Implement stats calculations for new calculated_stats_ container

src/HealthGPS/analysis_module.cpp

@@ -319,36 +319,88 @@
 }
 
 void AnalysisModule::calculate_population_statistics(RuntimeContext &context) {
- size_t num_factors_to_calculate =
-  context.mapping().entries().size() - factors_to_calculate_.size();
+
+ auto current_time = static_cast<unsigned int>(context.time_now());
 
  for (const auto &person : context.population()) {
- // Get the bin index for each factor
- std::vector<size_t> bin_indices;
- for (size_t i = 0; i < factors_to_calculate_.size(); i++) {
- double factor_value = person.get_risk_factor_value(factors_to_calculate_[i]);
- auto bin_index =
- static_cast<size_t>((factor_value - factor_min_values_[i]) / factor_bin_widths_[i]);
- bin_indices.push_back(bin_index);
- }
+ // First let's fetch the correct `calculated_stats_` bin index for this person
+ size_t index = calculate_index(person);
 
- // Calculate the index in the calculated_stats_ vector
- size_t index = 0;
- for (size_t i = 0; i < bin_indices.size() - 1; i++) {
- size_t accumulated_bins =
- std::accumulate(std::next(factor_bins_.cbegin(), i + 1), factor_bins_.cend(),
- size_t{1}, std::multiplies<>());
- index += bin_indices[i] * accumulated_bins * num_factors_to_calculate;
+ // Now we can add the calculated stats for this person to the correct index
+ if (!person.is_active()) {
+ if (!person.is_alive() && person.time_of_death() == current_time) {
+ calculated_stats_[index + get_channel_index("deaths")]++;
+ float expected_life =
+ definition_.life_expectancy().at(context.time_now(), person.gender);
+ double yll = std::max(expected_life - person.age, 0.0f) * DALY_UNITS;
+ calculated_stats_[index + get_channel_index("mean_yll")] += yll;
+ calculated_stats_[index + get_channel_index("mean_daly")] += yll;
+ }
+
+ if (person.has_emigrated() && person.time_of_migration() == current_time) {
+ calculated_stats_[index + get_channel_index("emigrations")]++;
+ }
+
+ continue;
  }
- index += bin_indices.back() * num_factors_to_calculate;
 
- // Now we can add the values of the factors that are not in factors_to_calculate_
+ calculated_stats_[index + get_channel_index("count")]++;
+
  for (const auto &factor : context.mapping().entries()) {
- if (std::find(factors_to_calculate_.cbegin(), factors_to_calculate_.cend(),
- factor.key()) == factors_to_calculate_.cend()) {
- calculated_stats_[index++] += person.get_risk_factor_value(factor.key());
+ double value = person.get_risk_factor_value(factor.key());
+ calculated_stats_[index + get_channel_index("mean_" + factor.key().to_string())] +=
+ value;
+ }
+
+ for (const auto &[disease_name, disease_state] : person.diseases) {
+ if (disease_state.status == DiseaseStatus::active) {
+ calculated_stats_[index +
+ get_channel_index("prevalence_" + disease_name.to_string())]++;
+ if (disease_state.start_time == context.time_now()) {
+ calculated_stats_[index +
+ get_channel_index("incidence_" + disease_name.to_string())]++;
+ }
  }
  }
+
+ double dw = calculate_disability_weight(person);
+ double yld = dw * DALY_UNITS;
+ calculated_stats_[index + get_channel_index("mean_yld")] += yld;
+ calculated_stats_[index + get_channel_index("mean_daly")] += yld;
+
+ classify_weight(person);
+ }
+
+ // For each bin in the calculated stats...
+ for (size_t i = 0; i < calculated_stats_.size(); i += channels_.size()) {
+ double count_F = calculated_stats_[i + get_channel_index("count")];
+ double count_M = calculated_stats_[i + get_channel_index("count")];
+ double deaths_F = calculated_stats_[i + get_channel_index("deaths")];
+ double deaths_M = calculated_stats_[i + get_channel_index("deaths")];
+
+ // Calculate in-place factor averages.
+ for (const auto &factor : context.mapping().entries()) {
+ calculated_stats_[i + get_channel_index("mean_" + factor.key().to_string())] /= count_F;
+ calculated_stats_[i + get_channel_index("mean_" + factor.key().to_string())] /= count_M;
+ }
+
+ // Calculate in-place disease prevalence and incidence rates.
+ for (const auto &disease : context.diseases()) {
+ calculated_stats_[i + get_channel_index("prevalence_" + disease.code.to_string())] /=
+ count_F;
+ calculated_stats_[i + get_channel_index("prevalence_" + disease.code.to_string())] /=
+ count_M;
+ calculated_stats_[i + get_channel_index("incidence_" + disease.code.to_string())] /=
+ count_F;
+ calculated_stats_[i + get_channel_index("incidence_" + disease.code.to_string())] /=
+ count_M;
+ }
+
+ // Calculate in-place YLL/YLD/DALY averages.
+ for (const auto &column : {"mean_yll", "mean_yld", "mean_daly"}) {
+ calculated_stats_[i + get_channel_index(column)] /= (count_F + deaths_F);
+ calculated_stats_[i + get_channel_index(column)] /= (count_M + deaths_M);
+ }
  }
 }
 
