Feature/find in events (#96)

* Updating for the find in events functionality

* fixing typo in find in event list function

Author: MJC598

include/hepce/utils/config.hpp

@@ -4,7 +4,7 @@
 // Created Date: 2025-04-18                                                  //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-05-08                                                  //
+// Last Modified: 2025-05-15                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -93,6 +93,19 @@ inline std::string GetStringFromConfig(std::string config_key,
     }
     return s;
 }
+
+inline bool FindInEventList(std::string event_name,
+                            datamanagement::ModelData &model_data) {
+    auto event_list = utils::ToLowerVector(utils::SplitToVecT<std::string>(
+        model_data.GetFromConfig("simulation.events"), ','));
+    auto event_name_lower = utils::ToLower(event_name);
+    if (std::find(event_list.begin(), event_list.end(), event_name_lower) !=
+        event_list.end()) {
+        return true;
+    }
+    return false;
+}
+
 } // namespace utils
 } // namespace hepce
 #endif // HEPCE_UTILS_CONFIG_HPP_

include/hepce/utils/formatting.hpp

@@ -4,7 +4,7 @@
 // Created Date: 2025-04-17                                                  //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-04-30                                                  //
+// Last Modified: 2025-05-15                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -78,6 +78,14 @@ inline std::string const BoolToString(bool b) {
     return b ? std::string("true") : std::string("false");
 }
 
+inline std::vector<std::string>
+ToLowerVector(const std::vector<std::string> &vec_str) {
+    std::vector<std::string> copy = vec_str;
+    std::transform(copy.begin(), copy.end(), copy.begin(),
+                   [](std::string &str) { return ToLower(str); });
+    return copy;
+}
+
 template <typename T>
 inline bool FindInVector(std::vector<T> searched, std::vector<T> queries) {
     for (T &query : queries) {

src/event/base/death.cpp

@@ -4,7 +4,7 @@
 // Created Date: 2025-04-18                                                  //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-05-14                                                  //
+// Last Modified: 2025-05-15                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -37,16 +37,19 @@ DeathImpl::DeathImpl(datamanagement::ModelData &model_data,
       _decomp_infected_probability(
           utils::GetDoubleFromConfig("mortality.decomp_infected", model_data)),
       _decomp_uninfected_probability(utils::GetDoubleFromConfig(
-          "mortality.decomp_uninfected", model_data)),
-      _hiv_mortality_probability(
-          utils::GetDoubleFromConfig("mortality.hiv", model_data)) {
+          "mortality.decomp_uninfected", model_data)) {
     LoadData(model_data);
 }
 
 // Execute
 void DeathImpl::Execute(model::Person &person, model::Sampler &sampler) {
-    if (ReachedMaxAge(person) || FatalOverdose(person, sampler) ||
-        HivDeath(person, sampler)) {
+    if (check_overdose && FatalOverdose(person, sampler)) {
+        return;
+    }
+    if (check_hiv && HivDeath(person, sampler)) {
+        return;
+    }
+    if (ReachedMaxAge(person)) {
         return;
     }
 
@@ -78,7 +81,15 @@ void DeathImpl::Execute(model::Person &person, model::Sampler &sampler) {
 }
 
 void DeathImpl::LoadData(datamanagement::ModelData &model_data) {
-    LoadOverdoseData(model_data);
+    if (utils::FindInEventList("overdose", model_data)) {
+        check_overdose = true;
+        LoadOverdoseData(model_data);
+    }
+    if (utils::FindInEventList("hivinfection", model_data)) {
+        check_hiv = true;
+        _hiv_mortality_probability =
+            utils::GetDoubleFromConfig("mortality.hiv", model_data);
+    }
     LoadBackgroundMortality(model_data);
 }
 

