Refactor/monitoring single core

model/CMakeLists.txt

@@ -80,8 +80,8 @@ set (Model_CPP
   Host/WithinHost/Diagnostic.cpp
   Host/WithinHost/Treatments.cpp
 
-  mon/mon.cpp
-  mon/misc.cpp
+  mon/Monitoring.cpp
+  mon/init.cpp
   mon/Continuous.cpp
 
   util/errors.cpp

model/Clinical/CM5DayCommon.cpp

@@ -36,8 +36,8 @@ using namespace ::OM::util;
 
 // These parameters are set by setHealthSystem() and do not need checkpointing.
 mon::Measure CM5DayCommon::measures[NumCaseTypes] = {
-    mon::MHT_TREATMENTS_1,  // first line official
-    mon::MHT_TREATMENTS_2   // second line official
+    mon::measure("nTreatments1"),  // first line official
+    mon::measure("nTreatments2")   // second line official
 };
 double CM5DayCommon::accessUCAny[NumCaseTypes];
 double CM5DayCommon::accessUCSelfTreat[NumCaseTypes];
@@ -135,21 +135,21 @@ void CM5DayCommon::severeMalaria (
     // expanded, separating in-hospital and without (q[0]):
     const double exHospitalDeath = p2 * (p3 * p4 + (1 - p3) * p5b);
     const double exDeath = exHospitalDeath + (1 - p2) * p5a;
-    mon::reportStatMHF( mon::MHF_EXPECTED_HOSPITAL_DEATHS, human, exHospitalDeath );
-    mon::reportStatMHF( mon::MHF_EXPECTED_DIRECT_DEATHS, human, exDeath );
+    mon::recordStat(mon::measure("expectedHospitalDeaths"), human, exHospitalDeath);
+    mon::recordStat(mon::measure("expectedDirectDeaths"), human, exDeath);
 
     // Expectation of sequelae is:
     // double exSeq = (q[7] - q[6]) + (q[4] - q[3]) + (q[1] - q[0]);
     // expanded and simplified, noting that p7 == p6 :
     const double exSeq = (p2 * (p3 * (1 - p4) + (1 - p3) * (1 - p5b)) + (1 - p2) * (1 - p5a)) * p6;
-    mon::reportStatMHF( mon::MHF_EXPECTED_SEQUELAE, human, exSeq );
+    mon::recordStat(mon::measure("expectedSequelae"), human, exSeq);
 
     double prandom = human.rng.uniform_01();
 
     //NOTE: we do not model diagnostics in this case
     if( prandom >= q[2] ){      // treated in hospital
         m_tLastTreatment = sim::ts0();
-        mon::reportEventMHI( mon::MHT_TREATMENTS_3, human, 1 );
+        mon::recordEvent(mon::measure("nTreatments3"), human, 1);
         Episode::State stateTreated = Episode::State (pgState | Episode::EVENT_IN_HOSPITAL);
 
         if( prandom >= q[5] ){  // treatment successful at clearing parasites

model/Clinical/CM5DayCommon.h

@@ -27,7 +27,7 @@
 #include "Clinical/ClinicalModel.h"
 #include "Host/Human.h"
 #include "Host/WithinHost/WHInterface.h"
-#include "mon/reporting.h"
+#include "mon/Monitoring.h"
 
 namespace OM {
 namespace Clinical {

model/Clinical/CMDecisionTree.cpp

@@ -404,7 +404,7 @@ class CMDTReport : public CMDecisionTree {
 
     virtual CMDTOut exec( CMHostData hostData ) const{
         for( const size_t outId : outIds ){
-            mon::reportEventMHI_CMDT( mon::MCD_CMDT_REPORT, hostData.human, 1, outId);
+            mon::recordStat(mon::measure("nCMDTReport"), hostData.human, 1, 0, 0, 0, outId);
         }
         return CMDTOut(false);
     }

model/Clinical/ClinicalModel.cpp

@@ -26,7 +26,7 @@
 #include "Clinical/ImmediateOutcomes.h"
 #include "Clinical/DecisionTree5Day.h"
 #include "Host/NeonatalMortality.h"
-#include "mon/reporting.h"
+#include "mon/Monitoring.h"
 #include "util/ModelOptions.h"
 #include "util/CommandLine.h"
 #include "util/errors.h"
@@ -143,14 +143,14 @@ void ClinicalModel::update (Human& human, double ageYears, bool newBorn) {
 