@@ -531,6 +583,26 @@
  }
 }
 
+void AnalysisModule::classify_weight(const Person &person) {
+ auto weight_class = weight_classifier_.classify_weight(person);
+ switch (weight_class) {
+ case WeightCategory::normal:
+ calculated_stats_[get_channel_index("normal_weight")]++;
+ break;
+ case WeightCategory::overweight:
+ calculated_stats_[get_channel_index("over_weight")]++;
+ calculated_stats_[get_channel_index("above_weight")]++;
+ break;
+ case WeightCategory::obese:
+ calculated_stats_[get_channel_index("obese_weight")]++;
+ calculated_stats_[get_channel_index("above_weight")]++;
+ break;
+ default:
+ throw std::logic_error("Unknown weight classification category.");
+ break;
+ }
+}
+
 void AnalysisModule::initialise_output_channels(RuntimeContext &context) {
  if (!channels_.empty()) {
  return;
@@ -560,8 +632,53 @@
  channels_.emplace_back("std_yld");
  channels_.emplace_back("mean_daly");
  channels_.emplace_back("std_daly");
+
+ // Since we will be performing frequent lookups, we will store the strings and indexes in a map
+ // for quick access.
+ for (size_t i = 0; i < channels_.size(); i++) {
+ channel_index_.emplace(channels_[i], i);
+ }
+}
+
+size_t AnalysisModule::calculate_index(const Person &person) const {
+ // Get the bin index for each factor
+ std::vector<size_t> bin_indices;
+ for (size_t i = 0; i < factors_to_calculate_.size(); i++) {
+ double factor_value = person.get_risk_factor_value(factors_to_calculate_[i]);
+ auto bin_index =
+ static_cast<size_t>((factor_value - factor_min_values_[i]) / factor_bin_widths_[i]);
+ bin_indices.push_back(bin_index);
+ }
+
+ // Calculate the index in the calculated_stats_ vector
+ size_t index = 0;
+ for (size_t i = 0; i < bin_indices.size() - 1; i++) {
+ size_t accumulated_bins =
+ std::accumulate(std::next(factor_bins_.cbegin(), i + 1), factor_bins_.cend(), size_t{1},
+ std::multiplies<>());
+ index += bin_indices[i] * accumulated_bins * channels_.size();
+ }
+ index += bin_indices.back() * channels_.size();
+
+ return index;
 }
 
+size_t AnalysisModule::get_channel_index(const std::string &channel) const {
+ auto it = channel_index_.find(channel);
+ if (it == channel_index_.end()) {
+ throw std::out_of_range("Unknown channel: " + channel);
+ }
+
+ return it->second;
+}
+
+void AnalysisModule::accumulate_squared_diffs(size_t bin_index, size_t channel_index) const {
+ for (const auto &factor : factors_to_calculate_) {
+ const double mean = calculated_stats_[bin_index + channel_index];
+ const double diff = value - mean;
+ }
+};
+
 std::unique_ptr<AnalysisModule> build_analysis_module(Repository &repository,
  const ModelInput &config) {
  auto analysis_entity = repository.manager().get_disease_analysis(config.settings().country());

src/HealthGPS/analysis_module.h

@@ -46,6 +46,7 @@ class AnalysisModule final : public UpdatableModule {
  WeightModel weight_classifier_;
  DoubleAgeGenderTable residual_disability_weight_;
  std::vector<std::string> channels_;
+ std::unordered_map<std::string, int> channel_index_;
  unsigned int comorbidities_;
  std::string name_{"Analysis"};
  std::vector<core::Identifier> factors_to_calculate_ = {"Gender"_id, "Age"_id};
@@ -70,8 +71,24 @@ class AnalysisModule final : public UpdatableModule {
  void calculate_population_statistics(RuntimeContext &context, DataSeries &series) const;
 
  void classify_weight(hgps::DataSeries &series, const hgps::Person &entity) const;
+ void classify_weight(const Person &person);
  void initialise_output_channels(RuntimeContext &context);
 
+ /// @brief Calculates the bin index in `calculated_stats_` for a given person
+ /// @param person The person to calculate the index for
+ /// @return The index in `calculated_stats_`
+ size_t calculate_index(const Person &person) const;
+
+ /// @brief Gets the index of the given channel name
+ /// @param channel The channel name
+ /// @return The channel index
+ size_t get_channel_index(const std::string &channel) const;
+
+ /// @brief Accumulates the squared differences between the given value and the mean
+ /// @param bin_index The index of the bin in `calculated_stats_`
+ /// @param channel_index The index of the channel in `channels_`
+ void accumulate_squared_diffs(size_t bin_index, size_t channel_index) const;
+
  /// @brief Calculates the standard deviation of factors given data series containing means
  /// @param context The runtime context
  /// @param series The data series containing factor means