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lenaploetzke merged 2 commits into from
Apr 11, 2024
Merged

965 use int instead of unsigned int in lct infection state #1002

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072d513
changed unsigned ints to ints
lenaploetzke Apr 11, 2024
d53a2f0
added reviewer suggestions
lenaploetzke Apr 11, 2024
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45 changes: 22 additions & 23 deletions cpp/examples/lct_secir.cpp
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Expand Up @@ -47,59 +47,58 @@ int main()
{50}, {10, 10, 5, 3, 2}, {20}, {10}};

// Assert that initial_populations has the right shape.
if (initial_populations.size() != (int)LctState::InfectionState::Count) {
if (initial_populations.size() != (size_t)LctState::InfectionState::Count) {
mio::log_error("The number of vectors in initial_populations does not match the number of InfectionStates.");
return 1;
}
if ((initial_populations[(int)LctState::InfectionState::Susceptible].size() !=
LctState::get_num_subcompartments<LctState::InfectionState::Susceptible>()) ||
(size_t)LctState::get_num_subcompartments<LctState::InfectionState::Susceptible>()) ||
(initial_populations[(int)LctState::InfectionState::Exposed].size() !=
LctState::get_num_subcompartments<LctState::InfectionState::Exposed>()) ||
(size_t)LctState::get_num_subcompartments<LctState::InfectionState::Exposed>()) ||
(initial_populations[(int)LctState::InfectionState::InfectedNoSymptoms].size() !=
LctState::get_num_subcompartments<LctState::InfectionState::InfectedNoSymptoms>()) ||
(size_t)LctState::get_num_subcompartments<LctState::InfectionState::InfectedNoSymptoms>()) ||
(initial_populations[(int)LctState::InfectionState::InfectedSymptoms].size() !=
LctState::get_num_subcompartments<LctState::InfectionState::InfectedSymptoms>()) ||
(size_t)LctState::get_num_subcompartments<LctState::InfectionState::InfectedSymptoms>()) ||
(initial_populations[(int)LctState::InfectionState::InfectedSevere].size() !=
LctState::get_num_subcompartments<LctState::InfectionState::InfectedSevere>()) ||
(size_t)LctState::get_num_subcompartments<LctState::InfectionState::InfectedSevere>()) ||
(initial_populations[(int)LctState::InfectionState::InfectedCritical].size() !=
LctState::get_num_subcompartments<LctState::InfectionState::InfectedCritical>()) ||
(size_t)LctState::get_num_subcompartments<LctState::InfectionState::InfectedCritical>()) ||
(initial_populations[(int)LctState::InfectionState::Recovered].size() !=
LctState::get_num_subcompartments<LctState::InfectionState::Recovered>()) ||
(size_t)LctState::get_num_subcompartments<LctState::InfectionState::Recovered>()) ||
(initial_populations[(int)LctState::InfectionState::Dead].size() !=
LctState::get_num_subcompartments<LctState::InfectionState::Dead>())) {
(size_t)LctState::get_num_subcompartments<LctState::InfectionState::Dead>())) {
mio::log_error("The length of at least one vector in initial_populations does not match the related number of "
"subcompartments.");
return 1;
}

