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1191 Initialization of ICU compartments after July 2024 #1192

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merged 12 commits into from
Jan 21, 2025
Merged

1191 Initialization of ICU compartments after July 2024 #1192

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0a1d340
use other init for icu after july 2024
HenrZu Jan 16, 2025
616174e
fix typos in date
HenrZu Jan 16, 2025
3956961
[ci skip] time constraint into set_divi_data
HenrZu Jan 17, 2025
e6b377b
test invalid dates in divi data
HenrZu Jan 17, 2025
cb35312
[ci skip] test set icu from case data
HenrZu Jan 17, 2025
4e6c809
typo test secirts
HenrZu Jan 17, 2025
897e3f0
tests into makro
HenrZu Jan 17, 2025
9a4225a
rm read_icu, adjust tests bc former bug, function if ICU data is avail
HenrZu Jan 20, 2025
b83bed0
[ci skip] date to iso format
HenrZu Jan 21, 2025
ff9ec02
[ci skip] Update cpp/memilio/io/epi_data.h
HenrZu Jan 21, 2025
5d3fcda
more detailed tests
HenrZu Jan 21, 2025
b30df0d
fix hardcoded age groups
HenrZu Jan 21, 2025
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12 changes: 12 additions & 0 deletions cpp/memilio/io/epi_data.h
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Original file line number Diff line number Diff line change
Expand Up @@ -230,6 +230,18 @@ class DiviEntry
}
};

/**
* @brief Checks if DIVI data is available for a given date.
* @param date The date to check.
* @return True if date is within 2020-04-23 and 2024-07-21, false otherwise.
*/
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;
}

/**
* Deserialize a list of DiviEntry from json.
* @param jsvalue Json value that contains DIVI data.
Expand Down
10 changes: 2 additions & 8 deletions cpp/models/ode_secir/parameters_io.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -123,8 +123,6 @@ IOResult<void> read_confirmed_cases_data(
auto date_df = region_entry.date;
auto age = size_t(region_entry.age_group);

bool read_icu = false; //params.populations.get({age, SecirCompartments::U}) == 0;

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if (date_df == offset_date_by_days(date, 0)) {
num_InfectedSymptoms[age] += scaling_factor_inf[age] * region_entry.num_confirmed;
num_rec[age] += region_entry.num_confirmed;
Expand All @@ -147,16 +145,12 @@ IOResult<void> read_confirmed_cases_data(
}
if (date_df == offset_date_by_days(date, -t_InfectedSymptoms[age] - t_InfectedSevere[age])) {
num_InfectedSevere[age] -= mu_I_H[age] * scaling_factor_inf[age] * region_entry.num_confirmed;
if (read_icu) {
num_icu[age] += mu_I_H[age] * mu_H_U[age] * scaling_factor_inf[age] * region_entry.num_confirmed;
}
num_icu[age] += mu_I_H[age] * mu_H_U[age] * scaling_factor_inf[age] * region_entry.num_confirmed;
}
if (date_df ==
offset_date_by_days(date, -t_InfectedSymptoms[age] - t_InfectedSevere[age] - t_InfectedCritical[age])) {
num_death[age] += region_entry.num_deaths;
if (read_icu) {
num_icu[age] -= mu_I_H[age] * mu_H_U[age] * scaling_factor_inf[age] * region_entry.num_confirmed;
}
num_icu[age] -= mu_I_H[age] * mu_H_U[age] * scaling_factor_inf[age] * region_entry.num_confirmed;
}
}
}
Expand Down
58 changes: 21 additions & 37 deletions cpp/models/ode_secir/parameters_io.h
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Expand Up @@ -134,8 +134,12 @@ IOResult<void> set_confirmed_cases_data(std::vector<Model<FP>>& model, std::vect
num_InfectedSymptoms[node][i];
model[node].populations[{AgeGroup(i), InfectionState::InfectedSymptomsConfirmed}] = 0;
model[node].populations[{AgeGroup(i), InfectionState::InfectedSevere}] = num_InfectedSevere[node][i];
model[node].populations[{AgeGroup(i), InfectionState::Dead}] = num_death[node][i];
model[node].populations[{AgeGroup(i), InfectionState::Recovered}] = num_rec[node][i];
// Only set the number of ICU patients here, if the date is not available in the data.
if (!is_divi_data_available(date)) {
model[node].populations[{AgeGroup(i), InfectionState::InfectedCritical}] = num_icu[node][i];
}
model[node].populations[{AgeGroup(i), InfectionState::Dead}] = num_death[node][i];
model[node].populations[{AgeGroup(i), InfectionState::Recovered}] = num_rec[node][i];
}
}
else {
Expand Down Expand Up @@ -190,6 +194,12 @@ template <typename FP = double>
IOResult<void> set_divi_data(std::vector<Model<FP>>& model, const std::string& path, const std::vector<int>& vregion,
Date date, double scaling_factor_icu)
{
// DIVI dataset will no longer be updated from CW29 2024 on.
if (!is_divi_data_available(date)) {
log_warning("No DIVI data available for date: {}-{}-{}", date.year, date.month, date.day,
". ICU compartment will be set based on Case data.");
return success();
}
std::vector<double> sum_mu_I_U(vregion.size(), 0);
std::vector<std::vector<double>> mu_I_U{model.size()};
for (size_t region = 0; region < vregion.size(); region++) {
Expand Down Expand Up @@ -306,13 +316,7 @@ IOResult<void> export_input_data_county_timeseries(
for (int t = 0; t <= num_days; ++t) {
auto offset_day = offset_date_by_days(date, t);

if (offset_day > Date(2020, 4, 23)) {
BOOST_OUTCOME_TRY(details::set_divi_data(models, divi_data_path, region, offset_day, scaling_factor_icu));
}
else {
log_warning("No DIVI data available for date: {}-{}-{}", offset_day.day, offset_day.month, offset_day.year);
}