     //indirect death: if this human's about to die, don't worry about further episodes:
     if (doomed <= DOOMED_EXPIRED) {	//clinical bout 6 intervals before
-        mon::reportEventMHI( mon::MHO_INDIRECT_DEATHS, human, 1 );
+        mon::recordEvent(mon::measure("nIndDeaths"), human, 1);
         doomed = DOOMED_INDIRECT;
         return;
     }
     if(newBorn /* i.e. first update since birth */) {
         // Chance of neonatal mortality:
         if (Host::NeonatalMortality::eventNeonatalMortality(human.rng)) {
-            mon::reportEventMHI( mon::MHO_INDIRECT_DEATHS, human, 1 );
+            mon::recordEvent(mon::measure("nIndDeaths"), human, 1);
             doomed = DOOMED_NEONATAL;
             return;
         }

model/Clinical/DecisionTree5Day.cpp

@@ -99,10 +99,10 @@ void DecisionTree5Day::uncomplicatedEvent ( Human& human, Episode::State pgState
 
         if( output.treated ){   // if any treatment or intervention deployed
             m_tLastTreatment = sim::ts0();
-            mon::reportEventMHI( measures[regimen], human, 1 );
+            mon::recordEvent(measures[regimen], human, 1);
         }
         if( output.screened ){
-            mon::reportEventMHI( mon::MHT_TREAT_DIAGNOSTICS, human, 1 );
+            mon::recordEvent(mon::measure("nTreatDiagnostics"), human, 1);
         }
 
         human.withinHostModel->optionalPqTreatment(human);

model/Clinical/Episode.cpp

@@ -71,55 +71,55 @@ void Episode::report () {
     if (state & Episode::MALARIA) {
         // Malarial fevers: report bout
         if (state & Episode::COMPLICATED) {
-            mon::reportMSACI( mon::MHE_SEVERE_EPISODES, surveyPeriod, ageGroup, cohortSet, 1 );
+            mon::record(mon::measure("nSevere"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
             if (state & Episode::SEVERE) {
-                mon::reportMSACI( mon::MHE_SEVERE_EPISODES_WITHOUT_COMORBIDITIES, surveyPeriod, ageGroup, cohortSet, 1 );
+                mon::record(mon::measure("nSevereWithoutComorbidities"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
             }
         } else { // UC or UC2
-            mon::reportMSACI( mon::MHE_UNCOMPLICATED_EPISODES, surveyPeriod, ageGroup, cohortSet, 1 );
+            mon::record(mon::measure("nUncomp"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
             if(infectionType == WithinHost::InfectionOrigin::Indigenous)
-                mon::reportMSACI( mon::MHE_UNCOMPLICATED_EPISODES_INDIGENOUS, surveyPeriod, ageGroup, cohortSet, 1 );
+                mon::record(mon::measure("nUncomp_Indigenous"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
             else if(infectionType == WithinHost::InfectionOrigin::Introduced)
-                mon::reportMSACI( mon::MHE_UNCOMPLICATED_EPISODES_INTRODUCED, surveyPeriod, ageGroup, cohortSet, 1 );
+                mon::record(mon::measure("nUncomp_Introduced"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
             else
-                mon::reportMSACI( mon::MHE_UNCOMPLICATED_EPISODES_IMPORTED, surveyPeriod, ageGroup, cohortSet, 1 );
+                mon::record(mon::measure("nUncomp_Imported"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
         }
 
