Merge pull request #430 from mrc-ide/MoreCalibChanges

Morecalibchanges
mrc-ide · Jul 8, 2020 · eb036bc · eb036bc
2 parents bdd4fea + 37171d5
commit eb036bc
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Showing 18 changed files with 1,691 additions and 1,146 deletions.
diff --git a/src/CLI.cpp b/src/CLI.cpp
@@ -10,6 +10,11 @@
 #include "Error.h"
 #include "Param.h"
 
+void parse_string(std::string const& input, std::string& output)
+{
+	output = input;
+}
+
 void parse_read_file(std::string const& input, std::string& output)
 {
 	// check to see if the file exists and error out if it doesn't
@@ -173,11 +178,26 @@ Optional arguments:
 
 void CmdLineArgs::print_help()
 {
+	// Wes: Temporary hack to reduce the number of /CLP: on the help text.
+	int clp_flag = 0;
+	const std::string CLP = "CLP";
 	std::stringstream ss;
+
 	ss << "CovidSim";
 	for (auto const& it : option_map_)
 	{
-		ss << " [/" << it.first << ']';
+		std::string option = it.first;
+		std::string option_first_3 = option.substr(0, 3);
+
+		if (option_first_3.compare(CLP) == 0) {
+			if (clp_flag == 0) {
+				ss << " [/CLP:00] .. [/CLP:99]";
+				clp_flag = 1;
+			}
+		}
+		else {
+			ss << " [/" << option << ']';
+		}
 	}
 	std::cerr << ss.str() << ' ' << USAGE << std::endl;
 }

diff --git a/src/CLI.h b/src/CLI.h
@@ -22,6 +22,11 @@ void parse_read_file(std::string const& input, std::string& output);
  */
 void parse_write_dir(std::string const& input, std::string& output);
 
+/**
+ *  handles general string.
+ */
+void parse_string(std::string const& input, std::string& output);
+
 /**
  * Parses and checks if the input string is an integer.
  */