src/event/base/internals/death_internals.hpp

@@ -4,7 +4,7 @@
 // Created Date: 2025-04-18                                                  //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-05-14                                                  //
+// Last Modified: 2025-05-15                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -51,7 +51,10 @@ class DeathImpl : public virtual Death, public EventBase {
     const double _f4_uninfected_probability;
     const double _decomp_infected_probability;
     const double _decomp_uninfected_probability;
-    const double _hiv_mortality_probability;
+    double _hiv_mortality_probability = 0.0;
+
+    bool check_overdose = false;
+    bool check_hiv = false;
 
     backgroundmap_t _background_data;
     overdosemap_t _overdose_data;

src/event/hcv/linking.cpp

@@ -4,7 +4,7 @@
 // Created Date: 2025-04-23                                                   //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-05-08                                                  //
+// Last Modified: 2025-05-15                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -39,7 +39,8 @@ LinkingImpl::LinkingImpl(datamanagement::ModelData &model_data,
 
 void LinkingImpl::LoadData(datamanagement::ModelData &model_data) {
     SetEventCostCategory(model::CostCategory::kLinking);
-    SetLinkingStratifiedByPregnancy(CheckForPregnancyEvent(model_data));
+    SetLinkingStratifiedByPregnancy(
+        utils::FindInEventList("Pregnancy", model_data));
     LoadLinkingData(model_data);
     SetInterventionCost(
         utils::GetDoubleFromConfig("linking.intervention_cost", model_data));

src/event/hiv/linking.cpp

@@ -4,7 +4,7 @@
 // Created Date: 2025-04-23                                                  //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-05-08                                                  //
+// Last Modified: 2025-05-15                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -35,7 +35,8 @@ LinkingImpl::LinkingImpl(datamanagement::ModelData &model_data,
 
 void LinkingImpl::LoadData(datamanagement::ModelData &model_data) {
     SetEventCostCategory(model::CostCategory::kHiv);
-    SetLinkingStratifiedByPregnancy(CheckForPregnancyEvent(model_data));
+    SetLinkingStratifiedByPregnancy(
+        utils::FindInEventList("pregnancy", model_data));
     LoadLinkingData(model_data);
 
     SetInterventionCost(utils::GetDoubleFromConfig(

src/event/internals/linking_internals.hpp

@@ -4,7 +4,7 @@
 // Created Date: 2025-04-18                                                  //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-05-12                                                  //
+// Last Modified: 2025-05-15                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -170,13 +170,6 @@ class LinkingBase : public EventBase {
     inline double ApplyMultiplier(double prob, double mult) {
         return utils::RateToProbability(utils::ProbabilityToRate(prob) * mult);
     }
-    inline bool CheckForPregnancyEvent(datamanagement::ModelData &model_data) {
-        std::vector<std::string> event_list = utils::SplitToVecT<std::string>(
-            utils::GetStringFromConfig("simulation.events", model_data), ',');
-
-        return (std::find(event_list.begin(), event_list.end(), "pregnancy") !=
-                event_list.end());
-    }
 
 private:
     // properties

tests/constants/config.hpp

@@ -4,7 +4,7 @@
 // Created Date: 2025-04-23                                                  //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-05-08                                                  //
+// Last Modified: 2025-05-15                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -147,6 +147,7 @@ inline void BuildAlternateSimConf(const std::string &name) {
       << "f4_uninfected = 0.0000271037696334409" << std::endl
       << "decomp_infected = 0.01734776" << std::endl
       << "decomp_uninfected = 0.005688756" << std::endl
+      << "hiv = 0.0" << std::endl
       << "[infection]" << std::endl
       << std::endl
       << "clearance_prob = 0.0489" << std::endl

tests/src/event/base/death_test.cpp

@@ -4,7 +4,7 @@
 // Created: 2025-01-06                                                        //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-05-08                                                  //
+// Last Modified: 2025-05-15                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -34,6 +34,7 @@
 #include <sampler_mock.hpp>
 
 using ::testing::_;
+using ::testing::NiceMock;
 using ::testing::Return;
 
