add new severe outcomes without counting comorbidities (#351)

SwissTPH · Jan 5, 2023 · 9699e63 · 9699e63
1 parent 3166042
commit 9699e63
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diff --git a/model/Clinical/Episode.cpp b/model/Clinical/Episode.cpp
@@ -61,6 +61,9 @@ void Episode::report () {
         // Malarial fevers: report bout
         if (state & Episode::COMPLICATED) {
             mon::reportMSACI( mon::MHE_SEVERE_EPISODES, surveyPeriod, ageGroup, cohortSet, 1 );
+            if (state & Episode::SEVERE) {
+                mon::reportMSACI( mon::MHE_SEVERE_EPISODES_WITHOUT_COMORBIDITIES, surveyPeriod, ageGroup, cohortSet, 1 );
+            }
         } else { // UC or UC2
             mon::reportMSACI( mon::MHE_UNCOMPLICATED_EPISODES, surveyPeriod, ageGroup, cohortSet, 1 );
         }

diff --git a/model/Clinical/Episode.h b/model/Clinical/Episode.h
@@ -61,6 +61,8 @@ class Episode{
         MALARIA             = WithinHost::Pathogenesis::MALARIA,          ///< Malaria sickness
         /// Used by ClinicalEventScheduler to indicate a second bout of malarial sickness within the same episode (roughly)
         SECOND_CASE         = 0x10,
+        SEVERE              = 0x8,      ///< Severe malaria case
+        COINFECTION         = 0x4,      ///< Malaria with a coinfection
         COMPLICATED         = WithinHost::Pathogenesis::COMPLICATED,         ///< Flag used to indicate SEVERE and/or COINFECTION
 
         //NEED_ANTIBIOTIC     = 0x40,         ///< Flag indicates a non-malaria fever requires (antibiotic) treatment

diff --git a/model/Host/WithinHost/Pathogenesis/PathogenesisModel.cpp b/model/Host/WithinHost/Pathogenesis/PathogenesisModel.cpp
@@ -117,6 +117,7 @@ Pathogenesis::StatePair PathogenesisModel::determineState(Host::Human& human,
         // Expectation of a severe bout:
         const double exSevere = prSevereEpisode + (1.0 - prSevereEpisode) * pCoinfection;
         mon::reportStatMHF( mon::MHF_EXPECTED_SEVERE, human, exSevere );
+        mon::reportStatMHF( mon::MHF_EXPECTED_SEVERE_WITHOUT_COMORBIDITIES, human, prSevereEpisode );
 
         if( human.rng().bernoulli( prSevereEpisode ) )
             result.state = STATE_SEVERE;

diff --git a/model/mon/OutputMeasures.h b/model/mon/OutputMeasures.h
@@ -455,15 +455,26 @@ void defineOutMeasures(){
      * the reporting period. */
     namedOutMeasures["innoculationsPerVector"] =
         OutMeasure::species( 79, MVF_INOCS, false );
+
     /** Number of custom intervention reports done */
     namedOutMeasures["nCMDTReport"] =
         OutMeasure::humanAC( 80, MCD_CMDT_REPORT, false );
+
+    /// Similar to nSevere. Number of severe episodes WITHOUT coinfection
+    namedOutMeasures["nSevereWithoutComorbidities"] =
+        OutMeasure::humanAC( 81, MHE_SEVERE_EPISODES_WITHOUT_COMORBIDITIES, false );
+    /** Similar to 'expectedSevere'.
+     * Expected number of severe bouts of malaria WITHOUT "complications due 
+     * to coinfection" (the same as the `nSevereWithoutComorbidities` output). */
+    namedOutMeasures["expectedSevereWithoutComorbidities"] =
+        OutMeasure::humanAC( 82, MHF_EXPECTED_SEVERE_WITHOUT_COMORBIDITIES, true );
 
     // Now initialise valid condition measures:
     for( const NamedMeasureMapT::value_type& v : namedOutMeasures ){
         Measure m = v.second.m;
         // Not the following:
         if( m == mon::MHE_SEVERE_EPISODES ||
+            m == mon::MHE_SEVERE_EPISODES_WITHOUT_COMORBIDITIES ||
             m == mon::MHE_UNCOMPLICATED_EPISODES ||
             m == mon::MHO_DIRECT_DEATHS ||
             m == mon::MHO_HOSPITAL_DEATHS ||

diff --git a/model/mon/reporting.h b/model/mon/reporting.h
@@ -84,6 +84,8 @@ enum Measure{
     MHE_UNCOMPLICATED_EPISODES,
     // Number of severe fever episodes in humans. Units: cases
     MHE_SEVERE_EPISODES,
+    // Number of severe fever episodes without counting episodes due to comorbidities in humans. Units: cases
+    MHE_SEVERE_EPISODES_WITHOUT_COMORBIDITIES,
     // Number of fever episodes in humans not due to malaria. Units: cases
     MHE_NON_MALARIA_FEVERS,
 
@@ -166,6 +168,8 @@ enum Measure{
     MHF_EXPECTED_SEQUELAE,
     // Expected severe bouts
     MHF_EXPECTED_SEVERE,
+    // Expected severe bouts without counting expected episodes due to comorbidites
+    MHF_EXPECTED_SEVERE_WITHOUT_COMORBIDITIES,
 
     // ———  MVF: vector (transmission) measures (doubles)  ———
     // Infectiousness of human population to mosquitoes