1268 Vaccination data no longer reported since July 2024 (#1269)

- Allow usage of DIVI data after July 2024
- Vaccination data is not available for dates after July 2024. Now we check if it needs to be considered in the simulation period
- Better handling of vaccination data when its not available

Co-authored-by: annawendler <106674756+annawendler@users.noreply.github.com>

Author: HenrZu

cpp/memilio/io/epi_data.h

@@ -238,8 +238,22 @@ class DiviEntry
 inline bool is_divi_data_available(const Date& date)
 {
     static const Date divi_data_start(2020, 4, 23);
-    static const Date divi_data_end(2024, 7, 21);
-    return date >= divi_data_start && date <= divi_data_end;
+    return date >= divi_data_start;
+}
+
+/**
+ * @brief Checks if vaccination data is available for any day within the given date interval, 
+ * only checking for overlap with the bounds of the simulation period.
+ * @param start_date The start date of the interval to check.
+ * @param end_date The end date of the interval to check.
+ * @return True if there is any overlap between the given date range and the vaccination data
+ *  availability period, false otherwise.
+ */
+inline bool is_vaccination_data_available(const Date& start_date, const Date& end_date)
+{
+    static const Date vaccination_data_start(2020, 12, 27);
+    static const Date vaccination_data_end(2024, 7, 9);
+    return !(end_date < vaccination_data_start || start_date > vaccination_data_end);
 }
 
 /**

cpp/models/ode_secirts/parameters_io.h

@@ -862,10 +862,15 @@ IOResult<void> set_vaccination_data(std::vector<Model<FP>>& model, const std::ve
     if (max_date_entry == vacc_data.end()) {
         return failure(StatusCode::InvalidFileFormat, "Vaccination data file is empty.");
     }
-    auto max_date = max_date_entry->date;
-    if (max_date < offset_date_by_days(date, num_days)) {
-        log_error("Vaccination data does not contain all dates. After the last day the data, vaccinations per day are "
-                  "set to 0.");
+    auto max_date       = max_date_entry->date;
+    auto min_date_entry = std::min_element(vacc_data.begin(), vacc_data.end(), [](auto&& a, auto&& b) {
+        return a.date < b.date;
+    });
+    auto min_date       = min_date_entry->date;
+    if (min_date > date || max_date < offset_date_by_days(date, num_days)) {
+        log_warning("Vaccination data only available from {} to {}. "
+                    "For days before and after, vaccinations will be set to 0.",
+                    min_date, max_date);
     }
 
     for (auto&& vacc_data_entry : vacc_data) {
@@ -952,6 +957,27 @@ template <typename FP = double>
 IOResult<void> set_vaccination_data(std::vector<Model<FP>>& model, const std::string& path, Date date,
                                     const std::vector<int>& vregion, int num_days)
 {
+    // Check if vaccination data is available for the given date range
+    auto end_date = offset_date_by_days(date, num_days);
+    if (!is_vaccination_data_available(date, end_date)) {
+        log_warning("No vaccination data available in range from {} to {}. "
+                    "Vaccination data will be set to 0.",
+                    date, end_date);
+        // Set vaccination data to 0 for all models
+        for (auto& m : model) {
+            m.parameters.template get<DailyPartialVaccinations<FP>>().resize(SimulationDay(num_days + 1));
+            m.parameters.template get<DailyFullVaccinations<FP>>().resize(SimulationDay(num_days + 1));
+            m.parameters.template get<DailyBoosterVaccinations<FP>>().resize(SimulationDay(num_days + 1));
+            for (auto d = SimulationDay(0); d < SimulationDay(num_days + 1); ++d) {
+                for (auto a = AgeGroup(0); a < m.parameters.get_num_groups(); ++a) {
+                    m.parameters.template get<DailyPartialVaccinations<FP>>()[{a, d}] = 0.0;
+                    m.parameters.template get<DailyFullVaccinations<FP>>()[{a, d}]    = 0.0;
+                    m.parameters.template get<DailyBoosterVaccinations<FP>>()[{a, d}] = 0.0;
+                }
+            }
+        }
+        return success();
+    }
     BOOST_OUTCOME_TRY(auto&& vacc_data, read_vaccination_data(path));
     BOOST_OUTCOME_TRY(set_vaccination_data(model, vacc_data, date, vregion, num_days));
     return success();

cpp/models/ode_secirvvs/parameters_io.h

@@ -727,6 +727,17 @@ IOResult<void> set_vaccination_data(std::vector<Model<FP>>& model, const std::ve
     }
     auto max_date = max_date_entry->date;
 