 using namespace hepce::data;
@@ -44,7 +45,7 @@ namespace testing {
 
 class DeathTest : public ::testing::Test {
 protected:
-    MockPerson mock_person;
+    NiceMock<MockPerson> mock_person;
     MockSampler mock_sampler;
     std::string test_db = "inputs.db";
     std::string test_conf = "sim.conf";
@@ -75,6 +76,13 @@ class DeathTest : public ::testing::Test {
         discounted_life = utils::Discount(1, 0.0025, 1, false);
         model_data = datamanagement::ModelData::Create(test_conf);
         model_data->AddSource(test_db);
+
+        ON_CALL(mock_person, GetAge()).WillByDefault(Return(300));
+        ON_CALL(mock_person, GetCurrentlyOverdosing())
+            .WillByDefault(Return(false));
+        ON_CALL(mock_person, GetSex()).WillByDefault(Return(data::Sex::kMale));
+        ON_CALL(mock_person, GetBehaviorDetails())
+            .WillByDefault(Return(behaviors));
     }
     void TearDown() override {
         std::filesystem::remove(test_db);
@@ -95,27 +103,14 @@ TEST_F(DeathTest, AgeDR) {
     auto event = event::base::Death::Create(*model_data, LOG_NAME);
     event->Execute(mock_person, mock_sampler);
 
-    // Testing the Overdose Table Logging
-    std::string expected = "No Overdose Table Found in the inputs database...";
-    std::string line;
-    std::ifstream f(LOG_FILE);
-    std::getline(f, line);
-    f.close();
-    ASSERT_TRUE(line.find(expected) != std::string::npos);
     std::filesystem::remove(LOG_FILE);
 }
 
 TEST_F(DeathTest, F4_Infected_BackgroundDR) {
     hcv_details.fibrosis_state = data::FibrosisState::kF4;
     hcv_details.hcv = data::HCV::kChronic;
 
-    EXPECT_CALL(mock_person, GetAge()).Times(2).WillRepeatedly(Return(300));
-    EXPECT_CALL(mock_person, GetCurrentlyOverdosing()).WillOnce(Return(false));
-    EXPECT_CALL(mock_person, GetHCVDetails())
-        .Times(2)
-        .WillRepeatedly(Return(hcv_details));
-    EXPECT_CALL(mock_person, GetSex()).WillOnce(Return(data::Sex::kMale));
-    EXPECT_CALL(mock_person, GetBehaviorDetails()).WillOnce(Return(behaviors));
+    ON_CALL(mock_person, GetHCVDetails()).WillByDefault(Return(hcv_details));
 
     EXPECT_CALL(mock_sampler, GetDecision(_)).WillOnce(Return(0));
     EXPECT_CALL(mock_person, Die(data::DeathReason::kBackground)).Times(1);
@@ -134,13 +129,7 @@ TEST_F(DeathTest, F4_Infected_LiverDR) {
     hcv_details.fibrosis_state = data::FibrosisState::kF4;
     hcv_details.hcv = data::HCV::kChronic;
 
-    EXPECT_CALL(mock_person, GetAge()).Times(2).WillRepeatedly(Return(300));
-    EXPECT_CALL(mock_person, GetCurrentlyOverdosing()).WillOnce(Return(false));
-    EXPECT_CALL(mock_person, GetHCVDetails())
-        .Times(2)
-        .WillRepeatedly(Return(hcv_details));
-    EXPECT_CALL(mock_person, GetSex()).WillOnce(Return(data::Sex::kMale));
-    EXPECT_CALL(mock_person, GetBehaviorDetails()).WillOnce(Return(behaviors));
+    ON_CALL(mock_person, GetHCVDetails()).WillByDefault(Return(hcv_details));
 
     EXPECT_CALL(mock_sampler, GetDecision(_)).WillOnce(Return(1));
     EXPECT_CALL(mock_person, Die(data::DeathReason::kLiver)).Times(1);
@@ -159,13 +148,7 @@ TEST_F(DeathTest, F4_Uninfected_BackgroundDR) {
     hcv_details.fibrosis_state = data::FibrosisState::kF4;
     hcv_details.hcv = data::HCV::kNone;
 
