1187 Make set_initial_flows() of IDE model usable with and without age resolution

cpp/examples/ide_initialization.cpp

@@ -23,6 +23,7 @@
 #include "ide_secir/simulation.h"
 #include "ide_secir/parameters_io.h"
 #include "memilio/config.h"
+#include "memilio/io/epi_data.h"
 #include "memilio/utils/time_series.h"
 #include "memilio/utils/date.h"
 #include "memilio/math/eigen.h"
@@ -88,7 +89,21 @@ int main(int argc, char** argv)
     }
     else {
         // Use the real data for initialization.
-        auto status = mio::isecir::set_initial_flows(model, dt, filename, mio::Date(2020, 12, 24));
+        // Here we assume that the file contains data without age resolution, hence we use read_confirmed_cases_noage()
+        // for reading the data and mio::ConfirmedCasesNoAgeEntry as EntryType in set_initial_flows().
+
+        auto status_read_data = mio::read_confirmed_cases_noage(filename);
+        if (!status_read_data) {
+            std::cout << "Error: " << status_read_data.error().formatted_message();
+            return -1;
+        }
+
+        std::vector<mio::ConfirmedCasesNoAgeEntry> rki_data = status_read_data.value();
+        mio::CustomIndexArray<ScalarType, mio::AgeGroup> scale_confirmed_cases =
+            mio::CustomIndexArray<ScalarType, mio::AgeGroup>(mio::AgeGroup(num_agegroups), 1.);
+
+        auto status = mio::isecir::set_initial_flows<mio::ConfirmedCasesNoAgeEntry>(
+            model, dt, rki_data, mio::Date(2020, 12, 24), scale_confirmed_cases);
         if (!status) {
             std::cout << "Error: " << status.error().formatted_message();
             return -1;

cpp/models/ide_secir/CMakeLists.txt

@@ -6,7 +6,6 @@ add_library(ide_secir
     simulation.cpp
     parameters.h
     parameters_io.h
-    parameters_io.cpp
 )
 target_link_libraries(ide_secir PUBLIC memilio)
 target_include_directories(ide_secir PUBLIC

cpp/models/ide_secir/model.cpp

@@ -46,8 +46,12 @@ Model::Model(TimeSeries<ScalarType>&& transitions_init, CustomIndexArray<ScalarT
     , m_num_agegroups{num_agegroups}
 
 {
+    // Assert that input arguments for the total population have the correct size regarding
+    // age groups.
+    assert((size_t)m_N.size() == m_num_agegroups);
+
     if (transitions.get_num_time_points() > 0) {
-        // Add first time point in populations according to last time point in transitions which is where we start
+        // Add first time point in m_populations according to last time point in m_transitions which is where we start
         // the simulation.
         populations.add_time_point<Eigen::VectorX<ScalarType>>(
             transitions.get_last_time(),
@@ -71,7 +75,7 @@ bool Model::check_constraints(ScalarType dt) const
 {
 
     if (!((size_t)transitions.get_num_elements() == (size_t)InfectionTransition::Count * m_num_agegroups)) {
-        log_error("A variable given for model construction is not valid. Number of elements in vector of"
+        log_error("A variable given for model construction is not valid. Number of elements in vector of "
                   "transitions does not match the required number.");
         return true;
     }
@@ -120,6 +124,21 @@ bool Model::check_constraints(ScalarType dt) const
         return true;
     }
 
+    if ((size_t)total_confirmed_cases.size() > 0 && (size_t)total_confirmed_cases.size() != m_num_agegroups) {
+        log_error("Initialization failed. Number of elements in total_confirmed_cases does not match the number "
+                  "of age groups.");
+        return true;
+    }
+
+    if ((size_t)total_confirmed_cases.size() > 0) {
+        for (AgeGroup group = AgeGroup(0); group < AgeGroup(m_num_agegroups); ++group) {
+            if (total_confirmed_cases[group] < 0) {
+                log_error("Initialization failed. One or more value of total_confirmed_cases is less than zero.");
+                return true;
+            }
+        }
+    }
+
     return parameters.check_constraints();
 }
 

cpp/models/ide_secir/model.h

@@ -26,6 +26,7 @@
 #include "memilio/config.h"
 #include "memilio/epidemiology/age_group.h"
 #include "memilio/utils/custom_index_array.h"
+#include "memilio/utils/date.h"
 #include "memilio/utils/time_series.h"
 
 #include "vector"
@@ -34,6 +35,13 @@ namespace mio
 {
 namespace isecir
 {
+// Forward declaration of friend classes/functions of Model.
+class Model;
+class Simulation;
+template <typename EntryType>
+IOResult<void> set_initial_flows(Model& model, const ScalarType dt, const std::vector<EntryType> rki_data,
+                                 const Date date, const CustomIndexArray<ScalarType, AgeGroup> scale_confirmed_cases);
+
 class Model
 {
     using ParameterSet = Parameters;
@@ -130,6 +138,16 @@ class Model
         return m_initialization_method;
     }
 
+    /**
+     * @brief Getter for number of age groups.
+     *
+     * @return Returns number of age groups. 
+     */
+    size_t get_num_agegroups() const
+    {
+        return m_num_agegroups;
+    }
+
     /**
      * @brief Setter for the tolerance used to calculate the maximum support of the TransitionDistributions.
      *
@@ -358,8 +376,10 @@ class Model
     friend class Simulation;
     // In set_initial_flows(), we compute initial flows based on RKI data using the (private) compute_flow() function
     // which is why it is defined as a friend function.
-    friend IOResult<void> set_initial_flows(Model& model, ScalarType dt, std::string const& path, Date date,
-                                            ScalarType scale_confirmed_cases);
+    template <typename EntryType>
+    friend IOResult<void> set_initial_flows(Model& model, const ScalarType dt, const std::vector<EntryType> rki_data,
+                                            const Date date,
+                                            const CustomIndexArray<ScalarType, AgeGroup> scale_confirmed_cases);
 };
 
 } // namespace isecir