ModelSIRD work OK

UofUEpiBio · Jul 25, 2023 · e6d92a5 · e6d92a5
1 parent 7b7ab20
commit e6d92a5
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Showing 14 changed files with 144 additions and 2 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -44,6 +44,7 @@ S3method(plot,epiworld_seir)
 S3method(plot,epiworld_seirconn)
 S3method(plot,epiworld_sir)
 S3method(plot,epiworld_sirconn)
+S3method(plot,epiworld_sird)
 S3method(plot,epiworld_sis)
 S3method(plot,epiworld_surv)
 S3method(print,epiworld_agent)
@@ -75,6 +76,7 @@ export(ModelSEIR)
 export(ModelSEIRCONN)
 export(ModelSIR)
 export(ModelSIRCONN)
+export(ModelSIRD)
 export(ModelSIRLogit)
 export(ModelSIS)
 export(ModelSURV)

diff --git a/R/cpp11.R b/R/cpp11.R
@@ -124,6 +124,10 @@ ModelSIR_cpp <- function(name, prevalence, transmission_rate, recovery_rate) {
   .Call(`_epiworldR_ModelSIR_cpp`, name, prevalence, transmission_rate, recovery_rate)
 }
 
+ModelSIRD_cpp <- function(name, prevalence, transmission_rate, recovery_rate, death_rate) {
+  .Call(`_epiworldR_ModelSIRD_cpp`, name, prevalence, transmission_rate, 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)
 }

diff --git a/inst/include/epiworld.hpp b/inst/include/epiworld.hpp
@@ -16720,6 +16720,125 @@ inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
 //////////////////////////////////////////////////////////////////////////////*/
 
 
+/*//////////////////////////////////////////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+ Start of -include/epiworld//models/sird.hpp-
+
+////////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////*/
+
+
+#ifndef EPIWORLD_SIRD_H 
+#define EPIWORLD_SIRD_H
+
+/**
+ * @brief Template for a Susceptible-Infected-Removed-Deceased (SIRD) model
+ * 
+ * @param model A Model<TSeq> object where to set up the SIRD.
+ * @param vname std::string Name of the virus
+ * @param initial_prevalence epiworld_double Initial prevalence
+ * @param initial_efficacy epiworld_double Initial susceptibility_reduction of the immune system
+ * @param initial_recovery epiworld_double Initial recovery_rate rate of the immune system
+ * @param initial_death epiworld_double Initial death_rate of the immune system 
+ */
+template<typename TSeq = int>
+class ModelSIRD : public epiworld::Model<TSeq>
+{
+public:
+
+    ModelSIRD() {};
+
+    ModelSIRD(
+        ModelSIRD<TSeq> & model,
+        std::string vname,
+        epiworld_double prevalence,
+        epiworld_double transmission_rate,
+        epiworld_double recovery_rate, 
+        epiworld_double death_rate
+    );
+
+    ModelSIRD(
+        std::string vname,
+        epiworld_double prevalence,
+        epiworld_double transmission_rate,
+        epiworld_double recovery_rate, 
+        epiworld_double death_rate
+    );
+
+};
+
+template<typename TSeq>
+inline ModelSIRD<TSeq>::ModelSIRD(
+    ModelSIRD<TSeq> & model,
+    std::string vname,
+    epiworld_double prevalence,
+    epiworld_double transmission_rate,
+    epiworld_double recovery_rate, 
+    epiworld_double death_rate
+    )
+{
+
+    // Adding statuses
+    model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
+    model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
+    model.add_state("Recovered"),
+    model.add_state("Deceased")
+    ;
+
+    // Setting up parameters
+    model.add_param(recovery_rate, "Recovery rate");
+    model.add_param(transmission_rate, "Transmission rate"),
+    model.add_param(death_rate, "Death rate");
+
+    // Preparing the virus -------------------------------------------
+    epiworld::Virus<TSeq> virus(vname);
+    virus.set_state(1,2,3);
+    virus.set_prob_recovery(&model("Recovery rate"));
+    virus.set_prob_infecting(&model("Transmission rate"));
+    virus.set_prob_death(&model("Death rate"));
+
+    model.add_virus(virus, prevalence);
+
+    model.set_name("Susceptible-Infected-Recovered-Deceased (SIRD)");
+
+    return;
+
+}
+
+template<typename TSeq>
+inline ModelSIRD<TSeq>::ModelSIRD(
+    std::string vname,
+    epiworld_double prevalence,
+    epiworld_double transmission_rate,
+    epiworld_double recovery_rate,
+    epiworld_double death_rate
+    )
+{
+
+    ModelSIRD<TSeq>(
+        *this,
+        vname,
+        prevalence,
+        transmission_rate,
+        recovery_rate, 
+        death_rate
+        );
+
+    return;
+
+}
+
+#endif
+/*//////////////////////////////////////////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+ End of -include/epiworld//models/sird.hpp-
+
+////////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////*/
+
+
 /*//////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 