// Transfer the initial values in initial_populations to the vector init.
Eigen::VectorXd init = Eigen::VectorXd::Zero(LctState::Count);
init[(int)LctState::get_first_index<LctState::InfectionState::Susceptible>()] =
init[LctState::get_first_index<LctState::InfectionState::Susceptible>()] =
initial_populations[(int)LctState::InfectionState::Susceptible][0];
for (unsigned int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::Exposed>(); i++) {
init[(int)LctState::get_first_index<LctState::InfectionState::Exposed>() + i] =
for (int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::Exposed>(); i++) {
init[LctState::get_first_index<LctState::InfectionState::Exposed>() + i] =
initial_populations[(int)LctState::InfectionState::Exposed][i];
}
for (unsigned int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::InfectedNoSymptoms>();
i++) {
init[(int)LctState::get_first_index<LctState::InfectionState::InfectedNoSymptoms>() + i] =
for (int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::InfectedNoSymptoms>(); i++) {
init[LctState::get_first_index<LctState::InfectionState::InfectedNoSymptoms>() + i] =
initial_populations[(int)LctState::InfectionState::InfectedNoSymptoms][i];
}
for (unsigned int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::InfectedSymptoms>(); i++) {
init[(int)LctState::get_first_index<LctState::InfectionState::InfectedSymptoms>() + i] =
for (int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::InfectedSymptoms>(); i++) {
init[LctState::get_first_index<LctState::InfectionState::InfectedSymptoms>() + i] =
initial_populations[(int)LctState::InfectionState::InfectedSymptoms][i];
}
for (unsigned int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::InfectedSevere>(); i++) {
init[(int)LctState::get_first_index<LctState::InfectionState::InfectedSevere>() + i] =
for (int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::InfectedSevere>(); i++) {
init[LctState::get_first_index<LctState::InfectionState::InfectedSevere>() + i] =
initial_populations[(int)LctState::InfectionState::InfectedSevere][i];
}
for (unsigned int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::InfectedCritical>(); i++) {
init[(int)LctState::get_first_index<LctState::InfectionState::InfectedCritical>() + i] =
for (int i = 0; i < LctState::get_num_subcompartments<LctState::InfectionState::InfectedCritical>(); i++) {
init[LctState::get_first_index<LctState::InfectionState::InfectedCritical>() + i] =
initial_populations[(int)LctState::InfectionState::InfectedCritical][i];
}
init[(int)LctState::get_first_index<LctState::InfectionState::Recovered>()] =
init[LctState::get_first_index<LctState::InfectionState::Recovered>()] =
initial_populations[(int)LctState::InfectionState::Recovered][0];
init[(int)LctState::get_first_index<LctState::InfectionState::Dead>()] =
init[LctState::get_first_index<LctState::InfectionState::Dead>()] =
initial_populations[(int)LctState::InfectionState::Dead][0];

// Initialize model.
Expand Down
19 changes: 10 additions & 9 deletions cpp/memilio/epidemiology/lct_infection_state.h
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Expand Up @@ -31,12 +31,12 @@ namespace mio
* @tparam Ns Number of subcompartments for each infection state defined in InfectionState.
* The number of given template arguments must be equal to the entry Count from InfectionState.
*/
template <class InfectionStates, unsigned int... Ns>
template <class InfectionStates, int... Ns>
class LctInfectionState
{
public:
using InfectionState = InfectionStates;
static_assert((unsigned int)InfectionState::Count == sizeof...(Ns),
static_assert((size_t)InfectionState::Count == sizeof...(Ns),
"The number of integers provided as template parameters must be "
"the same as the entry Count of InfectionState.");

Expand All @@ -46,10 +46,10 @@ class LctInfectionState
* @brief Gets the number of subcompartments in an infection state.
*
* @tparam State: Infection state for which the number of subcompartments should be returned.
* @return Number of subcompartments for State.
* @return Number of subcompartments for State. Returned value is always at least one.
*/
template <InfectionState State>
static constexpr unsigned int get_num_subcompartments()
static constexpr int get_num_subcompartments()
Comment thread
lenaploetzke marked this conversation as resolved.
{
static_assert(State < InfectionState::Count, "State must be a a valid InfectionState.");
return m_subcompartment_numbers[(int)State];
Expand All @@ -61,23 +61,24 @@ class LctInfectionState
* In a simulation, the number of individuals in the subcompartments are stored in vectors.
* Accordingly, the index of the first subcompartment of State in such a vector is returned.
* @tparam State: Infection state for which the index should be returned.
* @return Index of the first subcompartment for a vector with one entry per subcompartment.
* @return Index of the first subcompartment for a vector with one entry per subcompartment.
* Returned value is always non-negative.
*/
template <InfectionState State>
static constexpr unsigned int get_first_index()
static constexpr int get_first_index()
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lenaploetzke marked this conversation as resolved.
{
static_assert(State < InfectionState::Count, "State must be a a valid InfectionState.");
unsigned int index = 0;
int index = 0;
for (int i = 0; i < (int)(State); i++) {
index = index + m_subcompartment_numbers[i];
}
return index;
}

static constexpr unsigned int Count{(... + Ns)};
static constexpr int Count{(... + Ns)};

private:
static constexpr const std::array<unsigned int, sizeof...(Ns)> m_subcompartment_numbers{
static constexpr const std::array<int, sizeof...(Ns)> m_subcompartment_numbers{
Ns...}; ///< Vector which defines the number of subcompartments for each infection state of InfectionState.
};