         // Report outcomes of malarial fevers
         if (state & Episode::EVENT_IN_HOSPITAL) {
             if (state & Episode::DIRECT_DEATH) {
-                mon::reportMSACI( mon::MHO_DIRECT_DEATHS, surveyPeriod, ageGroup, cohortSet, 1 );
-                mon::reportMSACI( mon::MHO_HOSPITAL_DEATHS, surveyPeriod, ageGroup, cohortSet, 1 );
+                mon::record(mon::measure("nDirDeaths"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
+                mon::record(mon::measure("nHospitalDeaths"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
                 if (state & Episode::EVENT_FIRST_DAY){
-                    mon::reportMSACI( mon::MHO_FIRST_DAY_DEATHS, surveyPeriod, ageGroup, cohortSet, 1 );
-                    mon::reportMSACI( mon::MHO_HOSPITAL_FIRST_DAY_DEATHS, surveyPeriod, ageGroup, cohortSet, 1 );
+                    mon::record(mon::measure("Clinical_FirstDayDeaths"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
+                    mon::record(mon::measure("Clinical_HospitalFirstDayDeaths"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
                 }
             }
             else if (state & Episode::SEQUELAE) {
-                mon::reportMSACI( mon::MHO_SEQUELAE, surveyPeriod, ageGroup, cohortSet, 1 );
-                mon::reportMSACI( mon::MHO_HOSPITAL_SEQUELAE, surveyPeriod, ageGroup, cohortSet, 1 );
+                mon::record(mon::measure("nSeq"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
+                mon::record(mon::measure("nHospitalSeqs"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
             }
             else if (state & Episode::RECOVERY){
-                mon::reportMSACI( mon::MHO_HOSPITAL_RECOVERIES, surveyPeriod, ageGroup, cohortSet, 1 );
+                mon::record(mon::measure("nHospitalRecovs"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
             }
         } else {
             if (state & Episode::DIRECT_DEATH) {
-                mon::reportMSACI( mon::MHO_DIRECT_DEATHS, surveyPeriod, ageGroup, cohortSet, 1 );
+                mon::record(mon::measure("nDirDeaths"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
                 if (state & Episode::EVENT_FIRST_DAY){
-                    mon::reportMSACI( mon::MHO_FIRST_DAY_DEATHS, surveyPeriod, ageGroup, cohortSet, 1 );
+                    mon::record(mon::measure("Clinical_FirstDayDeaths"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
                 }
             }
             else if (state & Episode::SEQUELAE){
-                mon::reportMSACI( mon::MHO_SEQUELAE, surveyPeriod, ageGroup, cohortSet, 1 );
+                mon::record(mon::measure("nSeq"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
             }
             // Don't care about out-of-hospital recoveries
         }
     } else if (state & Episode::SICK) {
         // Report non-malarial fever and outcomes
-        mon::reportMSACI( mon::MHE_NON_MALARIA_FEVERS, surveyPeriod, ageGroup, cohortSet, 1 );
+        mon::record(mon::measure("nNMFever"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
 
         if (state & Episode::DIRECT_DEATH) {
-            mon::reportMSACI( mon::MHO_NMF_DEATHS, surveyPeriod, ageGroup, cohortSet, 1 );
+            mon::record(mon::measure("nNmfDeaths"), surveyPeriod, ageGroup, cohortSet, 0, 0, 0, 1);
         }
     }
 }

model/Clinical/Episode.h

@@ -26,8 +26,7 @@
 #include "Global.h"
 #include "Host/WithinHost/Pathogenesis/State.h"
 #include "Host/WithinHost/Infection/Infection.h"
-#include "mon/AgeGroup.h"
-#include "mon/info.h"
+#include "mon/Monitoring.h"
 #include "util/ModelOptions.h"
 #include <ostream>
 
@@ -84,7 +83,7 @@ class Episode{
     Episode() :
             time(sim::never()),
             surveyPeriod(mon::NOT_USED),
-            ageGroup(),
+            ageGroup(0),
             cohortSet(0),
             state(NONE)
     {
@@ -112,7 +111,7 @@ class Episode{
     /// Survey during which the event occured
     size_t surveyPeriod;
     /// Age group of the individual when the episode's first bout occurred
-    mon::AgeGroup ageGroup;
+    size_t ageGroup;
     /// Cohort membership
     uint32_t cohortSet;
     /// Descriptor of state, containing reporting info. Not all information will

model/Clinical/EventScheduler.cpp

@@ -23,7 +23,7 @@
 #include "Clinical/EventScheduler.h"
 #include "util/random.h"
 #include "Host/WithinHost/WHInterface.h"
-#include "mon/reporting.h"
+#include "mon/Monitoring.h"
 #include "util/ModelOptions.h"
 #include "util/errors.h"
 #include "util/StreamValidator.h"
@@ -174,7 +174,7 @@ void ClinicalEventScheduler::doClinicalUpdate (Human& human, double ageYears, Wi
         } else {
 	    if ( pgState & Episode::COMPLICATED ) {
                 const double pSequelae = pSequelaeInpatient.eval( ageYears );
-                mon::reportStatMHF( mon::MHF_EXPECTED_SEQUELAE, human, pSequelae );
+                mon::recordStat(mon::measure("expectedSequelae"), human, pSequelae);
 		if( human.rng.uniform_01() < pSequelae ){
 		    pgState = Episode::State (pgState | Episode::SEQUELAE);
                 }else{
@@ -253,17 +253,17 @@ void ClinicalEventScheduler::doClinicalUpdate (Human& human, double ageYears, Wi
         if( auxOut.treated ){	// I.E. some treatment was given
             timeLastTreatment = sim::ts0();
             if( pgState & Episode::COMPLICATED ){
-                mon::reportEventMHI( mon::MHT_TREATMENTS_3, human, 1 );
+                mon::recordEvent(mon::measure("nTreatments3"), human, 1);
             }else{
                 if( pgState & Episode::SECOND_CASE ){
-                    mon::reportEventMHI( mon::MHT_TREATMENTS_2, human, 1 );
+                    mon::recordEvent(mon::measure("nTreatments2"), human, 1);
                 }else{
-                    mon::reportEventMHI( mon::MHT_TREATMENTS_1, human, 1 );
+                    mon::recordEvent(mon::measure("nTreatments1"), human, 1);
                 }
             }
         }
         if( auxOut.screened ){
-            mon::reportEventMHI( mon::MHT_TREAT_DIAGNOSTICS, human, 1 );
+            mon::recordEvent(mon::measure("nTreatDiagnostics"), human, 1);
         }
 
