
-    model.add_virus(covid19, 0.01); 
+    model.add_virus(covid19); 
 
     model.add_tool(immune, 1.0);
     model.add_tool(vaccine, 0.5);

diff --git a/examples/05-user-data/main.cpp b/examples/05-user-data/main.cpp
@@ -21,7 +21,7 @@ int main()
     model.add_param(.3, "recovery");
 
     // Setting up virus --------------------------------------------------------
-    epiworld::Virus<> v("covid");
+    epiworld::Virus<> v("covid", 5, false);
     v.set_state(1,2,2);
 
     EPI_NEW_POSTRECOVERYFUN_LAMBDA(immunity, int)
@@ -51,7 +51,7 @@ int main()
 
     model.add_tool(is, 1.0);
     model.add_tool_n(postImm, 0u);
-    model.add_virus_n(v, 5);
+    model.add_virus(v);
     model.run(112, 30);
     model.print();
 

diff --git a/examples/07-surveillance/07-surveillance.md b/examples/07-surveillance/07-surveillance.md
@@ -57,7 +57,7 @@ int main()
 {
 
   // Creating a virus
-  epiworld::Virus<> covid19("covid 19");
+  epiworld::Virus<> covid19("covid 19", .01, true);
   covid19.set_infectiousness(.8);
 
   // Creating a tool
@@ -68,7 +68,7 @@ int main()
   epiworld::Model<> model;
 
   // Adding the tool and virus
-  model.add_virus(covid19, .01);
+  model.add_virus(covid19);
   model.add_tool(vax, .5);
 
   // Generating a random pop

diff --git a/include/epiworld/agent-bones.hpp b/include/epiworld/agent-bones.hpp
@@ -218,6 +218,7 @@ class Agent {
     int get_id() const; ///< Id of the individual
 
     VirusPtr<TSeq> & get_virus();
+    const VirusPtr<TSeq> & get_virus() const;
 
     ToolPtr<TSeq> & get_tool(int i);
     Tools<TSeq> get_tools();

diff --git a/include/epiworld/agent-meat.hpp b/include/epiworld/agent-meat.hpp
@@ -455,6 +455,11 @@ inline VirusPtr<TSeq> & Agent<TSeq>::get_virus() {
     return virus;
 }
 
+template<typename TSeq>
+inline const VirusPtr<TSeq> & Agent<TSeq>::get_virus() const {
+    return virus;
+}
+
 
 template<typename TSeq>
 inline Tools<TSeq> Agent<TSeq>::get_tools() {

diff --git a/include/epiworld/model-bones.hpp b/include/epiworld/model-bones.hpp
@@ -335,9 +335,7 @@ class Model {
      * indicating number of individuals.
      */
     ///@{
-    void add_virus(Virus<TSeq> & v, epiworld_double preval);
-    void add_virus_n(Virus<TSeq> & v, epiworld_fast_uint preval);
-    void add_virus_fun(Virus<TSeq> & v, VirusToAgentFun<TSeq> fun);
+    void add_virus(Virus<TSeq> & v);
     void add_tool(Tool<TSeq> & t, epiworld_double preval);
     void add_tool_n(Tool<TSeq> & t, epiworld_fast_uint preval);
     void add_tool_fun(Tool<TSeq> & t, ToolToAgentFun<TSeq> fun);

diff --git a/include/epiworld/model-meat-print.hpp b/include/epiworld/model-meat-print.hpp
@@ -157,13 +157,13 @@ inline const Model<TSeq> & Model<TSeq>::print(bool lite) const
         if (i < n_viruses_model)
         {
 
-            if (virus.get_prevalence_as_proportion())
+            if (virus->get_prevalence_as_proportion())
             {
 
                 printf_epiworld(
                     " - %s (baseline prevalence: %.2f%%)\n",
-                    virus.get_name().c_str(),
-                    virus.get_prevalence() * 100.00
+                    virus->get_name().c_str(),
+                    virus->get_prevalence() * 100.00
                 );
 
             }
@@ -172,8 +172,8 @@ inline const Model<TSeq> & Model<TSeq>::print(bool lite) const
 
                 printf_epiworld(
                     " - %s (baseline prevalence: %i seeds)\n",
-                    virus.get_name().c_str(),
-                    static_cast<int>(virus.get_prevalence())
+                    virus->get_name().c_str(),
+                    static_cast<int>(virus->get_prevalence())
                 );
 
             }
@@ -182,7 +182,7 @@ inline const Model<TSeq> & Model<TSeq>::print(bool lite) const
 
             printf_epiworld(
                 " - %s (originated in the model...)\n",
-                virus.get_name().c_str()
+                virus->get_name().c_str()
             );
 