+    auto min_date_entry = std::min_element(vacc_data.begin(), vacc_data.end(), [](auto&& a, auto&& b) {
+        return a.date < b.date;
+    });
+    auto min_date       = min_date_entry->date;
+    if (min_date > date || max_date < offset_date_by_days(date, num_days)) {
+        log_warning("Vaccination data only available from {} to {}. "
+                    "For days before, vaccination data will be set to 0. For days after, "
+                    "vaccination data will be set to the last available date.",
+                    min_date, max_date);
+    }
+
     for (auto&& vacc_data_entry : vacc_data) {
         auto it      = std::find_if(vregion.begin(), vregion.end(), [&vacc_data_entry](auto&& r) {
             return r == 0 || (vacc_data_entry.county_id && vacc_data_entry.county_id == regions::CountyId(r)) ||
@@ -833,6 +844,26 @@ template <typename FP = double>
 IOResult<void> set_vaccination_data(std::vector<Model<FP>>& model, const std::string& path, Date date,
                                     const std::vector<int>& vregion, int num_days)
 {
+    // Check if vaccination data is available for the given date range
+    auto end_date = offset_date_by_days(date, num_days);
+    if (!is_vaccination_data_available(date, end_date)) {
+        log_warning("No vaccination data available in range from {} to {}. "
+                    "Vaccination data will be set to 0.",
+                    date, end_date);
+        // Set vaccination data to 0 for all models
+        for (auto& m : model) {
+            m.parameters.template get<DailyPartialVaccinations<FP>>().resize(SimulationDay(num_days + 1));
+            m.parameters.template get<DailyFullVaccinations<FP>>().resize(SimulationDay(num_days + 1));
+
+            for (auto d = SimulationDay(0); d < SimulationDay(num_days + 1); ++d) {
+                for (auto a = AgeGroup(0); a < m.parameters.get_num_groups(); ++a) {
+                    m.parameters.template get<DailyPartialVaccinations<FP>>()[{a, d}] = 0.0;
+                    m.parameters.template get<DailyFullVaccinations<FP>>()[{a, d}]    = 0.0;
+                }
+            }
+        }
+        return success();
+    }
     BOOST_OUTCOME_TRY(auto&& vacc_data, read_vaccination_data(path));
     BOOST_OUTCOME_TRY(set_vaccination_data(model, vacc_data, date, vregion, num_days));
     return success();

cpp/tests/test_epi_data_io.cpp

@@ -300,10 +300,28 @@ TEST(TestEpiDataIo, read_divi_data)
 TEST(TestEpiDataIo, is_divi_data_available)
 {
     EXPECT_FALSE(mio::is_divi_data_available(mio::Date(2020, 4, 22))); // Before start
-    EXPECT_FALSE(mio::is_divi_data_available(mio::Date(2024, 7, 22))); // After end
     EXPECT_TRUE(mio::is_divi_data_available(mio::Date(2020, 4, 23))); // Start date
-    EXPECT_TRUE(mio::is_divi_data_available(mio::Date(2022, 1, 1))); // Inside range
-    EXPECT_TRUE(mio::is_divi_data_available(mio::Date(2024, 7, 21))); // End date
+    EXPECT_TRUE(mio::is_divi_data_available(mio::Date(2022, 1, 1))); // Day after start
+}
+
+TEST(TestEpiDataIo, is_vaccination_data_available)
+{
+    // Single date tests
+    EXPECT_FALSE(mio::is_vaccination_data_available(mio::Date(2020, 12, 26), mio::Date(2020, 12, 26))); // Before start
+    EXPECT_TRUE(mio::is_vaccination_data_available(mio::Date(2020, 12, 27), mio::Date(2020, 12, 27))); // Start date
+    EXPECT_TRUE(mio::is_vaccination_data_available(mio::Date(2024, 7, 9), mio::Date(2024, 7, 9))); // End date
+    EXPECT_FALSE(mio::is_vaccination_data_available(mio::Date(2024, 7, 10), mio::Date(2024, 7, 10))); // After end
+
+    // Date range tests
+    EXPECT_TRUE(
+        mio::is_vaccination_data_available(mio::Date(2020, 12, 20), mio::Date(2020, 12, 28))); // Overlap with start
+    EXPECT_TRUE(mio::is_vaccination_data_available(mio::Date(2024, 7, 5), mio::Date(2024, 7, 15))); // Overlap with end
+    EXPECT_TRUE(
+        mio::is_vaccination_data_available(mio::Date(2021, 1, 1), mio::Date(2021, 12, 31))); // Completely within range
+    EXPECT_TRUE(
+        mio::is_vaccination_data_available(mio::Date(2020, 1, 1), mio::Date(2025, 1, 1))); // Contains entire range
+    EXPECT_FALSE(mio::is_vaccination_data_available(mio::Date(2019, 1, 1), mio::Date(2020, 12, 26))); // Before start
+    EXPECT_FALSE(mio::is_vaccination_data_available(mio::Date(2024, 7, 10), mio::Date(2025, 1, 1))); // After end
 }
 