 	if ( true /*FIXME auxOut.hospitalisation != CMAuxOutput::NONE*/ ) {	// in hospital
@@ -283,9 +283,9 @@ void ClinicalEventScheduler::doClinicalUpdate (Human& human, double ageYears, Wi
 	    // community fatality rate when not in hospital or delayed hospital entry
             if( !inHospital )
                 pDeath = getCommunityCFR( pDeath );
-            mon::reportStatMHF( mon::MHF_EXPECTED_DIRECT_DEATHS, human, pDeath );
+            mon::recordStat(mon::measure("expectedDirectDeaths"), human, pDeath);
             if( inHospital )
-                mon::reportStatMHF( mon::MHF_EXPECTED_HOSPITAL_DEATHS, human, pDeath );
+                mon::recordStat(mon::measure("expectedHospitalDeaths"), human, pDeath);
 	    if (human.rng.uniform_01() < pDeath) {
 		pgState = Episode::State (pgState | Episode::DIRECT_DEATH | Episode::EVENT_FIRST_DAY);
 		// Human is killed at end of time at risk
@@ -370,9 +370,9 @@ void ClinicalEventScheduler::doClinicalUpdate (Human& human, double ageYears, Wi
 		// community fatality rate when not in hospital
 		if( !(pgState & Episode::EVENT_IN_HOSPITAL) )
 		    pDeath = getCommunityCFR( pDeath );
-                mon::reportStatMHF( mon::MHF_EXPECTED_DIRECT_DEATHS, human, pDeath );
+                mon::recordStat(mon::measure("expectedDirectDeaths"), human, pDeath);
                 if( pgState & Episode::EVENT_IN_HOSPITAL )
-                    mon::reportStatMHF( mon::MHF_EXPECTED_HOSPITAL_DEATHS, human, pDeath );
+                    mon::recordStat(mon::measure("expectedHospitalDeaths"), human, pDeath);
 		if (human.rng.uniform_01() < pDeath) {
 		    pgState = Episode::State (pgState | Episode::DIRECT_DEATH);
 		    // Human is killed at end of time at risk

model/Clinical/ImmediateOutcomes.cpp

@@ -190,14 +190,14 @@ void ImmediateOutcomes::uncomplicatedEvent (
         // UC2: official care only
 
         if( useDiagnosticUC ){
-            mon::reportEventMHI( mon::MHT_TREAT_DIAGNOSTICS, human, 1 );
+            mon::recordEvent(mon::measure("nTreatDiagnostics"), human, 1);
             auto diag = WithinHost::diagnostics::monitoringDiagnostic();
             if( !human.withinHostModel->diagnosticResult(human.rng, diag) )
                 return; // negative outcome: no treatment
         }
 
         m_tLastTreatment = sim::ts0();
-        mon::reportEventMHI( measures[regimen], human, 1 );
+        mon::recordEvent(measures[regimen], human, 1);
 
         double p = ( x < accessUCSelfTreat[regimen] * m_treatmentSeekingFactor ) ?
             cureRateUCSelfTreat[regimen] : cureRateUCOfficial[regimen];

model/Host/Human.cpp

@@ -31,7 +31,7 @@
 #include "util/StreamValidator.h"
 #include "Population.h"
 #include "interventions/InterventionManager.h"
-#include "mon/reporting.h"
+#include "mon/Monitoring.h"
 #include "schema/scenario.h"
 
 namespace OM { namespace Host {
@@ -147,7 +147,7 @@ void Human::removeFirstEvent(interventions::SubPopRemove::RemoveAtCode code )
                 clinicalModel->flushReports();     // reset HS memory
 