BOOST_OUTCOME_TRY(details::set_divi_data(models, divi_data_path, region, offset_day, scaling_factor_icu));
BOOST_OUTCOME_TRY(details::set_confirmed_cases_data(models, case_data, region, offset_day, scaling_factor_inf));
BOOST_OUTCOME_TRY(details::set_population_data(models, num_population, region));
for (size_t r = 0; r < region.size(); r++) {
Expand Down Expand Up @@ -355,13 +359,8 @@ IOResult<void> read_input_data_germany(std::vector<Model>& model, Date date,
const std::vector<double>& scaling_factor_inf, double scaling_factor_icu,
const std::string& dir)
{
if (date > Date(2020, 4, 23)) {
BOOST_OUTCOME_TRY(
details::set_divi_data(model, path_join(dir, "germany_divi.json"), {0}, date, scaling_factor_icu));
}
else {
log_warning("No DIVI data available for this date");
}
BOOST_OUTCOME_TRY(
details::set_divi_data(model, path_join(dir, "germany_divi.json"), {0}, date, scaling_factor_icu));
BOOST_OUTCOME_TRY(details::set_confirmed_cases_data(model, path_join(dir, "cases_all_age_ma7.json"), {0}, date,
scaling_factor_inf));
BOOST_OUTCOME_TRY(details::set_population_data(model, path_join(dir, "county_current_population.json"), {0}));
Expand All @@ -382,14 +381,9 @@ IOResult<void> read_input_data_state(std::vector<Model>& model, Date date, std::
const std::vector<double>& scaling_factor_inf, double scaling_factor_icu,
const std::string& dir)
{
if (date > Date(2020, 4, 23)) {
BOOST_OUTCOME_TRY(
details::set_divi_data(model, path_join(dir, "state_divi.json"), state, date, scaling_factor_icu));
}
else {
log_warning("No DIVI data available for this date");
}

BOOST_OUTCOME_TRY(
details::set_divi_data(model, path_join(dir, "state_divi.json"), state, date, scaling_factor_icu));
BOOST_OUTCOME_TRY(details::set_confirmed_cases_data(model, path_join(dir, "cases_all_state_age_ma7.json"), state,
date, scaling_factor_inf));
BOOST_OUTCOME_TRY(details::set_population_data(model, path_join(dir, "county_current_population.json"), state));
Expand All @@ -412,13 +406,8 @@ IOResult<void> read_input_data_county(std::vector<Model>& model, Date date, cons
const std::vector<double>& scaling_factor_inf, double scaling_factor_icu,
const std::string& dir, int num_days = 0, bool export_time_series = false)
{
if (date > Date(2020, 4, 23)) {
BOOST_OUTCOME_TRY(details::set_divi_data(model, path_join(dir, "pydata/Germany", "county_divi_ma7.json"),
county, date, scaling_factor_icu));
}
else {
log_warning("No DIVI data available for this date");
}
BOOST_OUTCOME_TRY(details::set_divi_data(model, path_join(dir, "pydata/Germany", "county_divi_ma7.json"), county,
date, scaling_factor_icu));
BOOST_OUTCOME_TRY(details::set_confirmed_cases_data(
model, path_join(dir, "pydata/Germany", "cases_all_county_age_ma7.json"), county, date, scaling_factor_inf));
BOOST_OUTCOME_TRY(details::set_population_data(
Expand Down Expand Up @@ -454,13 +443,8 @@ IOResult<void> read_input_data(std::vector<Model>& model, Date date, const std::
const std::vector<double>& scaling_factor_inf, double scaling_factor_icu,
const std::string& data_dir, int num_days = 0, bool export_time_series = false)
{
if (date > Date(2020, 4, 23)) {
BOOST_OUTCOME_TRY(details::set_divi_data(model, path_join(data_dir, "critical_cases.json"), node_ids, date,
scaling_factor_icu));
}
else {
log_warning("No DIVI data available for this date");
}
BOOST_OUTCOME_TRY(
details::set_divi_data(model, path_join(data_dir, "critical_cases.json"), node_ids, date, scaling_factor_icu));
BOOST_OUTCOME_TRY(details::set_confirmed_cases_data(model, path_join(data_dir, "confirmed_cases.json"), node_ids,
date, scaling_factor_inf));
BOOST_OUTCOME_TRY(details::set_population_data(model, path_join(data_dir, "population_data.json"), node_ids));
Expand Down
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