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1067 improve abm tests #1141

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a5fc536
Add comments and structure the test of household in infection
khoanguyen-dev Sep 30, 2024
0a1e39e
Add comments and structure the tests of mask
khoanguyen-dev Oct 1, 2024
044b21c
Merge branch 'main' into 1067-improve-abm-tests
khoanguyen-dev Oct 9, 2024
13054c0
Optimise tests for infection, lockdown, mobiliy rules and testing str…
khoanguyen-dev Oct 21, 2024
f4620ae
Merge branch 'main' into 1067-improve-abm-tests
khoanguyen-dev Oct 28, 2024
6b9ff47
Optimise tests for location, person and model
khoanguyen-dev Oct 31, 2024
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178 changes: 94 additions & 84 deletions cpp/models/abm/parameters.h
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Original file line number Diff line number Diff line change
Expand Up @@ -229,7 +229,7 @@ struct MaskProtection {
using Type = CustomIndexArray<UncertainValue<>, MaskType>;
static Type get_default(AgeGroup /*size*/)
{
Type defaut_value = Type(MaskType::Count, 0.0);
Type defaut_value = Type(MaskType::Count, 0.0);
// Initial values according to http://dx.doi.org/10.15585/mmwr.mm7106e1
defaut_value[MaskType::FFP2] = 0.83;
defaut_value[MaskType::Surgical] = 0.66;
Expand Down Expand Up @@ -637,108 +637,118 @@ class Parameters : public ParametersBase
*/
bool check_constraints() const
{
for (auto i = AgeGroup(0); i < AgeGroup(m_num_groups); ++i) {

if (this->get<IncubationPeriod>()[{VirusVariant::Wildtype, i}] < 0) {
log_error("Constraint check: Parameter IncubationPeriod of age group {:.0f} smaller than {:.4f}",
(size_t)i, 0);
return true;
}

if (this->get<InfectedNoSymptomsToSymptoms>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter InfectedNoSymptomsToSymptoms of age group {:.0f} smaller "
"than {:d}",
(size_t)i, 0);
return true;
}

if (this->get<InfectedNoSymptomsToRecovered>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter InfectedNoSymptomsToRecovered of age group {:.0f} smaller "
"than {:d}",
(size_t)i, 0);
return true;
}

if (this->get<InfectedSymptomsToRecovered>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error(
"Constraint check: Parameter InfectedSymptomsToRecovered of age group {:.0f} smaller than {:d}",
(size_t)i, 0);
return true;
}

if (this->get<InfectedSymptomsToSevere>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter InfectedSymptomsToSevere of age group {:.0f} smaller than {:d}",
(size_t)i, 0);
return true;
}

if (this->get<SevereToCritical>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter SevereToCritical of age group {:.0f} smaller than {:d}",
(size_t)i, 0);
return true;
}

if (this->get<SevereToRecovered>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter SevereToRecovered of age group {:.0f} smaller than {:d}",
(size_t)i, 0);
return true;
}

if (this->get<CriticalToDead>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter CriticalToDead of age group {:.0f} smaller than {:d}", (size_t)i,
0);
return true;
}

if (this->get<CriticalToRecovered>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter CriticalToRecovered of age group {:.0f} smaller than {:d}",
(size_t)i, 0);
return true;
}

if (this->get<RecoveredToSusceptible>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter RecoveredToSusceptible of age group {:.0f} smaller than {:d}",
(size_t)i, 0);
return true;
}

if (this->get<DetectInfection>()[{VirusVariant::Wildtype, i}] < 0.0 ||
this->get<DetectInfection>()[{VirusVariant::Wildtype, i}] > 1.0) {
log_error("Constraint check: Parameter DetectInfection of age group {:.0f} smaller than {:d} or "
"larger than {:d}",
(size_t)i, 0, 1);
return true;
for (auto age_group = AgeGroup(0); age_group < AgeGroup(m_num_groups); ++age_group) {
for (std::uint32_t variant_count = 0; variant_count < static_cast<std::uint32_t>(VirusVariant::Count); ++variant_count) {

auto virus_variant = static_cast<mio::abm::VirusVariant>(variant_count);
Comment on lines +640 to +643
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With a patch to make_index_range in index_range.h, this becomes