                 // report removal due to first infection/bout/treatment
-                mon::reportEventMHI( mon::MHR_SUB_POP_REM_FIRST_EVENT, *this, 1 );
+                mon::recordEvent(mon::measure("nSubPopRemovalFirstEvent"), *this, 1);
             }
             cohortSet = mon::updateCohortSet( cohortSet, expIt->first, false );
             // remove (affects reporting, restrictToSubPop and cumulative deployment):
@@ -163,7 +163,7 @@ void Human::updateCohortSet()
         if( !(expIt->second >= sim::ts0()) ){       // membership expired
             // don't flush reports
             // report removal due to expiry
-            mon::reportEventMHI( mon::MHR_SUB_POP_REM_TOO_OLD, *this, 1 );
+            mon::recordEvent(mon::measure("nSubPopRemovalTooOld"), *this, 1);
             cohortSet = mon::updateCohortSet( cohortSet, expIt->first, false );
             // erase element, but continue iteration
             expIt = subPopExp.erase( expIt );
@@ -211,8 +211,8 @@ void summarize(Human &human, bool surveyOnlyNewEp) {
         return;
     }
 
-    mon::reportStatMHI( mon::MHR_HOSTS, human, 1 );
-    mon::reportStatMHF( mon::MHF_AGE, human, sim::inYears(human.age(sim::now())) );
+    mon::recordStat(mon::measure("nHost"), human, 1);
+    mon::recordStat(mon::measure("sumAge"), human, sim::inYears(human.age(sim::now())) );
     bool patent = human.withinHostModel->summarize (human);
     human.infIncidence->summarize (human);
 
@@ -234,7 +234,7 @@ void update(Human &human, Transmission::TransmissionModel& transmission)
     util::streamValidate( age0 );
 
     // monitoringAgeGroup is the group for the start of the time step.
-    human.monitoringAgeGroup.update( age0 );
+    mon::updateAgeGroup(human.monitoringAgeGroup, age0);
 
     human.updateCohortSet();
 

model/Host/Human.h

@@ -25,7 +25,6 @@
 #include "Global.h"
 #include "Transmission/PerHost.h"
 #include "InfectionIncidenceModel.h"
-#include "mon/AgeGroup.h"
 #include "interventions/HumanComponents.h"
 #include "util/checkpoint_containers.h"
 #include <map>
@@ -118,7 +117,7 @@ class Human {
     interventions::PerHumanVaccine vaccine;
 
     /** Made persistant to save a lookup each time step (significant performance improvement) */
-    mon::AgeGroup monitoringAgeGroup;
+    size_t monitoringAgeGroup = 0;
 
     /** The next continuous distribution in the series */
     uint32_t nextCtsDist = 0;

model/Host/ImportedInfections.h

@@ -118,8 +118,8 @@ namespace Host {
                 for(Human& human : population){
                     if(human.rng.bernoulli( rateNow )){
                         human.withinHostModel->importInfection(human.rng);
-                        mon::reportEventMHI( mon::MHR_NEW_INFECTIONS, human, 1);
-                        mon::reportEventMHI( mon::MHR_NEW_INFECTIONS_IMPORTED, human, 1);
+                        mon::recordEvent(mon::measure("nNewInfections"), human, 1);
+                        mon::recordEvent(mon::measure("nNewInfections_Imported"), human, 1);
                     }
                 }
             }

model/Host/InfectionIncidenceModel.cpp

@@ -171,7 +171,7 @@ double LogNormalMAII::getAvailabilityFactor(LocalRng& rng, double baseAvailabili
 }
 
 void InfectionIncidenceModel::summarize (const Host::Human& human) {
-    mon::reportStatMHF( mon::MHF_EXPECTED_INFECTED, human, m_pInfected );
+    mon::recordStat(mon::measure("nExpectd"), human, m_pInfected);
 }
 
 
@@ -265,9 +265,9 @@ int InfectionIncidenceModel::numNewInfections (Human& human, double expectedNumI
 
 void InfectionIncidenceModel::reportNumNewInfections(Human& human, int newNumInfections_i, int newNumInfections_l)
 {
-    mon::reportEventMHI( mon::MHR_NEW_INFECTIONS, human, newNumInfections_i+newNumInfections_l);
-    mon::reportEventMHI( mon::MHR_NEW_INFECTIONS_INTRODUCED, human, newNumInfections_i);
-    mon::reportEventMHI( mon::MHR_NEW_INFECTIONS_INDIGENOUS, human, newNumInfections_l);
+    mon::recordEvent(mon::measure("nNewInfections"), human, newNumInfections_i+newNumInfections_l);
+    mon::recordEvent(mon::measure("nNewInfections_Introduced"), human, newNumInfections_i);
+    mon::recordEvent(mon::measure("nNewInfections_Indigenous"), human, newNumInfections_l);
     ctsNewInfections += newNumInfections_i+newNumInfections_l;
 }