Fixing ModelSISD

NAMESPACE

@@ -42,11 +42,14 @@ S3method(plot,epiworld_multiple_save_reproductive_number)
 S3method(plot,epiworld_repnum)
 S3method(plot,epiworld_seir)
 S3method(plot,epiworld_seirconn)
+S3method(plot,epiworld_seirdconn)
 S3method(plot,epiworld_sir)
 S3method(plot,epiworld_sirconn)
 S3method(plot,epiworld_sird)
 S3method(plot,epiworld_sis)
+S3method(plot,epiworld_sisd)
 S3method(plot,epiworld_surv)
+S3method(plot,epiworld_survd)
 S3method(print,epiworld_agent)
 S3method(print,epiworld_agents)
 S3method(print,epiworld_agents_tools)
@@ -74,12 +77,15 @@ S3method(verbose_on,epiworld_model)
 export(ModelDiffNet)
 export(ModelSEIR)
 export(ModelSEIRCONN)
+export(ModelSEIRDCONN)
 export(ModelSIR)
 export(ModelSIRCONN)
 export(ModelSIRD)
 export(ModelSIRLogit)
 export(ModelSIS)
+export(ModelSISD)
 export(ModelSURV)
+export(ModelSURVD)
 export(add_global_action)
 export(add_tool)
 export(add_tool_agent)

R/cpp11.R

@@ -128,6 +128,22 @@ ModelSIRD_cpp <- function(name, prevalence, transmission_rate, recovery_rate, de
   .Call(`_epiworldR_ModelSIRD_cpp`, name, prevalence, transmission_rate, recovery_rate, death_rate)
 }
 
+ModelSISD_cpp <- function(name, prevalence, transmission_rate, recovery_rate, death_rate) {
+  .Call(`_epiworldR_ModelSISD_cpp`, name, prevalence, transmission_rate, recovery_rate, death_rate)
+}
+
+ModelSURVD_cpp <- function(name, prevalence, efficacy_vax, latent_period, prob_symptoms, prop_vaccinated, prop_vax_redux_transm, infect_period, prop_vax_redux_infect, surveillance_prob, transmission_rate, prob_death, prob_noreinfect) {
+  .Call(`_epiworldR_ModelSURVD_cpp`, name, prevalence, efficacy_vax, latent_period, prob_symptoms, prop_vaccinated, prop_vax_redux_transm, infect_period, prop_vax_redux_infect, surveillance_prob, transmission_rate, prob_death, prob_noreinfect)
+}
+
+ModelSIRDCONN_cpp <- function(name, n, prevalence, contact_rate, transmission_rate, recovery_rate, death_rate) {
+  .Call(`_epiworldR_ModelSIRDCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, recovery_rate, death_rate)
+}
+
+ModelSEIRDCONN_cpp <- function(name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate, death_rate) {
+  .Call(`_epiworldR_ModelSEIRDCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate, death_rate)
+}
+
 ModelSEIRCONN_cpp <- function(name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate) {
   .Call(`_epiworldR_ModelSEIRCONN_cpp`, name, n, prevalence, contact_rate, transmission_rate, incubation_days, recovery_rate)
 }

inst/include/epiworld.hpp

@@ -3183,8 +3183,10 @@ inline void DataBase<TSeq>::record()
         // Now the diagonal must reflect the state
         for (size_t s_i = 0u; s_i < model->nstates; ++s_i)
         {
+
             for (size_t s_j = 0u; s_j < model->nstates; ++s_j)
             {
+
                 if ((s_i != s_j) && (transition_matrix[s_i + s_j * model->nstates] > 0))
                 {
                     transition_matrix[s_j + s_j * model->nstates] +=
@@ -3195,15 +3197,18 @@ inline void DataBase<TSeq>::record()
 
             }
 
-            #ifdef EPI_DEBUG
+        }
+
+        #ifdef EPI_DEBUG
+        for (size_t s_i = 0u; s_i < model->nstates; ++s_i)
+        {
             if (transition_matrix[s_i + s_i * model->nstates] != 
                 today_total[s_i])
                 throw std::logic_error(
                     "The diagonal of the updated transition Matrix should match the daily totals"
                     );
-            #endif
         }
-
+        #endif
 
     }
 
@@ -6949,7 +6954,6 @@ inline void Model<TSeq>::actions_run()
                 for (size_t t = 0u; t < p->n_tools; ++t)
                     db.update_tool(p->tools[t]->id, p->state, a.new_state);
 
-
                 // Saving the last state and setting the new one
                 p->state_prev = p->state;
                 p->state      = a.new_state;
@@ -16902,16 +16906,16 @@ inline ModelSISD<TSeq>::ModelSISD(
     // Adding statuses
     model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
     model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
-    model.add_state("Deceased")
+    model.add_state("Deceased");
 
     // Setting up parameters
     model.add_param(transmission_rate, "Transmission rate");
     model.add_param(recovery_rate, "Recovery rate");
-    model.add_param(death_rate, "Death rate")
+    model.add_param(death_rate, "Death rate");
 
     // Preparing the virus -------------------------------------------
     epiworld::Virus<TSeq> virus(vname);
-    virus.set_state(1,0,0);
+    virus.set_state(1,0,2);
 
     virus.set_prob_infecting(&model("Transmission rate"));
     virus.set_prob_recovery(&model("Recovery rate"));
@@ -16929,7 +16933,7 @@ inline ModelSISD<TSeq>::ModelSISD(
     epiworld_double prevalence,
     epiworld_double transmission_rate,
     epiworld_double recovery_rate,
-    epiworld_double death_rate,
+    epiworld_double death_rate
     )
 {