 TEST(TestEpiDataIo, read_confirmed_cases_data)

cpp/tests/test_odesecir.cpp

@@ -1454,11 +1454,6 @@ TEST(TestOdeSecir, set_divi_data_invalid_dates)
     EXPECT_THAT(print_wrap(model_vector[0].populations.array().cast<double>()),
                 MatrixNear(print_wrap(model.populations.array().cast<double>()), 1e-10, 1e-10));
 
-    // Test with data after DIVI dataset was no longer updated.
-    EXPECT_THAT(mio::osecir::details::set_divi_data(model_vector, "", {1001}, {2025, 12, 01}, 1.0), IsSuccess());
-    EXPECT_THAT(print_wrap(model_vector[0].populations.array().cast<double>()),
-                MatrixNear(print_wrap(model.populations.array().cast<double>()), 1e-10, 1e-10));
-
     mio::set_log_level(mio::LogLevel::warn);
 }
 
@@ -1479,7 +1474,7 @@ TEST_F(ModelTestOdeSecir, set_confirmed_cases_data_with_ICU)
 
     // Change dates of the case data so that no ICU data is available at that time.
     // Also, increase the number of confirmed cases by 1 each day.
-    const auto t0 = mio::Date(2025, 1, 1);
+    const auto t0 = mio::Date(2000, 1, 1);
     auto day_add  = 0;
     for (auto& entry : case_data) {
         entry.date          = offset_date_by_days(t0, day_add);

cpp/tests/test_odesecirts.cpp

@@ -768,12 +768,6 @@ TEST(TestOdeSECIRTS, set_divi_data_invalid_dates)
     // Assure that populations is the same as before.
     EXPECT_THAT(print_wrap(model_vector[0].populations.array().cast<double>()),
                 MatrixNear(print_wrap(model.populations.array().cast<double>()), 1e-10, 1e-10));
-
-    // Test with data after DIVI dataset was no longer updated.
-    EXPECT_THAT(mio::osecirts::details::set_divi_data(model_vector, "", {1001}, {2025, 12, 01}, 1.0), IsSuccess());
-    EXPECT_THAT(print_wrap(model_vector[0].populations.array().cast<double>()),
-                MatrixNear(print_wrap(model.populations.array().cast<double>()), 1e-10, 1e-10));
-
     mio::set_log_level(mio::LogLevel::warn);
 }
 
@@ -802,7 +796,7 @@ TEST(TestOdeSECIRTS, set_confirmed_cases_data_with_ICU)
 
     // Change dates of the case data so that no ICU data is available at that time.
     // Also, increase the number of confirmed cases by 1 each day.
-    const auto t0 = mio::Date(2025, 1, 1);
+    const auto t0 = mio::Date(2000, 1, 1);
     auto day_add  = 0;
     for (auto& entry : case_data) {
         entry.date          = offset_date_by_days(t0, day_add);
@@ -1079,6 +1073,91 @@ TEST(TestOdeSECIRTS, model_initialization)
                 MatrixNear(print_wrap(expected_values), 1e-5, 1e-5));
 }
 
