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1268 Vaccination data reporting expired #1269

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9932b75
vaccination data data restriction, rm for divi data
HenrZu Apr 28, 2025
2a6ea57
move into if makro
HenrZu Apr 28, 2025
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17 changes: 15 additions & 2 deletions cpp/memilio/io/epi_data.h
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Original file line number Diff line number Diff line change
Expand Up @@ -238,8 +238,21 @@ 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.
* @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);
}

/**
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21 changes: 21 additions & 0 deletions cpp/models/ode_secirts/parameters_io.h
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Expand Up @@ -952,6 +952,27 @@ 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();
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20 changes: 20 additions & 0 deletions cpp/models/ode_secirvvs/parameters_io.h
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Expand Up @@ -833,6 +833,26 @@ 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();
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24 changes: 21 additions & 3 deletions cpp/tests/test_epi_data_io.cpp
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Expand Up @@ -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)
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7 changes: 1 addition & 6 deletions cpp/tests/test_odesecir.cpp
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Expand Up @@ -1453,11 +1453,6 @@ 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);
}

Expand All @@ -1478,7 +1473,7 @@ 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);
Expand Down
56 changes: 49 additions & 7 deletions cpp/tests/test_odesecirts.cpp
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Expand Up @@ -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);
}

Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -1079,6 +1073,54 @@ 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);
}
}
}

#endif

TEST(TestOdeSECIRTS, parameter_percentiles)
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57 changes: 47 additions & 10 deletions cpp/tests/test_odesecirvvs.cpp
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Expand Up @@ -583,11 +583,6 @@ TEST(TestOdeSECIRVVS, 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::osecirvvs::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);
}

Expand All @@ -612,7 +607,7 @@ TEST(TestOdeSECIRVVS, 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);
Expand Down Expand Up @@ -666,14 +661,14 @@ TEST(TestOdeSECIRVVS, read_data)

auto read_result1 = mio::osecirvvs::read_input_data_county(model1, {2020, 12, 01}, {1002},
std::vector<double>(size_t(num_age_groups), 1.0), 1.0,
TEST_GERMANY_PYDATA_DIR, 10);
TEST_GERMANY_PYDATA_DIR, 30);

auto read_result2 = mio::osecirvvs::read_input_data(model2, {2020, 12, 01}, {1002},
std::vector<double>(size_t(num_age_groups), 1.0), 1.0,
TEST_GERMANY_PYDATA_DIR, 10);
TEST_GERMANY_PYDATA_DIR, 30);

auto read_result_district = mio::osecirvvs::read_input_data(
model3, {2020, 12, 01}, {1002}, std::vector<double>(size_t(num_age_groups), 1.0), 1.0, pydata_dir_District, 10);
model3, {2020, 12, 01}, {1002}, std::vector<double>(size_t(num_age_groups), 1.0), 1.0, pydata_dir_District, 30);

ASSERT_THAT(read_result1, IsSuccess());
ASSERT_THAT(read_result2, IsSuccess());
Expand Down Expand Up @@ -903,7 +898,7 @@ TEST(TestOdeSECIRVVS, model_initialization)

ASSERT_THAT(mio::osecirvvs::read_input_data_county(model_vector, {2020, 12, 01}, {0},
std::vector<double>(size_t(num_age_groups), 1.0), 1.0,
TEST_GERMANY_PYDATA_DIR, 2, false),
TEST_GERMANY_PYDATA_DIR, 30, false),
IsSuccess());

// Values from data/export_time_series_init_osecirvvs.h5, for reading in comparison
Expand Down Expand Up @@ -1088,6 +1083,48 @@ TEST(TestOdeSECIRVVS, run_simulation)
ASSERT_THAT(print_wrap(result.matrix()), MatrixNear(print_wrap(expected_result.matrix()), 1e-5, 1e-5));
}

TEST(TestOdeSECIRVVS, set_vaccination_data_not_avail)
{
const auto num_age_groups = 2;
const auto num_days = 5;
mio::osecirvvs::Model<double> model(num_age_groups);
std::vector<mio::osecirvvs::Model<double>> model_vector = {model};

// Setup initial non-zero vaccination data
auto& params = model_vector[0].parameters;
params.get<mio::osecirvvs::DailyPartialVaccinations<double>>().resize(mio::SimulationDay(num_days + 1));
params.get<mio::osecirvvs::DailyFullVaccinations<double>>().resize(mio::SimulationDay(num_days + 1));

const double initial_partial_vacc_val = 10.0;
const double initial_full_vacc_val = 5.0;

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::osecirvvs::DailyPartialVaccinations<double>>()[{g, d}] = initial_partial_vacc_val;
params.get<mio::osecirvvs::DailyFullVaccinations<double>>()[{g, d}] = initial_full_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::osecirvvs::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::osecirvvs::DailyPartialVaccinations<double>>()[{a, d}];
auto full_vacc = params.get<mio::osecirvvs::DailyFullVaccinations<double>>()[{a, d}];
EXPECT_NEAR(partial_vacc, 0.0, 1e-10);
EXPECT_NEAR(full_vacc, 0.0, 1e-10);
}
}
}

#endif

TEST(TestOdeSECIRVVS, parameter_percentiles)
Expand Down