         }

diff --git a/include/epiworld/model-meat.hpp b/include/epiworld/model-meat.hpp
@@ -754,7 +754,7 @@ inline void Model<TSeq>::dist_virus()
     for (auto & v: viruses)
     {
 
-        v.distribute(this);
+        v->distribute(this);
 
         // Apply the events
         events_run();
@@ -972,15 +972,11 @@ inline void Model<TSeq>::seed(size_t s) {
 }
 
 template<typename TSeq>
-inline void Model<TSeq>::add_virus(Virus<TSeq> & v, epiworld_double preval)
+inline void Model<TSeq>::add_virus(
+    Virus<TSeq> & v
+    )
 {
 
-    if (preval > 1.0)
-        throw std::range_error("Prevalence of virus cannot be above 1.0");
-
-    if (preval < 0.0)
-        throw std::range_error("Prevalence of virus cannot be negative");
-
     // Checking the state
     epiworld_fast_int init_, post_, rm_;
     v.get_state(&init_, &post_, &rm_);
@@ -1002,57 +998,6 @@ inline void Model<TSeq>::add_virus(Virus<TSeq> & v, epiworld_double preval)
 
 }
 
-template<typename TSeq>
-inline void Model<TSeq>::add_virus_n(Virus<TSeq> & v, epiworld_fast_uint preval)
-{
-
-    // Checking the ids
-    epiworld_fast_int init_, post_, rm_;
-    v.get_state(&init_, &post_, &rm_);
-
-    if (init_ == -99)
-        throw std::logic_error(
-            "The virus \"" + v.get_name() + "\" has no -init- state."
-            );
-    else if (post_ == -99)
-        throw std::logic_error(
-            "The virus \"" + v.get_name() + "\" has no -post- state."
-            );
-
-    // Setting the id
-    db.record_virus(v);
-
-    // Adding new virus
-    viruses.push_back(std::make_shared< Virus<TSeq> >(v));
-
-}
-
-template<typename TSeq>
-inline void Model<TSeq>::add_virus_fun(Virus<TSeq> & v, VirusToAgentFun<TSeq> fun)
-{
-
-    // Checking the ids
-    epiworld_fast_int init_, post_, rm_;
-    v.get_state(&init_, &post_, &rm_);
-
-    if (init_ == -99)
-        throw std::logic_error(
-            "The virus \"" + v.get_name() + "\" has no -init- state."
-            );
-    else if (post_ == -99)
-        throw std::logic_error(
-            "The virus \"" + v.get_name() + "\" has no -post- state."
-            );
-
-    // Setting the id
-    db.record_virus(v);
-    // v.set_id(viruses.size());
-
-    // Adding new virus
-    viruses.push_back(std::make_shared< Virus<TSeq> >(v));
-
-}
-
 template<typename TSeq>
 inline void Model<TSeq>::add_tool(Tool<TSeq> & t, epiworld_double preval)
 {

diff --git a/include/epiworld/models/diffnet.hpp b/include/epiworld/models/diffnet.hpp
@@ -164,12 +164,12 @@ inline ModelDiffNet<TSeq>::ModelDiffNet(
     model.add_param(prob_adopt, parname);
 
     // Preparing the virus -------------------------------------------
-    epiworld::Virus<TSeq> innovation(innovation_name);
+    epiworld::Virus<TSeq> innovation(innovation_name, prevalence, true);
     innovation.set_state(1,1,1);
 
     innovation.set_prob_infecting(&model(parname));
 
-    model.add_virus(innovation, prevalence);
+    model.add_virus(innovation);
 
     model.set_name(
         std::string("Diffusion of Innovations - ") + innovation_name);

diff --git a/include/epiworld/models/init-functions.hpp b/include/epiworld/models/init-functions.hpp
@@ -32,10 +32,10 @@ inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_sir(
         double n   = static_cast<double>(model->size());
         for (const auto & virus: model->get_viruses())
         {
-            if (virus.get_prevalence_as_proportion())
-                tot += virus.get_prevalence();
+            if (virus->get_prevalence_as_proportion())
+                tot += virus->get_prevalence();
             else
-                tot += virus.get_prevalence() / n;
+                tot += virus->get_prevalence() / n;
         }
 
         // Putting the total into context
@@ -106,10 +106,10 @@ inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_sird(
         double n   = static_cast<double>(model->size());
         for (const auto & virus: model->get_viruses())
         {
-            if (virus.get_prevalence_as_proportion())
-                tot += virus.get_prevalence();
+            if (virus->get_prevalence_as_proportion())
+                tot += virus->get_prevalence();
             else
-                tot += virus.get_prevalence() / n;
+                tot += virus->get_prevalence() / n;
         }
 
