Merge branch 'main' into data_source_from_config

.github/workflows/docs.yml

@@ -6,7 +6,6 @@ on:
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-    branches: [main]
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:

.pre-commit-config.yaml

@@ -8,13 +8,13 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.28.6
+    rev: 0.29.0
     hooks:
       - id: check-github-workflows
       - id: check-metaschema
         files: "schemas/.*"
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v18.1.7
+    rev: v18.1.8
     hooks:
       - id: clang-format
         files: '.*\.(h|cpp)'

src/HealthGPS/analysis_module.cpp

@@ -22,13 +22,13 @@ AnalysisModule::AnalysisModule(AnalysisDefinition &&definition, WeightModel &&cl
       residual_disability_weight_{create_age_gender_table<double>(age_range)},
       comorbidities_{comorbidities} {}
 
-// Overload constructor with additional parameter for calculated_factors_
+// Overload constructor with additional parameter for calculated_stats_
 AnalysisModule::AnalysisModule(AnalysisDefinition &&definition, WeightModel &&classifier,
                                const core::IntegerInterval age_range, unsigned int comorbidities,
-                               std::vector<double> calculated_factors)
+                               std::vector<double> calculated_stats)
     : definition_{std::move(definition)}, weight_classifier_{std::move(classifier)},
       residual_disability_weight_{create_age_gender_table<double>(age_range)},
-      comorbidities_{comorbidities}, calculated_factors_{std::move(calculated_factors)} {}
+      comorbidities_{comorbidities}, calculated_stats_{std::move(calculated_stats)} {}
 SimulationModuleType AnalysisModule::type() const noexcept {
     return SimulationModuleType::Analysis;
 }
@@ -59,17 +59,21 @@ void AnalysisModule::initialise_vector(RuntimeContext &context) {
         factor_bin_widths_.push_back((max_factor - min_factor) / factor_bins_.back());
     }
 
-    // The number of factors to calculate is the number of factors minus the length of the `factors`
-    // vector.
-    size_t num_factors_to_calc = context.mapping().entries().size() - factors_to_calculate_.size();
+    // The number of factors to calculate stats for is the number of factors minus the length of the
+    // `factors` vector.
+    size_t num_stats_to_calc = context.mapping().entries().size() - factors_to_calculate_.size();
+
+    // And for each factor, we calculate the stats described in `channels_`, so we
+    // multiply the size of `channels_` by the number of factors to calculate stats for.
+    num_stats_to_calc *= channels_.size();
 
     // The product of the number of bins for each factor can be used to calculate the size of the
-    // `calculated_factors_` in the next step
+    // `calculated_stats_` in the next step
     size_t total_num_bins =
         std::accumulate(factor_bins_.cbegin(), factor_bins_.cend(), size_t{1}, std::multiplies<>());
 
     // Set the vector size and initialise all values to 0.0
-    calculated_factors_.resize(total_num_bins * num_factors_to_calc);
+    calculated_stats_.resize(total_num_bins * num_stats_to_calc);
 }
 
 const std::string &AnalysisModule::name() const noexcept { return name_; }
@@ -115,7 +119,7 @@ void AnalysisModule::initialise_population(RuntimeContext &context) {
 void AnalysisModule::update_population(RuntimeContext &context) {
 
     // Reset the calculated factors vector to 0.0
-    std::ranges::fill(calculated_factors_, 0.0);
+    std::ranges::fill(calculated_stats_, 0.0);
 
     publish_result_message(context);
 }
@@ -328,7 +332,7 @@ void AnalysisModule::calculate_population_statistics(RuntimeContext &context) {
             bin_indices.push_back(bin_index);
         }
 
-        // Calculate the index in the calculated_factors_ vector
+        // 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 =
@@ -342,7 +346,7 @@ void AnalysisModule::calculate_population_statistics(RuntimeContext &context) {
         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_factors_[index++] += person.get_risk_factor_value(factor.key());
+                calculated_stats_[index++] += person.get_risk_factor_value(factor.key());
             }
         }
     }

src/HealthGPS/analysis_module.h

@@ -49,7 +49,7 @@ class AnalysisModule final : public UpdatableModule {
     unsigned int comorbidities_;
     std::string name_{"Analysis"};
     std::vector<core::Identifier> factors_to_calculate_ = {"Gender"_id, "Age"_id};
-    std::vector<double> calculated_factors_;
+    std::vector<double> calculated_stats_;
     std::vector<size_t> factor_bins_;
     std::vector<double> factor_bin_widths_;
     std::vector<double> factor_min_values_;