Expand Down
8 changes: 4 additions & 4 deletions cpp/models/lct_secir/model.h
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Expand Up @@ -43,8 +43,8 @@ namespace lsecir
* @tparam NumInfectedSevere The number of subcompartents used for the InfectedSevere compartment.
* @tparam NumInfectedCritical The number of subcompartents used for the InfectedCritical compartment.
*/
template <unsigned int NumExposed, unsigned int NumInfectedNoSymptoms, unsigned int NumInfectedSymptoms,
unsigned int NumInfectedSevere, unsigned int NumInfectedCritical>
template <int NumExposed, int NumInfectedNoSymptoms, int NumInfectedSymptoms, int NumInfectedSevere,
int NumInfectedCritical>
class Model
{

Expand Down Expand Up @@ -75,7 +75,7 @@ class Model
log_error("Size of the initial values does not match subcompartments.");
return true;
}
for (unsigned int i = 0; i < LctState::Count; i++) {
for (int i = 0; i < LctState::Count; i++) {
if (m_initial_values[i] < 0) {
log_warning(
"Initial values for one subcompartment are less than zero. Simulation results are not realistic.");
Expand Down Expand Up @@ -291,7 +291,7 @@ class Model
void set_initial_values(Eigen::VectorXd init)
{
m_initial_values = init;
m_N0 = m_initial_values.sum();
m_N0 = m_initial_values.sum();
}

Parameters parameters{}; ///< Parameters of the model.
Expand Down
13 changes: 6 additions & 7 deletions cpp/models/lct_secir/parameters_io.h
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Expand Up @@ -118,8 +118,8 @@ IOResult<void> set_initial_data_from_confirmed_cases(Model& model, const std::st
int idxInfectedNoSymptoms_last =
LctState::template get_first_index<InfectionState::InfectedNoSymptoms>() +
LctState::template get_num_subcompartments<InfectionState::InfectedNoSymptoms>() - 1;
for (int i = 0;
i < (int)LctState::template get_num_subcompartments<InfectionState::InfectedNoSymptoms>(); i++) {
for (int i = 0; i < LctState::template get_num_subcompartments<InfectionState::InfectedNoSymptoms>();
i++) {
if (offset == std::floor(i * timeInfectedNoSymptoms_i)) {
init[idxInfectedNoSymptoms_last - i] -=
(1 - (i * timeInfectedNoSymptoms_i - std::floor(i * timeInfectedNoSymptoms_i))) *
Expand Down Expand Up @@ -152,7 +152,7 @@ IOResult<void> set_initial_data_from_confirmed_cases(Model& model, const std::st
// Index of the last subcompartment of Exposed.
int idxExposed_last = LctState::template get_first_index<InfectionState::Exposed>() +
LctState::template get_num_subcompartments<InfectionState::Exposed>() - 1;
for (int i = 0; i < (int)LctState::template get_num_subcompartments<InfectionState::Exposed>(); i++) {
for (int i = 0; i < LctState::template get_num_subcompartments<InfectionState::Exposed>(); i++) {
if (offset == std::floor(timeInfectedNoSymptoms + i * timeExposed_i)) {
init[idxExposed_last - i] -= (1 - (timeInfectedNoSymptoms + i * timeExposed_i -
std::floor(timeInfectedNoSymptoms + i * timeExposed_i))) *
Expand Down Expand Up @@ -185,7 +185,7 @@ IOResult<void> set_initial_data_from_confirmed_cases(Model& model, const std::st
(ScalarType)LctState::template get_num_subcompartments<InfectionState::InfectedSymptoms>();
// Index of the first subcompartment of InfectedSymptoms.
int idxInfectedSymptoms_first = LctState::template get_first_index<InfectionState::InfectedSymptoms>();
for (int i = 0; i < (int)LctState::template get_num_subcompartments<InfectionState::InfectedSymptoms>();
for (int i = 0; i < LctState::template get_num_subcompartments<InfectionState::InfectedSymptoms>();
i++) {
if (offset == std::floor(-timeInfectedSymptoms_i * (i + 1))) {
init[idxInfectedSymptoms_first + i] -=
Expand Down Expand Up @@ -221,8 +221,7 @@ IOResult<void> set_initial_data_from_confirmed_cases(Model& model, const std::st
ScalarType prob_SeverePerInfectedSymptoms = model.parameters.template get<SeverePerInfectedSymptoms>();
// Index of the first subcompartment of InfectedSevere.
int idxInfectedSevere_first = LctState::template get_first_index<InfectionState::InfectedSevere>();
for (int i = 0; i < (int)LctState::template get_num_subcompartments<InfectionState::InfectedSevere>();
i++) {
for (int i = 0; i < LctState::template get_num_subcompartments<InfectionState::InfectedSevere>(); i++) {
if (offset == std::floor(-timeInfectedSymptoms - timeInfectedSevere_i * (i + 1))) {
init[idxInfectedSevere_first + i] -=
prob_SeverePerInfectedSymptoms *
Expand Down Expand Up @@ -265,7 +264,7 @@ IOResult<void> set_initial_data_from_confirmed_cases(Model& model, const std::st
ScalarType prob_CriticalPerSevere = model.parameters.template get<CriticalPerSevere>();
// Index of the first subcompartment of InfectedCritical.
int idxInfectedCritical_first = LctState::template get_first_index<InfectionState::InfectedCritical>();
for (int i = 0; i < (int)LctState::template get_num_subcompartments<InfectionState::InfectedCritical>();
for (int i = 0; i < LctState::template get_num_subcompartments<InfectionState::InfectedCritical>();
i++) {
if (offset ==
std::floor(-timeInfectedSymptoms - timeInfectedSevere - timeInfectedCritical_i * (i + 1))) {
Expand Down
2 changes: 1 addition & 1 deletion cpp/tests/test_lct_parameters_io.cpp
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Expand Up @@ -67,7 +67,7 @@ TEST(TestLCTParametersIo, ReadPopulationDataRKI)
Eigen::VectorXd compare(LctState::Count);
compare << 863.05, 14.30625, 8.53125, 30.1125, 36.1875, 3.8125, 9.88, 3.52, 0.09, 0.25, 0.6888, 27.8712, 1.7;