diff --git a/man/ModelDiffNet.Rd b/man/ModelDiffNet.Rd
diff --git a/man/ModelSEIR.Rd b/man/ModelSEIR.Rd
diff --git a/man/ModelSEIRCONN.Rd b/man/ModelSEIRCONN.Rd
diff --git a/man/ModelSIR.Rd b/man/ModelSIR.Rd
diff --git a/man/ModelSIRCONN.Rd b/man/ModelSIRCONN.Rd
diff --git a/man/ModelSIRLogit.Rd b/man/ModelSIRLogit.Rd
diff --git a/man/ModelSIS.Rd b/man/ModelSIS.Rd
diff --git a/man/ModelSURV.Rd b/man/ModelSURV.Rd
diff --git a/man/epiworld-data.Rd b/man/epiworld-data.Rd
diff --git a/src/cpp11.cpp b/src/cpp11.cpp
@@ -223,6 +223,13 @@ extern "C" SEXP _epiworldR_ModelSIR_cpp(SEXP name, SEXP prevalence, SEXP transmi
   END_CPP11
 }
 // epimodels.cpp
+SEXP ModelSIRD_cpp(std::string name, double prevalence, double transmission_rate, double recovery_rate, double death_rate);
+extern "C" SEXP _epiworldR_ModelSIRD_cpp(SEXP name, SEXP prevalence, SEXP transmission_rate, SEXP recovery_rate, SEXP death_rate) {
+  BEGIN_CPP11
+    return cpp11::as_sexp(ModelSIRD_cpp(cpp11::as_cpp<cpp11::decay_t<std::string>>(name), cpp11::as_cpp<cpp11::decay_t<double>>(prevalence), cpp11::as_cpp<cpp11::decay_t<double>>(transmission_rate), cpp11::as_cpp<cpp11::decay_t<double>>(recovery_rate), cpp11::as_cpp<cpp11::decay_t<double>>(death_rate)));
+  END_CPP11
+}
+// epimodels.cpp
 SEXP ModelSEIRCONN_cpp(std::string name, unsigned int n, double prevalence, double contact_rate, double transmission_rate, double incubation_days, double recovery_rate);
 extern "C" SEXP _epiworldR_ModelSEIRCONN_cpp(SEXP name, SEXP n, SEXP prevalence, SEXP contact_rate, SEXP transmission_rate, SEXP incubation_days, SEXP recovery_rate) {
   BEGIN_CPP11
@@ -740,6 +747,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_epiworldR_ModelSEIRCONN_cpp",                    (DL_FUNC) &_epiworldR_ModelSEIRCONN_cpp,                     7},
     {"_epiworldR_ModelSEIR_cpp",                        (DL_FUNC) &_epiworldR_ModelSEIR_cpp,                         5},
     {"_epiworldR_ModelSIRCONN_cpp",                     (DL_FUNC) &_epiworldR_ModelSIRCONN_cpp,                      6},
+    {"_epiworldR_ModelSIRD_cpp",                        (DL_FUNC) &_epiworldR_ModelSIRD_cpp,                         5},
     {"_epiworldR_ModelSIRLogit_cpp",                    (DL_FUNC) &_epiworldR_ModelSIRLogit_cpp,                    10},
     {"_epiworldR_ModelSIR_cpp",                         (DL_FUNC) &_epiworldR_ModelSIR_cpp,                          4},
     {"_epiworldR_ModelSIS_cpp",                         (DL_FUNC) &_epiworldR_ModelSIS_cpp,                          4},

diff --git a/src/epimodels.cpp b/src/epimodels.cpp
@@ -175,15 +175,15 @@ SEXP ModelSIR_cpp(
   cpp11::external_pointer<epiworld::epimodels::ModelSIRD<>> (a)
 
 [[cpp11::register]]
-SEXP ModelSIR_cpp(
+SEXP ModelSIRD_cpp(
     std::string name,
     double prevalence,
     double transmission_rate,
     double recovery_rate,
     double death_rate
 ) {
 
-  // Creating a pointer to a ModelSIR model
+  // Creating a pointer to a ModelSIRD model
   WrapSIRD(ptr)(
       new epiworld::epimodels::ModelSIRD<>(
           name,