Suggested change
for (auto age_group = AgeGroup(0); age_group < AgeGroup(m_num_groups); ++age_group) {
for (std::uint32_t variant_count = 0; variant_count < static_cast<std::uint32_t>(VirusVariant::Count); ++variant_count) {
auto virus_variant = static_cast<mio::abm::VirusVariant>(variant_count);
for (auto age_group : make_index_range(AgeGroup{m_num_groups})) {
for (auto virus_variant : make_index_range(Index<VirusVariant>{VirusVariant::Count})) {

Try to replace make_index_range with the following, so it can work with AgeGroup (otherwise Index<AgeGroup> is required):

/**
 * @brief Construct a range that can be used to iterate over all MultiIndices in the given dimensions.
 * The range spans over [0, d) for each category in the MultiIndex, where d is that category's value in dimensions.
 * @param[in] dimensions A MultiIndex that contains the dimension for each category.
 * @tparam Categories All categories of the given MultiIndex.
 * @return An iterable range over the given dimensions.
 */
template <class... Categories>
IndexRange<Index<Categories...>> make_index_range(const Index<Categories...>& dimensions)
{
    return IndexRange<Index<Categories...>>(dimensions);
}


if (this->get<IncubationPeriod>()[{virus_variant, age_group}] < 0) {
log_error("Constraint check: Parameter IncubationPeriod of age group {:.0f} smaller than {:.4f}",
(size_t)age_group, 0);
return true;
}

if (this->get<InfectedNoSymptomsToSymptoms>()[{virus_variant, age_group}] < 0.0) {
log_error("Constraint check: Parameter InfectedNoSymptomsToSymptoms of age group {:.0f} smaller "
"than {:d}",
(size_t)age_group, 0);
return true;
}

if (this->get<InfectedNoSymptomsToRecovered>()[{virus_variant, age_group}] < 0.0) {
log_error("Constraint check: Parameter InfectedNoSymptomsToRecovered of age group {:.0f} smaller "
"than {:d}",
(size_t)age_group, 0);
return true;
}

if (this->get<InfectedSymptomsToRecovered>()[{virus_variant, age_group}] < 0.0) {
log_error(
"Constraint check: Parameter InfectedSymptomsToRecovered of age group {:.0f} smaller than {:d}",
(size_t)age_group, 0);
return true;
}

if (this->get<InfectedSymptomsToSevere>()[{virus_variant, age_group}] < 0.0) {
log_error(
"Constraint check: Parameter InfectedSymptomsToSevere of age group {:.0f} smaller than {:d}",
(size_t)age_group, 0);
return true;
}

if (this->get<SevereToCritical>()[{virus_variant, age_group}] < 0.0) {
log_error("Constraint check: Parameter SevereToCritical of age group {:.0f} smaller than {:d}",
(size_t)age_group, 0);
return true;
}

if (this->get<SevereToRecovered>()[{virus_variant, age_group}] < 0.0) {
log_error("Constraint check: Parameter SevereToRecovered of age group {:.0f} smaller than {:d}",
(size_t)age_group, 0);
return true;
}

if (this->get<CriticalToDead>()[{virus_variant, age_group}] < 0.0) {
log_error("Constraint check: Parameter CriticalToDead of age group {:.0f} smaller than {:d}",
(size_t)age_group, 0);
return true;
}

if (this->get<CriticalToRecovered>()[{virus_variant, age_group}] < 0.0) {
log_error("Constraint check: Parameter CriticalToRecovered of age group {:.0f} smaller than {:d}",
(size_t)age_group, 0);
return true;
}

if (this->get<RecoveredToSusceptible>()[{virus_variant, age_group}] < 0.0) {
log_error(
"Constraint check: Parameter RecoveredToSusceptible of age group {:.0f} smaller than {:d}",
(size_t)age_group, 0);
return true;
}

if (this->get<DetectInfection>()[{virus_variant, age_group}] < 0.0 ||
this->get<DetectInfection>()[{virus_variant, age_group}] > 1.0) {
log_error("Constraint check: Parameter DetectInfection of age group {:.0f} smaller than {:d} or "
"larger than {:d}",
(size_t)age_group, 0, 1);
return true;
}
}

