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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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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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Original file line number Diff line number Diff line change
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 (date <= Date(2020, 4, 23) || date >= Date(2024, 7, 21)) {
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 (date <= Date(2020, 4, 23) || date >= Date(2024, 7, 21)) {
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log_warning("No DIVI data available for date: {}-{}-{}", date.day, date.month, date.year,
". ICU compartment will be set based on Case data.");
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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
83 changes: 45 additions & 38 deletions cpp/models/ode_secirts/parameters_io.h
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ IOResult<void> compute_confirmed_cases_data(
std::vector<std::vector<FP>>& vnum_InfectedSevere, std::vector<std::vector<FP>>& vnum_icu,
std::vector<std::vector<FP>>& vnum_death, std::vector<std::vector<FP>>& vnum_timm_i,
std::vector<int> const& vregion, Date date, const std::vector<Model>& model,
const std::vector<FP>& scaling_factor_inf, const size_t layer, bool read_icu = false)
const std::vector<FP>& scaling_factor_inf, const size_t layer)
{
auto max_date_entry = std::max_element(case_data.begin(), case_data.end(), [](auto&& a, auto&& b) {
return a.date < b.date;
Expand Down Expand Up @@ -211,17 +211,13 @@ IOResult<void> compute_confirmed_cases_data(
}
if (entry.date == offset_date_by_days(date, -t_InfectedSymptoms - t_InfectedSevere)) {
num_InfectedSevere[age] -= severePerInfectedSymptoms * scaling_factor_inf[age] * entry.num_confirmed;
if (read_icu) {
num_icu[age] +=
severePerInfectedSymptoms * criticalPerSevere * scaling_factor_inf[age] * entry.num_confirmed;
}
num_icu[age] +=
severePerInfectedSymptoms * criticalPerSevere * scaling_factor_inf[age] * entry.num_confirmed;
}
if (entry.date == offset_date_by_days(date, -t_InfectedSymptoms - t_InfectedSevere - t_InfectedCritical)) {
num_death[age] += entry.num_deaths;
if (read_icu) {
num_icu[age] -=
severePerInfectedSymptoms * criticalPerSevere * scaling_factor_inf[age] * entry.num_confirmed;
}
num_icu[age] -=
severePerInfectedSymptoms * criticalPerSevere * scaling_factor_inf[age] * entry.num_confirmed;
}
if (entry.date == offset_date_by_days(date, 0 - t_imm_interval_i)) {
num_imm[age] -= entry.num_confirmed;
Expand Down Expand Up @@ -305,13 +301,12 @@ IOResult<void> read_confirmed_cases_data(
std::vector<std::vector<FP>>& vnum_InfectedNoSymptoms, std::vector<std::vector<FP>>& vnum_InfectedSymptoms,
std::vector<std::vector<FP>>& vnum_InfectedSevere, std::vector<std::vector<FP>>& vnum_icu,
std::vector<std::vector<FP>>& vnum_death, std::vector<std::vector<FP>>& vnum_timm_i,
const std::vector<Model>& model, const std::vector<FP>& scaling_factor_inf, const size_t layer,
bool read_icu = false)
const std::vector<Model>& model, const std::vector<FP>& scaling_factor_inf, const size_t layer)
{
BOOST_OUTCOME_TRY(auto&& case_data, mio::read_confirmed_cases_data(path));
return compute_confirmed_cases_data(case_data, vnum_Exposed, vnum_InfectedNoSymptoms, vnum_InfectedSymptoms,
vnum_InfectedSevere, vnum_icu, vnum_death, vnum_timm_i, vregion, date, model,
scaling_factor_inf, layer, read_icu);
scaling_factor_inf, layer);
}

/**
Expand Down Expand Up @@ -354,7 +349,7 @@ set_confirmed_cases_data(std::vector<Model>& model, const std::vector<ConfirmedC
std::vector<FP> denom_E(num_age_groups, 0.0);
std::vector<FP> denom_I_NS(num_age_groups, 0.0);
std::vector<FP> denom_I_Sy(num_age_groups, 0.0);
std::vector<FP> denom_I_Sev(num_age_groups, 0.0);
std::vector<FP> denom_I_Sev_Cr(num_age_groups, 0.0);

/*----------- Naive immunity -----------*/
for (size_t county = 0; county < model.size(); county++) {
Expand Down Expand Up @@ -391,7 +386,7 @@ set_confirmed_cases_data(std::vector<Model>& model, const std::vector<ConfirmedC
model[county]
.parameters.template get<ReducInfectedSymptomsImprovedImmunity<FP>>()[(AgeGroup)group]);

