1315 support io without age groups

cpp/memilio/geography/regions.h

@@ -77,6 +77,8 @@ DECL_TYPESAFE(int, CountyId);
 
 DECL_TYPESAFE(int, DistrictId);
 
+DECL_TYPESAFE(int, ProvinciaId);
+
 /**
          * get the id of the state that the specified county is in. 
          * @param[in, out] county a county id.

cpp/memilio/io/epi_data.cpp

@@ -27,10 +27,10 @@ namespace mio
 
 std::vector<const char*> ConfirmedCasesDataEntry::age_group_names = {"A00-A04", "A05-A14", "A15-A34",
                                                                      "A35-A59", "A60-A79", "A80+"};
-
-std::vector<const char*> 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"};
+// std::vector<const char*> PopulationDataEntrySpain::age_group_names = {"Population"};
 
 std::vector<const char*> VaccinationDataEntry::age_group_names = {"0-4", "5-14", "15-34", "35-59", "60-79", "80-99"};
 
@@ -49,11 +49,14 @@ IOResult<std::vector<int>> get_node_ids(const std::string& path, bool is_node_fo
             }
         }
         else {
-            if (entry.district_id) {
+            if (entry.state_id) {
+                id.push_back(entry.state_id->get());
+            }
+            else if (entry.district_id) {
                 id.push_back(entry.district_id->get());
             }
             else {
-                return failure(StatusCode::InvalidValue, "Population data file is missing district ids.");
+                return failure(StatusCode::InvalidValue, "Population data file is missing district and state ids.");
             }
         }
     }
@@ -62,6 +65,13 @@ IOResult<std::vector<int>> get_node_ids(const std::string& path, bool is_node_fo
     id.erase(std::unique(id.begin(), id.end()), id.end());
     return success(id);
 }
+
+IOResult<std::vector<int>> get_country_id(const std::string& /*path*/, bool /*is_node_for_county*/,
+                                          bool /*rki_age_groups*/)
+{
+    std::vector<int> id = {0};
+    return success(id);
+}
 } // namespace mio
 
 #endif //MEMILIO_HAS_JSONCPP

cpp/memilio/io/epi_data.h

@@ -77,6 +77,9 @@ class ConfirmedCasesNoAgeEntry
     double num_recovered;
     double num_deaths;
     Date date;
+    boost::optional<regions::StateId> state_id;
+    boost::optional<regions::CountyId> county_id;
+    boost::optional<regions::DistrictId> district_id;
 
     template <class IOContext>
     static IOResult<ConfirmedCasesNoAgeEntry> deserialize(IOContext& io)
@@ -86,12 +89,15 @@ class ConfirmedCasesNoAgeEntry
         auto num_recovered = obj.expect_element("Recovered", Tag<double>{});
         auto num_deaths    = obj.expect_element("Deaths", Tag<double>{});
         auto date          = obj.expect_element("Date", Tag<StringDate>{});
+        auto state_id      = obj.expect_optional("ID_State", Tag<regions::StateId>{});
+        auto county_id     = obj.expect_optional("ID_County", Tag<regions::CountyId>{});
+        auto district_id   = obj.expect_optional("ID_District", Tag<regions::DistrictId>{});
         return apply(
             io,
-            [](auto&& nc, auto&& nr, auto&& nd, auto&& d) {
-                return ConfirmedCasesNoAgeEntry{nc, nr, nd, d};
+            [](auto&& nc, auto&& nr, auto&& nd, auto&& d, auto&& sid, auto&& cid, auto&& did) {
+                return ConfirmedCasesNoAgeEntry{nc, nr, nd, d, sid, cid, did};
             },
-            num_confirmed, num_recovered, num_deaths, date);
+            num_confirmed, num_recovered, num_deaths, date, state_id, county_id, district_id);
     }
 };
 
@@ -331,6 +337,35 @@ class PopulationDataEntry
     }
 };
 
+// class PopulationDataEntrySpain
+// {
+// public:
+//     static std::vector<const char*> age_group_names;
+
+//     CustomIndexArray<double, AgeGroup> population;
+//     boost::optional<regions::ProvinciaId> provincia_id;
+
+//     template <class IoContext>
+//     static IOResult<PopulationDataEntrySpain> deserialize(IoContext& io)
+//     {
+//         auto obj      = io.expect_object("PopulationDataEntrySpain");
+//         auto state_id = obj.expect_optional("ID_Provincia", Tag<regions::ProvinciaId>{});
+//         std::vector<IOResult<double>> age_groups;
+//         age_groups.reserve(age_group_names.size());
+//         std::transform(age_group_names.begin(), age_group_names.end(), std::back_inserter(age_groups),
+//                        [&obj](auto&& age_name) {
+//                            return obj.expect_element(age_name, Tag<double>{});
+//                        });
+//         return apply(
+//             io,
+//             [](auto&& ag, auto&& pid) {
+//                 return PopulationDataEntrySpain{
+//                     CustomIndexArray<double, AgeGroup>(AgeGroup(ag.size()), ag.begin(), ag.end()), pid};
+//             },
+//             details::unpack_all(age_groups), provincia_id);
+//     }
+// };
+
 namespace details
 {
 inline void get_rki_age_interpolation_coefficients(const std::vector<double>& age_ranges,
@@ -435,6 +470,19 @@ inline IOResult<std::vector<PopulationDataEntry>> deserialize_population_data(co
     }
 }
 