-    EXPECT_CALL(mock_person, GetAge()).Times(2).WillRepeatedly(Return(300));
-    EXPECT_CALL(mock_person, GetCurrentlyOverdosing()).WillOnce(Return(false));
-    EXPECT_CALL(mock_person, GetHCVDetails())
-        .Times(2)
-        .WillRepeatedly(Return(hcv_details));
-    EXPECT_CALL(mock_person, GetSex()).WillOnce(Return(data::Sex::kMale));
-    EXPECT_CALL(mock_person, GetBehaviorDetails()).WillOnce(Return(behaviors));
+    ON_CALL(mock_person, GetHCVDetails()).WillByDefault(Return(hcv_details));
 
     EXPECT_CALL(mock_sampler, GetDecision(_)).WillOnce(Return(0));
     EXPECT_CALL(mock_person, Die(data::DeathReason::kBackground)).Times(1);
@@ -184,13 +167,7 @@ TEST_F(DeathTest, F4_Uninfected_LiverDR) {
     hcv_details.fibrosis_state = data::FibrosisState::kF4;
     hcv_details.hcv = data::HCV::kNone;
 
-    EXPECT_CALL(mock_person, GetAge()).Times(2).WillRepeatedly(Return(300));
-    EXPECT_CALL(mock_person, GetCurrentlyOverdosing()).WillOnce(Return(false));
-    EXPECT_CALL(mock_person, GetHCVDetails())
-        .Times(2)
-        .WillRepeatedly(Return(hcv_details));
-    EXPECT_CALL(mock_person, GetSex()).WillOnce(Return(data::Sex::kMale));
-    EXPECT_CALL(mock_person, GetBehaviorDetails()).WillOnce(Return(behaviors));
+    ON_CALL(mock_person, GetHCVDetails()).WillByDefault(Return(hcv_details));
 
     EXPECT_CALL(mock_sampler, GetDecision(_)).WillOnce(Return(1));
     EXPECT_CALL(mock_person, Die(data::DeathReason::kLiver)).Times(1);
@@ -209,13 +186,7 @@ TEST_F(DeathTest, Decomp_Infected_BackgroundDR) {
     hcv_details.fibrosis_state = data::FibrosisState::kDecomp;
     hcv_details.hcv = data::HCV::kChronic;
 
-    EXPECT_CALL(mock_person, GetAge()).Times(2).WillRepeatedly(Return(300));
-    EXPECT_CALL(mock_person, GetCurrentlyOverdosing()).WillOnce(Return(false));
-    EXPECT_CALL(mock_person, GetHCVDetails())
-        .Times(3)
-        .WillRepeatedly(Return(hcv_details));
-    EXPECT_CALL(mock_person, GetSex()).WillOnce(Return(data::Sex::kMale));
-    EXPECT_CALL(mock_person, GetBehaviorDetails()).WillOnce(Return(behaviors));
+    ON_CALL(mock_person, GetHCVDetails()).WillByDefault(Return(hcv_details));
 
     EXPECT_CALL(mock_sampler, GetDecision(_)).WillOnce(Return(0));
     EXPECT_CALL(mock_person, Die(data::DeathReason::kBackground)).Times(1);
@@ -234,13 +205,7 @@ TEST_F(DeathTest, Decomp_Infected_LiverDR) {
     hcv_details.fibrosis_state = data::FibrosisState::kDecomp;
     hcv_details.hcv = data::HCV::kChronic;
 