denom_I_Sev[group] =
denom_I_Sev_Cr[group] =
1 / (immunity_population[0][group] +
immunity_population[1][group] *
model[county].parameters.template get<ReducInfectedSevereCriticalDeadPartialImmunity<FP>>()[(
Expand All @@ -418,7 +413,12 @@ set_confirmed_cases_data(std::vector<Model>& model, const std::vector<ConfirmedC
immunity_population[0][i] * denom_I_Sy[i] * num_InfectedSymptoms[county][i];
model[county].populations[{AgeGroup(i), InfectionState::InfectedSymptomsNaiveConfirmed}] = 0;
model[county].populations[{AgeGroup(i), InfectionState::InfectedSevereNaive}] =
immunity_population[0][i] * denom_I_Sev[i] * num_InfectedSevere[county][i];
immunity_population[0][i] * denom_I_Sev_Cr[i] * num_InfectedSevere[county][i];
// Only set the number of ICU patients here, if the date is not available in the data.
if (date <= Date(2020, 4, 23) || date >= Date(2024, 7, 21)) {
model[county].populations[{AgeGroup(i), InfectionState::InfectedCriticalNaive}] =
immunity_population[0][i] * denom_I_Sev_Cr[i] * num_icu[county][i];
}
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}
if (std::accumulate(num_InfectedSymptoms[county].begin(), num_InfectedSymptoms[county].end(), 0.0) == 0) {
log_warning("No infections for unvaccinated reported on date " + std::to_string(date.year) + "-" +
Expand Down Expand Up @@ -462,7 +462,15 @@ set_confirmed_cases_data(std::vector<Model>& model, const std::vector<ConfirmedC
immunity_population[1][i] *
model[county]
.parameters.template get<ReducInfectedSevereCriticalDeadPartialImmunity<FP>>()[(AgeGroup)i] *
denom_I_Sev[i] * num_InfectedSevere[county][i];
denom_I_Sev_Cr[i] * num_InfectedSevere[county][i];
// Only set the number of ICU patients here, if the date is not available in the data.
if (date <= Date(2020, 4, 23) || date >= Date(2024, 7, 21)) {
model[county].populations[{AgeGroup(i), InfectionState::InfectedCriticalPartialImmunity}] =
immunity_population[1][i] *
model[county]
.parameters.template get<ReducInfectedSevereCriticalDeadPartialImmunity<FP>>()[(AgeGroup)i] *
denom_I_Sev_Cr[i] * num_icu[county][i];
}
// the += is necessary because we already set the previous vaccinated individuals
model[county].populations[{AgeGroup(i), InfectionState::TemporaryImmunePartialImmunity}] +=
immunity_population[1][i] *
Expand Down Expand Up @@ -511,7 +519,16 @@ set_confirmed_cases_data(std::vector<Model>& model, const std::vector<ConfirmedC
immunity_population[2][i] *
model[county]
.parameters.template get<ReducInfectedSevereCriticalDeadImprovedImmunity<FP>>()[(AgeGroup)i] *
denom_I_Sev[i] * num_InfectedSevere[county][i];
denom_I_Sev_Cr[i] * num_InfectedSevere[county][i];
// Only set the number of ICU patients here, if the date is not available in the data.
if (date <= Date(2020, 4, 23) || date >= Date(2024, 7, 21)) {
model[county].populations[{AgeGroup(i), InfectionState::InfectedCriticalImprovedImmunity}] =
immunity_population[2][i] *
model[county]
.parameters.template get<ReducInfectedSevereCriticalDeadImprovedImmunity<FP>>()[(AgeGroup)i] *
denom_I_Sev_Cr[i] * num_icu[county][i];
}

// the += is necessary because we already set the previous vaccinated individuals
model[county].populations[{AgeGroup(i), InfectionState::TemporaryImmuneImprovedImmunity}] +=
immunity_population[2][i] *
Expand Down Expand Up @@ -644,6 +661,12 @@ template <class Model, typename FP = double>
IOResult<void> set_divi_data(std::vector<Model>& model, const std::string& path, const std::vector<int>& vregion,
Date date, FP scaling_factor_icu)
{
// DIVI dataset will no longer be updated from CW29 2024 on.
if (date <= Date(2020, 4, 23) || date >= Date(2024, 7, 21)) {
log_warning("No DIVI data available for date: {}-{}-{}", date.day, date.month, date.year,
". ICU compartment will be set based on Case data.");
return success();
}
std::vector<FP> sum_mu_I_U(vregion.size(), 0);
std::vector<std::vector<FP>> mu_I_U{model.size()};
for (size_t region = 0; region < vregion.size(); region++) {
Expand Down Expand Up @@ -993,13 +1016,7 @@ IOResult<void> export_input_data_county_timeseries(

// TODO: Reuse more code, e.g., set_divi_data (in secir) and a set_divi_data (here) only need a different ModelType.
// TODO: add option to set ICU data from confirmed cases if DIVI or other data is not available.
if (offset_day > Date(2020, 4, 23)) {
BOOST_OUTCOME_TRY(details::set_divi_data(models, divi_data_path, counties, offset_day, scaling_factor_icu));
}
else {
log_warning("No DIVI data available for for date: {}-{}-{}", offset_day.day, offset_day.month,
offset_day.year);
}
BOOST_OUTCOME_TRY(details::set_divi_data(models, divi_data_path, counties, offset_day, scaling_factor_icu));

BOOST_OUTCOME_TRY(details::set_confirmed_cases_data(models, case_data, counties, offset_day, scaling_factor_inf,
immunity_population));
Expand Down Expand Up @@ -1073,13 +1090,8 @@ IOResult<void> read_input_data_county(std::vector<Model>& model, Date date, cons

// TODO: Reuse more code, e.g., set_divi_data (in secir) and a set_divi_data (here) only need a different ModelType.
// TODO: add option to set ICU data from confirmed cases if DIVI or other data is not available.
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"),
Expand Down Expand Up @@ -1136,13 +1148,8 @@ IOResult<void> read_input_data(std::vector<Model>& model, Date date, const std::

// TODO: Reuse more code, e.g., set_divi_data (in secir) and a set_divi_data (here) only need a different ModelType.
// TODO: add option to set ICU data from confirmed cases if DIVI or other data is not available.
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, immunity_population));
Expand Down
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