Gadgil48/175 new core data structures

src/IO.cpp

@@ -152,7 +152,7 @@ InferenceConfig ReadInferenceConfig(const std::string& configDir, Utilities::log
         inferenceConfig.toleranceLimit[ii] = ReadNumberFromFile<double>(KeyName.str(), "Tolerance settings", ParamsPath);
     }
 
-    inferenceConfig.observations = ReadInferenceObservations(configDir, log);
+    inferenceConfig.observations = ReadInferenceObservations(configDir, log, inferenceConfig.herd_id);
 
     return inferenceConfig;
 }
@@ -195,10 +195,8 @@ PredictionConfig ReadPredictionConfig(const std::string& configDir, int index, U
     return predictionConfig;
 }
 
-ObservationsForInference ReadInferenceObservations(const std::string& configDir, Utilities::logging_stream::Sptr log)
-{
-    ObservationsForInference observations;
-
+HealthBoardData ReadInferenceObservations(const std::string& configDir, Utilities::logging_stream::Sptr log, int herd_id)
+{    
     (*log) << "Observations For Inference Config:" << std::endl;
 
     const std::string scot_data_file = configDir + "/scot_data.csv";
@@ -209,39 +207,41 @@ ObservationsForInference ReadInferenceObservations(const std::string& configDir,
     //rows from 1 are indivudual health board
     //last row is for all of scotland
     (*log) << "\t- " << scot_data_file << std::endl;
-    observations.cases = Utilities::read_csv<int>(scot_data_file, ',');
+    std::vector<std::vector<int>> cases_in = Utilities::read_csv<int>(scot_data_file, ',');    
 
     //Uploading observed death data
     //Note: first vector is the vector of time. value of -1 indicate number of pigs in the herd
     //rows from 1 are indivudual health board
     //last row is for all of scotland
     (*log) << "\t- " << scot_deaths_file << std::endl;
-    observations.deaths = Utilities::read_csv<int>(scot_deaths_file, ',');
-
+    std::vector<std::vector<int>> deaths_in = Utilities::read_csv<int>(scot_deaths_file, ',');
+    
     const std::string settings_file = configDir + "/parameters.ini";
 
     ValidationParameters validationParams = ImportValidationParameters(configDir);
     int nHealthBoards = validationParams.nHealthBoards;
     int nCasesDays = validationParams.nCasesDays;
 
-    unsigned int cases_rows = observations.cases.size();
-    unsigned int cases_cols = observations.cases[0].size();
+    unsigned int cases_rows = cases_in.size();
+    unsigned int cases_cols = cases_in[0].size();
 
     ImportConsistencyCheck(scot_data_file, cases_rows, (nHealthBoards + 1), "rows");
     ImportConsistencyCheck(scot_data_file, cases_cols, nCasesDays, "columns");
 
-    unsigned int deaths_rows = observations.deaths.size();
-    unsigned int deaths_cols = observations.deaths[0].size();
+    unsigned int deaths_rows = deaths_in.size();
+    unsigned int deaths_cols = deaths_in[0].size();
 
     ImportConsistencyCheck(scot_deaths_file, deaths_rows, (nHealthBoards + 1), "rows");
     ImportConsistencyCheck(scot_deaths_file, deaths_cols, nCasesDays, "columns");
 
+    HealthBoardData observations(herd_id, cases_in, deaths_in);
+
     return observations;
 }
 
-ObservationsForModels ReadModelObservations(const std::string& configDir, Utilities::logging_stream::Sptr log)
+HealthBoardData ReadModelObservations(const std::string& configDir, Utilities::logging_stream::Sptr log, int herd_id)
 {
-    ObservationsForModels observations;
+    // ObservationsForModels observations;
 
     (*log) << "Observations For Models:" << std::endl;
 
@@ -265,27 +265,44 @@ ObservationsForModels ReadModelObservations(const std::string& configDir, Utilit
     //rows from 1 are indivudual health board
     //last row is for all of scotland
     (*log) << "\t- " << scot_data_file << std::endl;
-    observations.cases = Utilities::read_csv<int>(scot_data_file, ',');
+    // observations.cases = Utilities::read_csv<int>(scot_data_file, ',');
+    std::vector<std::vector<int>> cases_in = Utilities::read_csv<int>(scot_data_file, ',');
 
-    unsigned int cases_rows = observations.cases.size();
-    unsigned int cases_cols = observations.cases[0].size();
+    unsigned int cases_rows = cases_in.size();
+    unsigned int cases_cols = cases_in[0].size();
 
     ImportConsistencyCheck(scot_data_file, cases_rows, (nHealthBoards + 1), "rows");
     ImportConsistencyCheck(scot_data_file, cases_cols, nCasesDays, "columns");
 