-    EXPECT_CALL(mock_person, GetAge()).Times(2).WillRepeatedly(Return(300));
-    EXPECT_CALL(mock_person, GetCurrentlyOverdosing()).WillOnce(Return(false));
-    EXPECT_CALL(mock_person, GetHCVDetails())
-        .Times(3)
-        .WillRepeatedly(Return(hcv_details));
-    EXPECT_CALL(mock_person, GetSex()).WillOnce(Return(data::Sex::kMale));
-    EXPECT_CALL(mock_person, GetBehaviorDetails()).WillOnce(Return(behaviors));
+    ON_CALL(mock_person, GetHCVDetails()).WillByDefault(Return(hcv_details));
 
     EXPECT_CALL(mock_sampler, GetDecision(_)).WillOnce(Return(1));
     EXPECT_CALL(mock_person, Die(data::DeathReason::kLiver)).Times(1);
@@ -259,13 +224,7 @@ TEST_F(DeathTest, Decomp_Uninfected_BackgroundDR) {
     hcv_details.fibrosis_state = data::FibrosisState::kDecomp;
     hcv_details.hcv = data::HCV::kNone;
 
-    EXPECT_CALL(mock_person, GetAge()).Times(2).WillRepeatedly(Return(300));
-    EXPECT_CALL(mock_person, GetCurrentlyOverdosing()).WillOnce(Return(false));
-    EXPECT_CALL(mock_person, GetHCVDetails())
-        .Times(3)
-        .WillRepeatedly(Return(hcv_details));
-    EXPECT_CALL(mock_person, GetSex()).WillOnce(Return(data::Sex::kMale));
-    EXPECT_CALL(mock_person, GetBehaviorDetails()).WillOnce(Return(behaviors));
+    ON_CALL(mock_person, GetHCVDetails()).WillByDefault(Return(hcv_details));
 
     EXPECT_CALL(mock_sampler, GetDecision(_)).WillOnce(Return(0));
     EXPECT_CALL(mock_person, Die(data::DeathReason::kBackground)).Times(1);
@@ -284,13 +243,7 @@ TEST_F(DeathTest, Decomp_Uninfected_LiverDR) {
     hcv_details.fibrosis_state = data::FibrosisState::kDecomp;
     hcv_details.hcv = data::HCV::kNone;
 
-    EXPECT_CALL(mock_person, GetAge()).Times(2).WillRepeatedly(Return(300));
-    EXPECT_CALL(mock_person, GetCurrentlyOverdosing()).WillOnce(Return(false));
-    EXPECT_CALL(mock_person, GetHCVDetails())
-        .Times(3)
-        .WillRepeatedly(Return(hcv_details));
-    EXPECT_CALL(mock_person, GetSex()).WillOnce(Return(data::Sex::kMale));
-    EXPECT_CALL(mock_person, GetBehaviorDetails()).WillOnce(Return(behaviors));
+    ON_CALL(mock_person, GetHCVDetails()).WillByDefault(Return(hcv_details));
 
     EXPECT_CALL(mock_sampler, GetDecision(_)).WillOnce(Return(1));
     EXPECT_CALL(mock_person, Die(data::DeathReason::kLiver)).Times(1);
@@ -309,13 +262,7 @@ TEST_F(DeathTest, NoDeath) {
     hcv_details.fibrosis_state = data::FibrosisState::kDecomp;
     hcv_details.hcv = data::HCV::kNone;
 
-    EXPECT_CALL(mock_person, GetAge()).Times(2).WillRepeatedly(Return(300));
-    EXPECT_CALL(mock_person, GetCurrentlyOverdosing()).WillOnce(Return(false));
-    EXPECT_CALL(mock_person, GetHCVDetails())
-        .Times(3)
-        .WillRepeatedly(Return(hcv_details));
-    EXPECT_CALL(mock_person, GetSex()).WillOnce(Return(data::Sex::kMale));
-    EXPECT_CALL(mock_person, GetBehaviorDetails()).WillOnce(Return(behaviors));
+    ON_CALL(mock_person, GetHCVDetails()).WillByDefault(Return(hcv_details));
 
     EXPECT_CALL(mock_sampler, GetDecision(_)).WillOnce(Return(2));
     EXPECT_CALL(mock_person, Die(_)).Times(0);