for (unsigned int i = 0; i < LctState::Count; i++) {
for (int i = 0; i < LctState::Count; i++) {
EXPECT_NEAR(model.get_initial_values()[i], compare[i], 1e-4) << "at subcompartment number " << i;
}
}
Expand Down
10 changes: 5 additions & 5 deletions cpp/tests/test_lct_secir.cpp
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Expand Up @@ -226,15 +226,15 @@ TEST(TestLCTSecir, testEvalRightHandSide)
model.parameters.get<mio::lsecir::DeathsPerCritical>() = 0.3;

// Compare the result of eval_right_hand_side() with a hand calculated result.
unsigned int num_subcompartments = LctState::Count;
int num_subcompartments = LctState::Count;
Eigen::VectorXd dydt(num_subcompartments);
model.eval_right_hand_side(model.get_initial_values(), 0, dydt);

Eigen::VectorXd compare(num_subcompartments);
compare << -15.3409, -3.4091, 6.25, -17.5, 15, 0, 3.3052, 3.4483, -7.0417, 6.3158, -2.2906, -2.8169, 12.3899,
1.6901;

for (unsigned int i = 0; i < num_subcompartments; i++) {
for (int i = 0; i < num_subcompartments; i++) {
ASSERT_NEAR(compare[i], dydt[i], 1e-3);
}
}
Expand Down Expand Up @@ -460,17 +460,17 @@ TEST(TestLCTSecir, testConstraints)
using LctState = Model::LctState;

// Check wrong size of initial value vector.
Model model1(std::move(Eigen::VectorXd::Ones((int)LctState::Count - 1)), std::move(parameters_lct));
Model model1(std::move(Eigen::VectorXd::Ones(LctState::Count - 1)), std::move(parameters_lct));
constraint_check = model1.check_constraints();
EXPECT_TRUE(constraint_check);

// Check with values smaller than zero.
Model model2(std::move(Eigen::VectorXd::Constant((int)LctState::Count, -1)), std::move(parameters_lct));
Model model2(std::move(Eigen::VectorXd::Constant(LctState::Count, -1)), std::move(parameters_lct));
constraint_check = model2.check_constraints();
EXPECT_TRUE(constraint_check);

// Check with correct conditions.
Model model3(std::move(Eigen::VectorXd::Constant((int)LctState::Count, 1)));
Model model3(std::move(Eigen::VectorXd::Constant(LctState::Count, 1)));
constraint_check = model3.check_constraints();
EXPECT_FALSE(constraint_check);

Expand Down