     //Uploading population per age group
-    //columns are for each individual Health Borad
-    //last column is for Scotland
-    //rows are for each age group: [0] Under20,[1] 20-29,[2] 30-39,[3] 40-49,[4] 50-59,[5] 60-69,[6] Over70,[7] HCW
+    //rows are for each individual Health Board
+    //last row is for Scotland
+    //columns are for each age group: [0] Under20,[1] 20-29,[2] 30-39,[3] 40-49,[4] 50-59,[5] 60-69,[6] Over70,[7] HCW
     (*log) << "\t- " << scot_ages_file << std::endl;
-    observations.age_pop = Utilities::read_csv<double>(scot_ages_file, ',');
+    // observations.age_pop = Utilities::read_csv<double>(scot_ages_file, ',');
+    std::vector<std::vector<double>> age_pop_in = Utilities::read_csv<double>(scot_ages_file, ',');
 
-    unsigned int age_pop_rows = observations.age_pop.size();
-    unsigned int age_pop_cols = observations.age_pop[0].size();
+    unsigned int age_pop_rows = age_pop_in.size();
+    unsigned int age_pop_cols = age_pop_in[0].size();
 
     ImportConsistencyCheck(scot_ages_file, age_pop_rows, nHealthBoards, "rows");
     ImportConsistencyCheck(scot_ages_file, age_pop_cols, (nAgeGroups - 1), "columns");
 
+    //Upload frailty probability p_f by age group
+    //columns are for each age group: [0] Under20,[1] 20-29,[2] 30-39,[3] 40-49,[4] 50-59,[5] 60-69,[6] Over70,[7] HCW
+    //rows are for each individual Health Board
+    //last row is for Scotland
+    (*log) << "\t- " << scot_frail_file << std::endl;
+    // observations.pf_pop = Utilities::read_csv<double>(scot_frail_file, ',');
+    std::vector<std::vector<double>> pf_pop_in = Utilities::read_csv<double>(scot_frail_file, ',');
+
+    unsigned int pf_pop_rows = pf_pop_in.size();
+    unsigned int pf_pop_cols = pf_pop_in[0].size();
+
+    ImportConsistencyCheck(scot_frail_file, pf_pop_rows, nHealthBoards, "rows");
+    ImportConsistencyCheck(scot_frail_file, pf_pop_cols, nAgeGroups, "columns");
+
+    HealthBoardData observations(herd_id, cases_in, age_pop_in, pf_pop_in);
 
     //mean number of daily contacts per age group (overall)	
     (*log) << "\t- " << waifw_norm_file << std::endl;
@@ -331,19 +348,6 @@ ObservationsForModels ReadModelObservations(const std::string& configDir, Utilit
     ImportConsistencyCheck(cfr_byage_file, cfr_rows, nAgeGroups, "rows");
     ImportConsistencyCheck(cfr_byage_file, cfr_cols, nCfrCategories, "columns");
 
-    //Upload frailty probability p_f by age group
-    //columns are for each age group: [0] Under20,[1] 20-29,[2] 30-39,[3] 40-49,[4] 50-59,[5] 60-69,[6] Over70,[7] HCW
-    //rows are for each individual Health Borad
-    //last row is for Scotland
-    (*log) << "\t- " << scot_frail_file << std::endl;
-    observations.pf_pop = Utilities::read_csv<double>(scot_frail_file, ',');
-
-    unsigned int pf_pop_rows = observations.pf_pop.size();
-    unsigned int pf_pop_cols = observations.pf_pop[0].size();
-
-    ImportConsistencyCheck(scot_frail_file, pf_pop_rows, nHealthBoards, "rows");
-    ImportConsistencyCheck(scot_frail_file, pf_pop_cols, nAgeGroups, "columns");
-
     return observations;
 }
 

src/IO.h

@@ -121,7 +121,7 @@ std::vector<double> ReadPredictionParametersFromFile(const std::string& filePath
  * 
  * @return Observations needed for Inference framework
  */
-ObservationsForInference ReadInferenceObservations(const std::string& configDir, Utilities::logging_stream::Sptr log);
+HealthBoardData ReadInferenceObservations(const std::string& configDir, Utilities::logging_stream::Sptr log, int herd_id);
 
 /**
  * @brief Read observations needed for all models
@@ -131,7 +131,7 @@ ObservationsForInference ReadInferenceObservations(const std::string& configDir,
  * 
  * @return Observations needed for all models
  */
-ObservationsForModels ReadModelObservations(const std::string& configDir, Utilities::logging_stream::Sptr log);
+HealthBoardData ReadModelObservations(const std::string& configDir, Utilities::logging_stream::Sptr log, int herd_id);
 