+TEST(TestOdeSECIRTS, set_vaccination_data_not_avail)
+{
+    const auto num_age_groups = 2;
+    const auto num_days       = 5;
+    mio::osecirts::Model<double> model(num_age_groups);
+    std::vector<mio::osecirts::Model<double>> model_vector = {model};
+
+    // Setup initial non-zero vaccination data
+    auto& params = model_vector[0].parameters;
+    params.get<mio::osecirts::DailyPartialVaccinations<double>>().resize(mio::SimulationDay(num_days + 1));
+    params.get<mio::osecirts::DailyFullVaccinations<double>>().resize(mio::SimulationDay(num_days + 1));
+    params.get<mio::osecirts::DailyBoosterVaccinations<double>>().resize(mio::SimulationDay(num_days + 1));
+
+    const double initial_partial_vacc_val = 10.0;
+    const double initial_full_vacc_val    = 5.0;
+    const double initial_booster_vacc_val = 2.0;
+
+    for (auto g = mio::AgeGroup(0); g < mio::AgeGroup(num_age_groups); ++g) {
+        for (auto d = mio::SimulationDay(0); d < mio::SimulationDay(num_days + 1); ++d) {
+            params.get<mio::osecirts::DailyPartialVaccinations<double>>()[{g, d}] = initial_partial_vacc_val;
+            params.get<mio::osecirts::DailyFullVaccinations<double>>()[{g, d}]    = initial_full_vacc_val;
+            params.get<mio::osecirts::DailyBoosterVaccinations<double>>()[{g, d}] = initial_booster_vacc_val;
+        }
+    }
+
+    // Call set_vaccination_data with an unavailable date
+    mio::Date unavailable_date(2019, 1, 1); // Date before vaccinations started
+    std::vector<int> region = {1001};
+    std::string any_path    = "dummy_vacc_path.json";
+
+    auto result =
+        mio::osecirts::details::set_vaccination_data(model_vector, any_path, unavailable_date, region, num_days);
+
+    ASSERT_THAT(result, IsSuccess());
+
+    // Check that vaccinations are set to zero for all days and age groups
+    for (auto d = mio::SimulationDay(0); d < mio::SimulationDay(num_days + 1); ++d) {
+        for (auto a = mio::AgeGroup(0); a < mio::AgeGroup(num_age_groups); ++a) {
+            auto partial_vacc = params.get<mio::osecirts::DailyPartialVaccinations<double>>()[{a, d}];
+            auto full_vacc    = params.get<mio::osecirts::DailyFullVaccinations<double>>()[{a, d}];
+            auto booster_vacc = params.get<mio::osecirts::DailyBoosterVaccinations<double>>()[{a, d}];
+            EXPECT_NEAR(partial_vacc, 0.0, 1e-10);
+            EXPECT_NEAR(full_vacc, 0.0, 1e-10);
+            EXPECT_NEAR(booster_vacc, 0.0, 1e-10);
+        }
+    }
+}
+
+TEST(TestOdeSECIRTS, set_vaccination_data_min_date_not_avail)
+{
+    mio::set_log_level(mio::LogLevel::off);
+
+    // create model
+    const auto num_age_groups = 1;
+    const auto num_days       = 5;
+    mio::osecirts::Model<double> model(num_age_groups);
+    std::vector<mio::osecirts::Model<double>> model_vector = {model};
+    auto& params                                           = model_vector[0].parameters;
+
+    // create simple vaccination data
+    std::vector<mio::VaccinationDataEntry> vacc_data = {
+        mio::VaccinationDataEntry{10.0, 5.0, 2.0, 0.0, mio::Date(2021, 1, 15), mio::AgeGroup(0), {}, {}, {}}};
+
+    // simulation date before vaccination data
+    mio::Date earlier_date(2021, 1, 1);
+    std::vector<int> region = {0};
+
+    auto result = mio::osecirts::details::set_vaccination_data(model_vector, vacc_data, earlier_date, region, num_days);
+    ASSERT_THAT(result, IsSuccess());
+
+    // check that vaccinations are set to zero for all days and age groups
+    for (auto d = mio::SimulationDay(0); d < mio::SimulationDay(num_days + 1); ++d) {
+        for (auto a = mio::AgeGroup(0); a < mio::AgeGroup(num_age_groups); ++a) {
+            auto partial_vacc = params.get<mio::osecirts::DailyPartialVaccinations<double>>()[{a, d}];
+            auto full_vacc    = params.get<mio::osecirts::DailyFullVaccinations<double>>()[{a, d}];
+            auto booster_vacc = params.get<mio::osecirts::DailyBoosterVaccinations<double>>()[{a, d}];
+            EXPECT_NEAR(partial_vacc, 0.0, 1e-10);
+            EXPECT_NEAR(full_vacc, 0.0, 1e-10);
+            EXPECT_NEAR(booster_vacc, 0.0, 1e-10);
+        }
+    }
+
+    mio::set_log_level(mio::LogLevel::warn);
+}
+
 #endif
 
 TEST(TestOdeSECIRTS, parameter_percentiles)