if (this->get<GotoWorkTimeMinimum>()[i].seconds() < 0.0 ||
this->get<GotoWorkTimeMinimum>()[i].seconds() > this->get<GotoWorkTimeMaximum>()[i].seconds()) {
if (this->get<GotoWorkTimeMinimum>()[age_group].seconds() < 0.0 ||
this->get<GotoWorkTimeMinimum>()[age_group].seconds() >
this->get<GotoWorkTimeMaximum>()[age_group].seconds()) {
log_error("Constraint check: Parameter GotoWorkTimeMinimum of age group {:.0f} smaller {:d} or "
"larger {:d}",
(size_t)i, 0, this->get<GotoWorkTimeMaximum>()[i].seconds());
(size_t)age_group, 0, this->get<GotoWorkTimeMaximum>()[age_group].seconds());
return true;
}

if (this->get<GotoWorkTimeMaximum>()[i].seconds() < this->get<GotoWorkTimeMinimum>()[i].seconds() ||
this->get<GotoWorkTimeMaximum>()[i] > days(1)) {
if (this->get<GotoWorkTimeMaximum>()[age_group].seconds() <
this->get<GotoWorkTimeMinimum>()[age_group].seconds() ||
this->get<GotoWorkTimeMaximum>()[age_group] > days(1)) {
log_error("Constraint check: Parameter GotoWorkTimeMaximum of age group {:.0f} smaller {:d} or larger "
"than one day time span",
(size_t)i, this->get<GotoWorkTimeMinimum>()[i].seconds());
(size_t)age_group, this->get<GotoWorkTimeMinimum>()[age_group].seconds());
return true;
}

if (this->get<GotoSchoolTimeMinimum>()[i].seconds() < 0.0 ||
this->get<GotoSchoolTimeMinimum>()[i].seconds() > this->get<GotoSchoolTimeMaximum>()[i].seconds()) {
if (this->get<GotoSchoolTimeMinimum>()[age_group].seconds() < 0.0 ||
this->get<GotoSchoolTimeMinimum>()[age_group].seconds() >
this->get<GotoSchoolTimeMaximum>()[age_group].seconds()) {
log_error("Constraint check: Parameter GotoSchoolTimeMinimum of age group {:.0f} smaller {:d} or "
"larger {:d}",
(size_t)i, 0, this->get<GotoWorkTimeMaximum>()[i].seconds());
(size_t)age_group, 0, this->get<GotoWorkTimeMaximum>()[age_group].seconds());
return true;
}

if (this->get<GotoSchoolTimeMaximum>()[i].seconds() < this->get<GotoSchoolTimeMinimum>()[i].seconds() ||
this->get<GotoSchoolTimeMaximum>()[i] > days(1)) {
if (this->get<GotoSchoolTimeMaximum>()[age_group].seconds() <
this->get<GotoSchoolTimeMinimum>()[age_group].seconds() ||
this->get<GotoSchoolTimeMaximum>()[age_group] > days(1)) {
log_error("Constraint check: Parameter GotoWorkTimeMaximum of age group {:.0f} smaller {:d} or larger "
"than one day time span",
(size_t)i, this->get<GotoSchoolTimeMinimum>()[i].seconds());
(size_t)age_group, this->get<GotoSchoolTimeMinimum>()[age_group].seconds());
return true;
}
}
Expand Down
67 changes: 41 additions & 26 deletions cpp/tests/test_abm_household.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,69 +21,82 @@
#include "abm_helpers.h"
#include <gtest/gtest.h>


/**
* @brief Test adding a household to a model.
* Verifies correct number of persons, age groups, and location assignments.
*/
TEST(TestHouseholds, test_add_household_to_model)
{
// Create household members
auto member1 = mio::abm::HouseholdMember(num_age_groups);
member1.set_age_weight(age_group_0_to_4, 1);
member1.set_age_weight(age_group_0_to_4, 1); // Member is a child (age 0-4)

auto member2 = mio::abm::HouseholdMember(num_age_groups);
member2.set_age_weight(age_group_5_to_14, 1);
member2.set_age_weight(age_group_5_to_14, 1); // Member is a child (age 5-14)

