721 Munich graph sim (#791)

Co-authored-by: Henrik Zunker <69154294+HenrZu@users.noreply.github.com>

Author: jubicker

cpp/memilio/io/epi_data.cpp

@@ -25,19 +25,18 @@
 namespace mio
 {
 
-const std::array<const char*, 6> ConfirmedCasesDataEntry::age_group_names = {"A00-A04", "A05-A14", "A15-A34",
-                                                                             "A35-A59", "A60-A79", "A80+"};
+std::vector<const char*> ConfirmedCasesDataEntry::age_group_names = {"A00-A04", "A05-A14", "A15-A34",
+                                                                     "A35-A59", "A60-A79", "A80+"};
 
-const std::array<const char*, 11> PopulationDataEntry::age_group_names = {
+std::vector<const char*> PopulationDataEntry::age_group_names = {
     "<3 years",    "3-5 years",   "6-14 years",  "15-17 years", "18-24 years", "25-29 years",
     "30-39 years", "40-49 years", "50-64 years", "65-74 years", ">74 years"};
 
-const std::array<const char*, 6> VaccinationDataEntry::age_group_names = {"0-4",   "5-14",  "15-34",
-                                                                          "35-59", "60-79", "80-99"};
+std::vector<const char*> VaccinationDataEntry::age_group_names = {"0-4", "5-14", "15-34", "35-59", "60-79", "80-99"};
 
-IOResult<std::vector<int>> get_node_ids(const std::string& path, bool is_node_for_county)
+IOResult<std::vector<int>> get_node_ids(const std::string& path, bool is_node_for_county, bool rki_age_groups)
 {
-    BOOST_OUTCOME_TRY(population_data, read_population_data(path));
+    BOOST_OUTCOME_TRY(population_data, read_population_data(path, rki_age_groups));
     std::vector<int> id;
     id.reserve(population_data.size());
     for (auto&& entry : population_data) {

cpp/memilio/io/epi_data.h

@@ -74,7 +74,7 @@ class StringDate : public Date
 class ConfirmedCasesDataEntry
 {
 public:
-    static const std::array<const char*, 6> age_group_names;
+    static std::vector<const char*> age_group_names;
 
     double num_confirmed;
     double num_recovered;
@@ -223,7 +223,7 @@ IOResult<std::vector<T>> unpack_all(const std::vector<IOResult<T>>& v)
 class PopulationDataEntry
 {
 public:
-    static const std::array<const char*, 11> age_group_names;
+    static std::vector<const char*> age_group_names;
 
     CustomIndexArray<double, AgeGroup> population;
     boost::optional<regions::StateId> state_id;
@@ -260,8 +260,8 @@ inline void get_rki_age_interpolation_coefficients(const std::vector<double>& ag
                                                    std::vector<bool>& carry_over)
 {
     std::array<double, 6> param_ranges = {5., 10., 20., 25., 20., 20.};
-    static_assert(param_ranges.size() == ConfirmedCasesDataEntry::age_group_names.size(),
-                  "Number of RKI age groups does not match number of age ranges.");
+    assert(param_ranges.size() == ConfirmedCasesDataEntry::age_group_names.size() &&
+           "Number of RKI age groups does not match number of age ranges.");
 
     //counter for parameter age groups
     size_t counter = 0;
@@ -342,12 +342,19 @@ interpolate_to_rki_age_groups(const std::vector<PopulationDataEntry>& population
  * Deserialize population data from a JSON value.
  * Age groups are interpolated to RKI age groups.
  * @param jsvalue JSON value that contains the population data.
+ * @param rki_age_groups Specifies whether population data should be interpolated to rki age groups.
  * @return list of population data.
  */
-inline IOResult<std::vector<PopulationDataEntry>> deserialize_population_data(const Json::Value& jsvalue)
+inline IOResult<std::vector<PopulationDataEntry>> deserialize_population_data(const Json::Value& jsvalue,
+                                                                              bool rki_age_groups = true)
 {
     BOOST_OUTCOME_TRY(population_data, deserialize_json(jsvalue, Tag<std::vector<PopulationDataEntry>>{}));
-    return success(details::interpolate_to_rki_age_groups(population_data));
+    if (rki_age_groups) {
+        return success(details::interpolate_to_rki_age_groups(population_data));
+    }
+    else {
+        return success(population_data);
+    }
 }
 
