Merge branch '917-improve-code-coverage-of-ide-secir' into 958-implement-a-check-for-the-results-of-the-initialization

Author: lenaploetzke

cpp/models/ide_secir/model.h

@@ -53,25 +53,24 @@ class Model
           const ParameterSet& Parameterset_init = ParameterSet());
 
     /**
-    * @brief Checks constraints on model parameters.
+    * @brief Checks constraints on model parameters and initial data.
+    * @return Returns true if one (or more) constraint(s) are not satisfied, otherwise false.
     */
-    void check_constraints(ScalarType dt) const
+    bool check_constraints(ScalarType dt) const
     {
-        if (!(m_populations.get_num_time_points() > 0)) {
-            log_error("Model construction failed. No initial time point for populations.");
+        if (!((int)m_transitions.get_num_elements() == (int)InfectionTransition::Count)) {
+            log_error(
+                "Initialization failed. Number of elements in transition vector does not match the required number.");
+            return true;
         }
 
         for (int i = 0; i < (int)InfectionState::Count; i++) {
             if (m_populations[0][i] < 0) {
                 log_error("Initialization failed. Initial values for populations are less than zero.");
+                return true;
             }
         }
 
-        if (!((int)m_transitions.get_num_elements() == (int)InfectionTransition::Count)) {
-            log_error(
-                "Initialization failed. Number of elements in transition vector does not match the required number.");
-        }
-
         ScalarType support_max = std::max(
             {parameters.get<TransitionDistributions>()[(int)InfectionTransition::ExposedToInfectedNoSymptoms]
                  .get_support_max(dt, m_tol),
@@ -95,9 +94,10 @@ class Model
         if (m_transitions.get_num_time_points() < (Eigen::Index)std::ceil(support_max / dt)) {
             log_error(
                 "Initialization failed. Not enough time points for transitions given before start of simulation.");
+            return true;
         }
 
-        parameters.check_constraints();
+        return parameters.check_constraints();
     }
 
     /**

cpp/tests/test_ide_secir.cpp

@@ -348,8 +348,97 @@ TEST(IdeSecir, checkInitializations)
     mio::set_log_level(mio::LogLevel::warn);
 }
 