// Create household and add members
auto household = mio::abm::Household();
household.add_members(member1, 2);
household.add_members(member2, 2);
household.add_members(member1, 2); // Add two members of age group 0-4
household.add_members(member2, 2); // Add two members of age group 5-14

// Create model and add the household
auto model = mio::abm::Model(num_age_groups);

add_household_to_model(model, household);
auto persons = model.get_persons();

// Test size
// Test: Correct number of persons added to the model
EXPECT_EQ(persons.size(), 4);

// Test age
// Test: Correct age groups assigned to persons
EXPECT_EQ(persons[0].get_age(), age_group_0_to_4);
EXPECT_EQ(persons[1].get_age(), age_group_0_to_4);
EXPECT_EQ(persons[2].get_age(), age_group_5_to_14);
EXPECT_EQ(persons[3].get_age(), age_group_5_to_14);

// Test location
// Test: Ensure persons of the same age group are in the same location
EXPECT_EQ(persons[0].get_location(), persons[1].get_location());
EXPECT_EQ(persons[2].get_location(), persons[3].get_location());
}

/**
* @brief Test adding a group of households to a model.
* Checks correct number of persons, age distribution, and location assignments.
*/
TEST(TestHouseholds, test_add_household_group_to_model)
{

// Create household members
auto member1 = mio::abm::HouseholdMember(num_age_groups);
member1.set_age_weight(age_group_35_to_59, 1);
member1.set_age_weight(age_group_35_to_59, 1); // Member is an adult (age 35-59)

auto member2 = mio::abm::HouseholdMember(num_age_groups);
member2.set_age_weight(age_group_5_to_14, 1);

auto household_group = mio::abm::HouseholdGroup();
member2.set_age_weight(age_group_5_to_14, 1); // Member is a child (age 5-14)

// Create the first household and add members
auto household1 = mio::abm::Household();
household1.add_members(member1, 10);
household1.add_members(member2, 2);
household_group.add_households(household1, 5);
household1.add_members(member1, 10); // Add ten members of age group 35-59
household1.add_members(member2, 2); // Add two members of age group 5-14

// Create the second household and add members
auto household2 = mio::abm::Household();
household2.add_members(member1, 2);
household2.add_members(member2, 2);
household_group.add_households(household2, 10);
household2.add_members(member1, 2); // Add two members of age group 35-59
household2.add_members(member2, 2); // Add two members of age group 5-14

auto model = mio::abm::Model(num_age_groups);
// Create a household group and add households
auto household_group = mio::abm::HouseholdGroup();
household_group.add_households(household1, 5); // Add household1 5 times
household_group.add_households(household2, 10); // Add household2 10 times

// Create model and add the household group
auto model = mio::abm::Model(num_age_groups);
add_household_group_to_model(model, household_group);
auto persons = model.get_persons();

// Test size
// Test: Correct number of persons in the model (5 * 12 + 10 * 4 = 100 persons)
EXPECT_EQ(persons.size(), 100);

// Test age
// Test: Count persons in each age group
int number_of_age5to14_year_olds = 0, number_of_age35to59_year_olds = 0;

for (auto& person : persons) {
if (person.get_age() == age_group_5_to_14) {
number_of_age5to14_year_olds++;
Expand All @@ -92,10 +105,12 @@ TEST(TestHouseholds, test_add_household_group_to_model)
number_of_age35to59_year_olds++;
}
}
EXPECT_EQ(number_of_age5to14_year_olds, 30);
EXPECT_EQ(number_of_age35to59_year_olds, 70);

// Test location for some people
// Verify the age group distribution
EXPECT_EQ(number_of_age5to14_year_olds, 30); // 30 children (age 5-14)
EXPECT_EQ(number_of_age35to59_year_olds, 70); // 70 adults (age 35-59)

// Test: Ensure people in the same household share the same location (for a few checks)
EXPECT_EQ(persons[0].get_location(), persons[1].get_location());
EXPECT_EQ(persons[1].get_location(), persons[5].get_location());
EXPECT_EQ(persons[5].get_location(), persons[10].get_location());
Expand Down
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