         // Putting the total into context
@@ -184,10 +184,10 @@ inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_seir(
         double n   = static_cast<double>(model->size());
         for (const auto & virus: model->get_viruses())
         {
-            if (virus.get_prevalence_as_proportion())
-                tot += virus.get_prevalence();
+           if (virus->get_prevalence_as_proportion())
+                tot += virus->get_prevalence();
             else
-                tot += virus.get_prevalence() / n;
+                tot += virus->get_prevalence() / n;
         }
 
         // Putting the total into context
@@ -266,10 +266,10 @@ inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_seird(
         double n   = static_cast<double>(model->size());
         for (const auto & virus: model->get_viruses())
         {
-            if (virus.get_prevalence_as_proportion())
-                tot += virus.get_prevalence();
+            if (virus->get_prevalence_as_proportion())
+                tot += virus->get_prevalence();
             else
-                tot += virus.get_prevalence() / n;
+                tot += virus->get_prevalence() / n;
         }
 
         // Putting the total into context

diff --git a/include/epiworld/models/seir.hpp b/include/epiworld/models/seir.hpp
@@ -104,15 +104,15 @@ inline ModelSEIR<TSeq>::ModelSEIR(
     model.add_param(recovery_rate, "Recovery rate");
 
     // Preparing the virus -------------------------------------------
-    epiworld::Virus<TSeq> virus(vname);
+    epiworld::Virus<TSeq> virus(vname, prevalence, true);
     virus.set_state(ModelSEIR<TSeq>::EXPOSED, ModelSEIR<TSeq>::REMOVED, ModelSEIR<TSeq>::REMOVED);
 
     virus.set_prob_infecting(&model("Transmission rate"));
     virus.set_incubation(&model("Incubation days"));
     virus.set_prob_recovery(&model("Recovery rate"));
 
     // Adding the tool and the virus
-    model.add_virus(virus, prevalence);
+    model.add_virus(virus);
 
     model.set_name("Susceptible-Exposed-Infected-Removed (SEIR)");
 

diff --git a/include/epiworld/models/seirconnected.hpp b/include/epiworld/models/seirconnected.hpp
@@ -322,7 +322,7 @@ inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
 
 
     // Preparing the virus -------------------------------------------
-    epiworld::Virus<TSeq> virus(vname);
+    epiworld::Virus<TSeq> virus(vname, prevalence, true);
     virus.set_state(
         ModelSEIRCONN<TSeq>::EXPOSED,
         ModelSEIRCONN<TSeq>::RECOVERED,
@@ -333,7 +333,7 @@ inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
     virus.set_prob_recovery(&model("Prob. Recovery"));
     virus.set_incubation(&model("Avg. Incubation days"));
 
-    model.add_virus(virus, prevalence);
+    model.add_virus(virus);
 
     model.queuing_off(); // No queuing need
 

diff --git a/include/epiworld/models/seird.hpp b/include/epiworld/models/seird.hpp
@@ -168,7 +168,7 @@ inline ModelSEIRD<TSeq>::ModelSEIRD(
   model.add_param(death_rate, "Death rate");
 
   // Preparing the virus -------------------------------------------
-  epiworld::Virus<TSeq> virus(vname);
+  epiworld::Virus<TSeq> virus(vname, prevalence, true);
   virus.set_state(ModelSEIRD<TSeq>::EXPOSED, ModelSEIRD<TSeq>::REMOVED, ModelSEIRD<TSeq>::DECEASED);
 
   virus.set_prob_infecting(&model("Transmission rate"));
@@ -177,7 +177,7 @@ inline ModelSEIRD<TSeq>::ModelSEIRD(
   virus.set_prob_recovery(&model("Recovery rate"));
 
   // Adding the tool and the virus
-  model.add_virus(virus, prevalence);
+  model.add_virus(virus);
 
   model.set_name("Susceptible-Exposed-Infected-Removed-Deceased (SEIRD)");
 

diff --git a/include/epiworld/models/seirdconnected.hpp b/include/epiworld/models/seirdconnected.hpp
@@ -341,7 +341,7 @@ inline ModelSEIRDCONN<TSeq>::ModelSEIRDCONN(
 
 
     // Preparing the virus -------------------------------------------
-    epiworld::Virus<TSeq> virus(vname);
+    epiworld::Virus<TSeq> virus(vname, prevalence, true);
     virus.set_state(
         ModelSEIRDCONN<TSeq>::EXPOSED,
         ModelSEIRDCONN<TSeq>::REMOVED,
@@ -352,7 +352,7 @@ inline ModelSEIRDCONN<TSeq>::ModelSEIRDCONN(
     virus.set_prob_recovery(&model("Prob. Recovery"));
     virus.set_incubation(&model("Avg. Incubation days"));
     virus.set_prob_death(&model("Death rate"));
-    model.add_virus(virus, prevalence);
+    model.add_virus(virus);
 
     model.queuing_off(); // No queuing need