 /**
  * @brief Read seed settings from the parameters file

src/InferenceFramework.cpp

@@ -70,9 +70,9 @@ void InferenceFramework::Run()
     SimpleTimer runTimer;
 
 	const int time_back = GetTimeOffSet(inferenceConfig_);
-	const std::vector<int>& regionalCases = inferenceConfig_.observations.cases[inferenceConfig_.herd_id];
-	const std::vector<int>& regionalDeaths = inferenceConfig_.observations.deaths[inferenceConfig_.herd_id];
-	const std::vector<int>& timeStamps = inferenceConfig_.observations.cases[0];
+	const std::vector<int>& regionalCases = inferenceConfig_.observations.cases;
+	const std::vector<int>& regionalDeaths = inferenceConfig_.observations.deaths;
+	const std::vector<int>& timeStamps = inferenceConfig_.observations.timeStamps;
 
 	const Observations::ObsSelect obs_selections = Observations::SelectObservations(
 		inferenceConfig_.day_shut, timeStamps, regionalCases,

src/IrishModel.cpp

@@ -4,7 +4,7 @@ namespace EERAModel {
 namespace Model {
 
 IrishModel::IrishModel(const CommonModelInputParameters& commonParameters,
-    const ObservationsForModels& observations, Random::RNGInterface::Sptr rng, Utilities::logging_stream::Sptr log) 
+    const HealthBoardData& observations, Random::RNGInterface::Sptr rng, Utilities::logging_stream::Sptr log) 
     : rng_(rng) {
 
     fixedParameters_ = BuildFixedParameters(
@@ -16,19 +16,19 @@ IrishModel::IrishModel(const CommonModelInputParameters& commonParameters,
             observations.waifw_home,
             observations.waifw_sdist,
             observations.cfr_byage,
-            observations.pf_pop[commonParameters.herd_id - 1]
+            observations.pf_byage
     };
 
     int regionalPopulation = GetPopulationOfRegion(
-        observations, commonParameters.herd_id
+        observations
     );
 
     int healthCareWorkers = ComputeNumberOfHCWInRegion(
         regionalPopulation, commonParameters.totN_hcw, observations
     );
 
     ageNums_ = ComputeAgeNums(
-        commonParameters.herd_id, regionalPopulation, healthCareWorkers, observations
+        regionalPopulation, healthCareWorkers, observations
     );
 
     (*log) << "[Model settings]" << std::endl;

src/IrishModel.h

@@ -21,7 +21,7 @@ class IrishModel : public ModelInterface
      * @param rng Random number generator to be used by the model
      * @param log Logger
      */
-    IrishModel(const CommonModelInputParameters& commonParameters, const ObservationsForModels& observations,
+    IrishModel(const CommonModelInputParameters& commonParameters, const HealthBoardData& observations,
         Random::RNGInterface::Sptr rng, Utilities::logging_stream::Sptr log);
 
     /**

src/ModelCommon.cpp

@@ -16,12 +16,12 @@ std::vector<params> BuildFixedParameters(unsigned int size, params parameters)
     return std::vector<params>(size, parameters);
 }
 
-std::vector<int> ComputeAgeNums(int shb_id, int Npop, int N_hcw, const ObservationsForModels& obs) {
+std::vector<int> ComputeAgeNums(int Npop, int N_hcw, const HealthBoardData& obs) {
 	std::vector<int> agenums;
 
 	// define age structure of the shb of interest. the -1 is to account for difference in number of
 	// rows between two datasets (age_pop does not have a row with column name)
-	const auto& agedist = obs.age_pop[shb_id - 1];
+	const auto& agedist = obs.age_structure;
 
 	for (const auto& var : agedist) {
 		// modulate the population of non-hcw now to proportion in each age group recorded in 2011	
@@ -33,17 +33,17 @@ std::vector<int> ComputeAgeNums(int shb_id, int Npop, int N_hcw, const Observati
 	return agenums;
 }
 
-int GetPopulationOfRegion(const ObservationsForModels& obs, int region_id)
+int GetPopulationOfRegion(const HealthBoardData& obs)
 {
-	return obs.cases[region_id][0];
+	return obs.cases[0];
 }
 
-int ComputeNumberOfHCWInRegion(int regionalPopulation, int totalHCW, const ObservationsForModels& obs)
+int ComputeNumberOfHCWInRegion(int regionalPopulation, int totalHCW, const HealthBoardData& obs)
 {
-    int scotlandPopulation = 0;
-	for (unsigned int region = 0; region < obs.cases.size() - 1; ++region) {
-		scotlandPopulation += obs.cases[region][0];
-	}
+    int scotlandPopulation = obs.totScotPopulation;
+	// for (unsigned int region = 0; region < obs.cases.size() - 1; ++region) {
+	// 	scotlandPopulation += obs.cases[region][0];
+	// }
 	double regionalProportion = static_cast<double>(regionalPopulation) / scotlandPopulation;
 
     return static_cast<int>(round(totalHCW * regionalProportion)); 

src/ModelCommon.h

@@ -129,7 +129,7 @@ int accumulate_compartments(const Compartments& comp);
  * 
  * @return The population of the region
  */
-int GetPopulationOfRegion(const ObservationsForModels& obs, int region_id);
+int GetPopulationOfRegion(const HealthBoardData& obs);
 
