Merge pull request #216 from SwissTPH/logdens

Guard against usage of log(dens) when specificity of diagnostic < 1
SwissTPH · Dec 11, 2018 · bb5f5cf · bb5f5cf
2 parents 7739452 + d3faab7
commit bb5f5cf
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Showing 3 changed files with 18 additions and 1 deletion.
diff --git a/model/WithinHost/Diagnostic.cpp b/model/WithinHost/Diagnostic.cpp
@@ -107,6 +107,11 @@ bool Diagnostic::isPositive( double dens ) const {
     }
 }
 
+bool Diagnostic::allowsFalsePositives() const{
+    if( (boost::math::isnan)(specificity) ) return dens_lim <= 0.0;
+    return specificity < 1.0;
+}
+
 
 // ———  diagnostics (static)  ———
 

diff --git a/model/WithinHost/Diagnostic.h b/model/WithinHost/Diagnostic.h
@@ -45,7 +45,10 @@ class Diagnostic {
         return specificity != that.specificity ||
             dens_lim != that.dens_lim;
     }
-
+
+    /// True if false positives are possible
+    bool allowsFalsePositives() const;
+
 private:
     /** Construct from XML parameters. */
     Diagnostic( const Parameters& parameters, const scnXml::Diagnostic& elt );

diff --git a/model/mon/mon.cpp b/model/mon/mon.cpp
@@ -23,6 +23,7 @@
 #include "mon/management.h"
 #define H_OM_mon_cpp
 #include "mon/OutputMeasures.h"
+#include "WithinHost/Diagnostic.h"
 #include "WithinHost/Genotypes.h"
 #include "Clinical/CaseManagementCommon.h"
 #include "Host/Human.h"
@@ -451,6 +452,14 @@ void internal::initReporting( const scnXml::Scenario& scenario ){
             } else TRACED_EXCEPTION_DEFAULT("invalid measure code");
         }
 
+        if( om.m == MHF_LOG_DENSITY || om.m == MHF_LOG_DENSITY_GENOTYPE){
+            if( WithinHost::diagnostics::monitoringDiagnostic().allowsFalsePositives() ){
+                throw util::xml_scenario_error( (boost::format("measure %1% "
+                    "may not be used when monitoring diagnostic sensitivity "
+                    "< 1") %optElt.getName()).str() );
+            }
+        }
+
         // Categorisation can be disabled but not enabled. We check each now.
         if( optElt.getByAge().present() ){
             if( om.byAge ){