 /**
@@ -356,27 +363,46 @@ inline IOResult<std::vector<PopulationDataEntry>> deserialize_population_data(co
  * @param filename JSON file that contains the population data.
  * @return list of population data.
  */
-inline IOResult<std::vector<PopulationDataEntry>> read_population_data(const std::string& filename)
+inline IOResult<std::vector<PopulationDataEntry>> read_population_data(const std::string& filename,
+                                                                       bool rki_age_group = true)
 {
     BOOST_OUTCOME_TRY(jsvalue, read_json(filename));
-    return deserialize_population_data(jsvalue);
+    return deserialize_population_data(jsvalue, rki_age_group);
 }
 
+/**
+ * @brief Sets the age groups' names for the ConfirmedCasesDataEntry%s.
+ * @param[in] names age group names
+*/
+IOResult<void> set_confirmed_cases_age_group_names(std::vector<const char*> names);
+
+/**
+ * @brief Sets the age groups' names for the PopulationDataEntry%s.
+ * @param[in] names age group names
+*/
+IOResult<void> set_population_data_age_group_names(std::vector<const char*> names);
+
+/**
+ * @brief Sets the age groups' names for the VaccinationDataEntry%s.
+ * @param[in] names age group names
+*/
+IOResult<void> set_vaccination_data_age_group_names(std::vector<const char*> names);
+
 /**
  * @brief returns a vector with the ids of all nodes.
  * @param[in] path directory to population data
  * @param[in] is_node_for_county boolean specifying whether the nodes should be counties or districts
  * @return list of node ids.
  */
-IOResult<std::vector<int>> get_node_ids(const std::string& path, bool is_node_for_county);
+IOResult<std::vector<int>> get_node_ids(const std::string& path, bool is_node_for_county, bool rki_age_groups = true);
 
 /**
  * Represents an entry in a vaccination data file.
  */
 class VaccinationDataEntry
 {
 public:
-    static const std::array<const char*, 6> age_group_names;
+    static std::vector<const char*> age_group_names;
 
     double num_vaccinations_completed;
     Date date;

cpp/memilio/mobility/graph.h

@@ -258,16 +258,18 @@ class Graph
  * @param[in] tnt_capacity_factor Factor for test and trace capacity.
  * @param[in] num_days Number of days to be simulated; required to load data for vaccinations during the simulation.
  * @param[in] export_time_series If true, reads data for each day of simulation and writes it in the same directory as the input files.
+ * @param[in] rki_age_groups Specifies whether rki-age_groups should be used.
  */
 template <class TestAndTrace, class ContactPattern, class Model, class MigrationParams, class Parameters,
           class ReadFunction, class NodeIdFunction>
-IOResult<void>
-set_nodes(const Parameters& params, Date start_date, Date end_date, const fs::path& data_dir,
-          const std::string& population_data_path, bool is_node_for_county, Graph<Model, MigrationParams>& params_graph,
-          ReadFunction&& read_func, NodeIdFunction&& node_func, const std::vector<double>& scaling_factor_inf,
-          double scaling_factor_icu, double tnt_capacity_factor, int num_days = 0, bool export_time_series = false)
+IOResult<void> set_nodes(const Parameters& params, Date start_date, Date end_date, const fs::path& data_dir,
+                         const std::string& population_data_path, bool is_node_for_county,
+                         Graph<Model, MigrationParams>& params_graph, ReadFunction&& read_func,
+                         NodeIdFunction&& node_func, const std::vector<double>& scaling_factor_inf,
+                         double scaling_factor_icu, double tnt_capacity_factor, int num_days = 0,
+                         bool export_time_series = false, bool rki_age_groups = true)
 {
-    BOOST_OUTCOME_TRY(node_ids, node_func(population_data_path, is_node_for_county));
+    BOOST_OUTCOME_TRY(node_ids, node_func(population_data_path, is_node_for_county, rki_age_groups));
     std::vector<Model> nodes(node_ids.size(), Model(int(size_t(params.get_num_groups()))));
     for (auto& node : nodes) {
         node.parameters = params;