 /**
  * @brief Compute number of health care workers (HCW) in the region
@@ -141,7 +141,7 @@ int GetPopulationOfRegion(const ObservationsForModels& obs, int region_id);
  * @param totalHCW Total number of HCWs in the country
  * @param obs Input observations
  */
-int ComputeNumberOfHCWInRegion(int regionalPopulation, int totalHCW, const ObservationsForModels& obs);
+int ComputeNumberOfHCWInRegion(int regionalPopulation, int totalHCW, const HealthBoardData& obs);
 
 /**
  * @brief Compute the agenums 
@@ -152,7 +152,7 @@ int ComputeNumberOfHCWInRegion(int regionalPopulation, int totalHCW, const Obser
  * 
  * @return agenums
  */
-std::vector<int> ComputeAgeNums(int shb_id, int Npop, int N_hcw, const ObservationsForModels& obs);
+std::vector<int> ComputeAgeNums(int Npop, int N_hcw, const HealthBoardData& obs);
 
 /**
  * @brief Build the fixed parameters data structure

src/ModelTypes.h

@@ -2,6 +2,8 @@
 
 #include <vector>
 #include <string>
+#include <map>
+#include <iostream>
 
 namespace EERAModel {
 
@@ -155,6 +157,79 @@ struct Status
 		pop_array;								/*!< Population per epidemiological state and per age group on every day. */
 };
 
+/**
+ * @brief Enumerated type to access data with axis/axes corresponding to Age Groups.
+ */
+enum AgeGroup {
+	Age_Pre_20 = 0,
+	Age_20_29 = 1,
+	Age_30_39 = 2,
+	Age_40_49 = 3,
+	Age_50_59 = 4,
+	Age_60_69 = 5,
+	Age_Post_70 = 6,
+	HealthCareWorkers = 7
+};
+
+/**
+ * @brief Enumerated type to access data with axis/axes corresponding to 
+ * case fatality ratio identifiers
+ */
+enum CFRCategories {
+	ProbabilityOfHospitalisation = 0,
+	CaseFatalityRatio = 1,
+	ProbabilityOfDeath = 2
+};
+
+/**
+ * @brief Class that holds health board data.
+ * 		  The overloaded constructors allow name consistency between,
+ * 		  Health Board data needed for the Model and Inference framework.
+ */
+class HealthBoardData
+{
+	public:
+		int HealthBoardID;
+		int totScotPopulation;
+		std::string HealthBoardLabel;
+		std::vector<int> cases;
+		std::vector<int> deaths;
+		std::vector<double> age_structure;
+		std::vector<double> pf_byage;
+		std::vector<int> timeStamps;
+		std::vector<std::vector<double>> waifw_norm;
+		std::vector<std::vector<double>> waifw_home;
+		std::vector<std::vector<double>> waifw_sdist;
+		std::vector<std::vector<double>> cfr_byage;
+
+		HealthBoardData() {}
+
+		HealthBoardData(
+			const int& HealthBoardID_in,
+			const std::vector<std::vector<int>>& cases_in,
+			const std::vector<std::vector<int>>& deaths_in
+		) {
+			HealthBoardID = HealthBoardID_in;
+			HealthBoardLabel = "Health Board " + std::to_string(HealthBoardID);
+			cases = cases_in[HealthBoardID];
+			deaths = deaths_in[HealthBoardID];
+			timeStamps = cases_in[0];
+		}
+		HealthBoardData(
+			const int& HealthBoardID_in,
+			const std::vector<std::vector<int>>& cases_in,
+			const std::vector<std::vector<double>>& age_structure_in,
+			const std::vector<std::vector<double>>& pf_byage_in
+		) {
+			HealthBoardID = HealthBoardID_in;
+			HealthBoardLabel = "Health Board " + std::to_string(HealthBoardID);
+			cases = cases_in[HealthBoardID];
+			age_structure = age_structure_in[HealthBoardID - 1];
+			pf_byage = pf_byage_in[HealthBoardID - 1];
+			totScotPopulation = cases_in[cases_in.size() - 1][0];
+		}
+};
+
 /**
  * @brief Structure containing population counters after infection
  * 
@@ -230,7 +305,7 @@ struct InferenceConfig
 	int nSim;
 	int nParticleLimit;
 	std::vector<double> toleranceLimit;
-	ObservationsForInference observations;
+	HealthBoardData observations;
 };
 
 /**