diff --git a/src/CalcInfSusc.cpp b/src/CalcInfSusc.cpp
@@ -14,25 +14,33 @@ double CalcHouseInf(int j, unsigned short int ts)
 	return	((HOST_ISOLATED(j) && (Hosts[j].digitalContactTraced != 1)) ? P.CaseIsolationHouseEffectiveness : 1.0)
 		*	((Hosts[j].digitalContactTraced==1) ? P.DCTCaseIsolationHouseEffectiveness : 1.0)
 		*	((HOST_QUARANTINED(j) && (Hosts[j].digitalContactTraced != 1) && (!(HOST_ISOLATED(j))))? P.HQuarantineHouseEffect : 1.0)
-		*	P.HouseholdDenomLookup[Households[Hosts[j].hh].nhr - 1] * CalcPersonInf(j, ts);
+		*	P.HouseholdDenomLookup[Households[Hosts[j].hh].nhr - 1]
+		*   ((Hosts[j].care_home_resident) ? P.CareHomeResidentHouseholdScaling : 1.0)
+		*   (HOST_TREATED(j) ? P.TreatInfDrop : 1.0)
+		*   (HOST_VACCED(j) ? P.VaccInfDrop : 1.0)
+		*   ((P.NoInfectiousnessSDinHH)? ((Hosts[j].infectiousness < 0) ? P.SymptInfectiousness : P.AsymptInfectiousness):fabs(Hosts[j].infectiousness))  // removed call to CalcPersonInf to allow infectiousness to be const in hh
+		*   P.infectiousness[ts - Hosts[j].latent_time - 1];
 }
+
 double CalcPlaceInf(int j, int k, unsigned short int ts)
 {
 	return	((HOST_ISOLATED(j) && (Hosts[j].digitalContactTraced != 1)) ? P.CaseIsolationEffectiveness : 1.0)
 		*	((Hosts[j].digitalContactTraced==1) ? P.DCTCaseIsolationEffectiveness : 1.0)
-		*	((HOST_QUARANTINED(j) && (Hosts[j].digitalContactTraced != 1) && (!(HOST_ISOLATED(j)))) ? P.HQuarantinePlaceEffect[k] : 1.0)
-		*	((Hosts[j].inf == InfStat_Case) ? P.SymptPlaceTypeContactRate[k] : 1.0)
+		*	((HOST_QUARANTINED(j) && (!Hosts[j].care_home_resident) && (Hosts[j].digitalContactTraced != 1) && (!(HOST_ISOLATED(j)))) ? P.HQuarantinePlaceEffect[k] : 1.0)
+		*	(((Hosts[j].inf == InfStat_Case) && (!Hosts[j].care_home_resident)) ? P.SymptPlaceTypeContactRate[k] : 1.0)
 		*	P.PlaceTypeTrans[k] / P.PlaceTypeGroupSizeParam1[k] * CalcPersonInf(j, ts);
 }
+
 double CalcSpatialInf(int j, unsigned short int ts)
 {
 	return	((HOST_ISOLATED(j) && (Hosts[j].digitalContactTraced != 1)) ? P.CaseIsolationEffectiveness : 1.0)
 		*	((Hosts[j].digitalContactTraced==1) ? P.DCTCaseIsolationEffectiveness : 1.0)
-		*   ((HOST_QUARANTINED(j) && (Hosts[j].digitalContactTraced != 1) && (!(HOST_ISOLATED(j)))) ? P.HQuarantineSpatialEffect : 1.0)
+		*   ((HOST_QUARANTINED(j) && (!Hosts[j].care_home_resident) && (Hosts[j].digitalContactTraced != 1) && (!(HOST_ISOLATED(j)))) ? P.HQuarantineSpatialEffect : 1.0)
 		*	((Hosts[j].inf == InfStat_Case) ? P.SymptSpatialContactRate : 1.0)
 		*	P.RelativeSpatialContact[HOST_AGE_GROUP(j)]
 		*	CalcPersonInf(j, ts); 		/*	*Hosts[j].spatial_norm */
 }
+
 double CalcPersonInf(int j, unsigned short int ts)
 {
 	return	(HOST_TREATED(j) ? P.TreatInfDrop : 1.0)
@@ -47,19 +55,20 @@ double CalcHouseSusc(int ai, unsigned short int ts, int infector, int tn)
 {
 	return CalcPersonSusc(ai, ts, infector, tn)
 		* ((Mcells[Hosts[ai].mcell].socdist == 2) ? ((Hosts[ai].esocdist_comply) ? P.EnhancedSocDistHouseholdEffectCurrent : P.SocDistHouseholdEffectCurrent) : 1.0)
-		* (Hosts[ai].digitalContactTraced==1 ? P.DCTCaseIsolationHouseEffectiveness : 1.0);
+		* ((Hosts[ai].digitalContactTraced==1) ? P.DCTCaseIsolationHouseEffectiveness : 1.0)
+		* ((Hosts[ai].care_home_resident) ? P.CareHomeResidentHouseholdScaling : 1.0);
 }
 double CalcPlaceSusc(int ai, int k, unsigned short int ts, int infector, int tn)
 {
-	return		((HOST_QUARANTINED(ai) && (Hosts[ai].digitalContactTraced != 1)) ? P.HQuarantinePlaceEffect[k] : 1.0)
+	return		((HOST_QUARANTINED(ai) && (!Hosts[ai].care_home_resident) && (Hosts[ai].digitalContactTraced != 1)) ? P.HQuarantinePlaceEffect[k] : 1.0)
 		* ((Mcells[Hosts[ai].mcell].socdist == 2) ? ((Hosts[ai].esocdist_comply) ? P.EnhancedSocDistPlaceEffectCurrent[k] : P.SocDistPlaceEffectCurrent[k]) : 1.0)
-		*	(Hosts[ai].digitalContactTraced==1 ? P.DCTCaseIsolationEffectiveness : 1.0);
+		* ((Hosts[ai].digitalContactTraced==1) ? P.DCTCaseIsolationEffectiveness : 1.0);
 }
 double CalcSpatialSusc(int ai, unsigned short int ts, int infector, int tn)
 {
-	return	 ((HOST_QUARANTINED(ai) && (Hosts[ai].digitalContactTraced != 1)) ? P.HQuarantineSpatialEffect : 1.0)
+	return	 ((HOST_QUARANTINED(ai) && (!Hosts[ai].care_home_resident) && (Hosts[ai].digitalContactTraced != 1)) ? P.HQuarantineSpatialEffect : 1.0)
 		* ((Mcells[Hosts[ai].mcell].socdist == 2) ? ((Hosts[ai].esocdist_comply) ? P.EnhancedSocDistSpatialEffectCurrent : P.SocDistSpatialEffectCurrent) : 1.0)
-		*	(Hosts[ai].digitalContactTraced==1 ? P.DCTCaseIsolationEffectiveness : 1.0);
+		* ((Hosts[ai].digitalContactTraced == 1) ? P.DCTCaseIsolationEffectiveness : 1.0);
 }
 double CalcPersonSusc(int ai, unsigned short int ts, int infector, int tn)
 {

diff --git a/src/Constants.h b/src/Constants.h
@@ -67,6 +67,8 @@ const int OUTPUT_DIST_SCALE = 1000;
 const int MAX_PLACE_SIZE = 20000;
 const int MAX_NUM_SEED_LOCATIONS = 10000;
 
+const int MAX_CLP_COPIES = 50;
+
 const int CDF_RES = 20;
 const int INFPROF_RES = 56;
 

diff --git a/src/Country.h b/src/Country.h
@@ -8,7 +8,7 @@ const int MAX_INTERVENTIONS_PER_ADUNIT = 10;
 
 const int ADUNIT_LOOKUP_SIZE = 1000000;
 const int MAX_COUNTRIES = 100;
-const int NUM_PLACE_TYPES = 4;
+const int NUM_PLACE_TYPES = 5;
 const int MAX_ADUNITS = 3200;
 
 // Maximal absent time - used for array sizing