+/**
+ * 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<PopulationDataEntrySpain>> deserialize_population_data_spain(const Json::Value& jsvalue)
+// {
+//     BOOST_OUTCOME_TRY(auto&& population_data, deserialize_json(jsvalue, Tag<std::vector<PopulationDataEntrySpain>>{}));
+//     return success(population_data);
+// }
+
 /**
  * Deserialize population data from a JSON file.
  * Age groups are interpolated to RKI age groups.
@@ -448,6 +496,18 @@ inline IOResult<std::vector<PopulationDataEntry>> read_population_data(const std
     return deserialize_population_data(jsvalue, rki_age_group);
 }
 
+/**
+ * Deserialize population data from a JSON file.
+ * Age groups are interpolated to RKI age groups.
+ * @param filename JSON file that contains the population data.
+ * @return list of population data.
+ */
+// inline IOResult<std::vector<PopulationDataEntrySpain>> read_population_data_spain(const std::string& filename)
+// {
+//     BOOST_OUTCOME_TRY(auto&& jsvalue, read_json(filename));
+//     return deserialize_population_data_spain(jsvalue);
+// }
+
 /**
  * @brief Sets the age groups' names for the ConfirmedCasesDataEntry%s.
  * @param[in] names age group names
@@ -474,6 +534,8 @@ IOResult<void> set_vaccination_data_age_group_names(std::vector<const char*> nam
  * @return list of node ids.
  */
 IOResult<std::vector<int>> get_node_ids(const std::string& path, bool is_node_for_county, bool rki_age_groups = true);
+IOResult<std::vector<int>> get_country_id(const std::string& /*path*/, bool /*is_node_for_county*/,
+                                          bool /*rki_age_groups*/ = true);
 
 /**
  * Represents an entry in a vaccination data file.

cpp/memilio/io/parameters_io.cpp

@@ -62,6 +62,31 @@ IOResult<std::vector<std::vector<double>>> read_population_data(const std::vecto
     return success(vnum_population);
 }
 
+// IOResult<std::vector<std::vector<double>>>
+// read_population_data_spain(const std::vector<PopulationDataEntrySpain>& population_data,
+//                            const std::vector<int>& vregion)
+// {
+//     std::vector<std::vector<double>> vnum_population(vregion.size(), std::vector<double>(1, 0.0));
+
+//     for (auto&& provincia_entry : population_data) {
+//         printf("Test");
+//         //find region that this county belongs to
+//         //all counties belong to the country (id = 0)
+//         auto it = std::find_if(vregion.begin(), vregion.end(), [&provincia_entry](auto r) {
+//             return r == 0 || (provincia_entry.provincia_id && regions::ProvinciaId(r) == provincia_entry.provincia_id);
+//         });
+//         if (it != vregion.end()) {
+//             auto region_idx      = size_t(it - vregion.begin());
+//             auto& num_population = vnum_population[region_idx];
+//             for (size_t age = 0; age < num_population.size(); age++) {
+//                 num_population[age] += provincia_entry.population[AgeGroup(age)];
+//             }
+//         }
+//     }
+
+//     return success(vnum_population);
+// }
+
 IOResult<std::vector<std::vector<double>>> read_population_data(const std::string& path,
                                                                 const std::vector<int>& vregion)
 {

cpp/memilio/mobility/graph.h

@@ -368,7 +368,7 @@ IOResult<void> set_edges(const fs::path& mobility_data_file, Graph<Model, Mobili
             for (auto age = AgeGroup(0); age < populations.template size<mio::AgeGroup>(); ++age) {
                 for (auto compartment : mobile_compartments) {
                     auto coeff_index = populations.get_flat_index({age, compartment});
-                    mobility_coeffs[size_t(ContactLocation::Work)].get_baseline()[coeff_index] =
+                    mobility_coeffs[size_t(ContactLocation::Home)].get_baseline()[coeff_index] =
                         commuter_coeff_ij * commuting_weights[size_t(age)];
                 }
             }