-// a) Test if check_constraints() function correctly reports wrongly set parameters.
-// b) Test if check_constraints() does not complain if parameters are set within correct ranges.
+// a) Test if the function check_constraints() of the class Model correctly reports errors in the model constraints.
+// b) Test if check_constraints() does not complain if the conditions are met.
+TEST(IdeSecir, testModelConstraints)
+{
+    using Vec = mio::TimeSeries<ScalarType>::Vector;
+    // Deactivate temporarily log output for next tests.
+    mio::set_log_level(mio::LogLevel::off);
+
+    // Set wrong initial data and use check_constraints().
+    // Follow the same order as in check_constraints().
+
+    // --- Test with wrong size of the initial value vector for the flows.
+    ScalarType N      = 10000;
+    ScalarType deaths = 10;
+    ScalarType dt     = 1;
+
+    int num_transitions = (int)mio::isecir::InfectionTransition::Count;
+
+    // Create TimeSeries of the wrong size.
+    mio::TimeSeries<ScalarType> init_wrong_size(num_transitions + 1);
+    // Add time points with vectors of the wrong size.
+    Vec vec_init_wrong_size = Vec::Constant(num_transitions + 1, 0.);
+    vec_init_wrong_size[(int)mio::isecir::InfectionTransition::ExposedToInfectedNoSymptoms] = 10.0;
+    init_wrong_size.add_time_point(-3, vec_init_wrong_size);
+    while (init_wrong_size.get_last_time() < 0) {
+        init_wrong_size.add_time_point(init_wrong_size.get_last_time() + dt, vec_init_wrong_size);
+    }
+
+    // Initialize a model.
+    mio::isecir::Model model_wrong_size(std::move(init_wrong_size), N, deaths);
+
+    // Return true for negative entry in m_populations.
+    auto constraint_check = model_wrong_size.check_constraints(dt);
+    EXPECT_TRUE(constraint_check);
+
+    // --- Test with negative number of deaths.
+    deaths = -10;
+    // Create TimeSeries with num_transitions elements.
+    mio::TimeSeries<ScalarType> init(num_transitions);
+    // Add time points for initialization of transitions.
+    Vec vec_init                                                                 = Vec::Constant(num_transitions, 0.);
+    vec_init[(int)mio::isecir::InfectionTransition::ExposedToInfectedNoSymptoms] = 10.0;
+    init.add_time_point(-3, vec_init);
+    while (init.get_last_time() < 0) {
+        init.add_time_point(init.get_last_time() + dt, vec_init);
+    }
+
+    // Initialize a model.
+    mio::TimeSeries<ScalarType> init_copy(init);
+    mio::isecir::Model model_negative_deaths(std::move(init_copy), N, deaths);
+
+    // Return true for negative entry in m_populations.
+    constraint_check = model_negative_deaths.check_constraints(dt);
+    EXPECT_TRUE(constraint_check);
+
+    // --- Test with too few time points.
+    deaths = 10;
+    // Initialize a model.
+    mio::isecir::Model model_few_timepoints(std::move(init), N, deaths);
+
+    mio::ExponentialDecay expdecay(4.0);
+    mio::StateAgeFunctionWrapper delaydistribution(expdecay);
+    std::vector<mio::StateAgeFunctionWrapper> vec_delaydistrib(num_transitions, delaydistribution);
+    model_few_timepoints.parameters.set<mio::isecir::TransitionDistributions>(vec_delaydistrib);
+
+    constraint_check = model_few_timepoints.check_constraints(dt);
+    EXPECT_TRUE(constraint_check);
+
+    // --- The check_constraints() function of parameters is tested in its own test below. ---
+
+    // --- Correct wrong setup so that next check can go through.
+    mio::TimeSeries<ScalarType> init_enough_timepoints(num_transitions);
+    init_enough_timepoints.add_time_point(-5, vec_init);
+    while (init_enough_timepoints.get_last_time() < 0) {
+        init_enough_timepoints.add_time_point(init_enough_timepoints.get_last_time() + dt, vec_init);
+    }
+
+    // Initialize a model.
+    mio::isecir::Model model(std::move(init_enough_timepoints), N, deaths);
+
+    model.parameters.set<mio::isecir::TransitionDistributions>(vec_delaydistrib);
+
+    constraint_check = model.check_constraints(dt);
+    EXPECT_FALSE(constraint_check);
+
+    // Reactive log output.
+    mio::set_log_level(mio::LogLevel::warn);
+}
+
+// a) Test if check_constraints() function of Parameters correctly reports wrongly set parameters.
+// b) Test if check_constraints() function of Parameters does not complain if parameters are set within correct ranges.
 TEST(IdeSecir, testValueConstraints)
 {
     using Vec = mio::TimeSeries<ScalarType>::Vector;
@@ -442,8 +531,8 @@ TEST(IdeSecir, testValueConstraints)
     model.parameters
         .get<mio::isecir::TransitionProbabilities>()[(int)mio::isecir::InfectionTransition::SusceptibleToExposed] = 1.0;
     model.parameters.get<mio::isecir::TransitionProbabilities>()[(
-        int)mio::isecir::InfectionTransition::ExposedToInfectedNoSymptoms] = -1.0;
-    constraint_check                                                       = model.parameters.check_constraints();
+        int)mio::isecir::InfectionTransition::ExposedToInfectedNoSymptoms]                                        = 0.6;
+    constraint_check = model.parameters.check_constraints();
     EXPECT_TRUE(constraint_check);
 
     // Check sum InfectedNoSymptomsToInfectedSymptoms + InfectedNoSymptomsToRecovered.