Merge pull request #199 from SwissTPH/name-cleanup

Name cleanup

model/CMakeLists.txt

@@ -55,7 +55,7 @@ set (Model_CPP
   #Transmission/Anopheles/LCEmergence.cpp
   #Transmission/Anopheles/LifeCycle.cpp
   #Transmission/Anopheles/ResourceFitter.cpp
-  Transmission/Anopheles/PerHost.cpp
+  Transmission/Anopheles/PerHostAnoph.cpp
 
   WithinHost/WHInterface.cpp
   WithinHost/WHFalciparum.cpp

model/Transmission/Anopheles/AnophelesModel.h

@@ -22,7 +22,7 @@
 #define Hmod_AnophelesModel
 
 #include "Global.h"
-#include "Transmission/Anopheles/PerHost.h"
+#include "Transmission/Anopheles/PerHostAnoph.h"
 #include "Transmission/PerHost.h"
 #include "Transmission/Anopheles/MosqTransmission.h"
 #include "Transmission/Anopheles/FixedEmergence.h"
@@ -126,7 +126,7 @@ class AnophelesModel
     void initVectorTrap( const scnXml::Description1& desc, size_t instance );
 
     /** Return base-line human parameters for the mosquito. */
-    inline const Anopheles::PerHostBase& getHumanBaseParams () {
+    inline const PerHostAnophParams& getHumanBaseParams () {
         return humanBase;
     }
 
@@ -261,7 +261,7 @@ class AnophelesModel
      * descriptions.
      *
      * Read from XML by initialise; no need to checkpoint. */
-    Anopheles::PerHostBase humanBase;
+    PerHostAnophParams humanBase;
 
 
     /** Duration of host-seeking per day; the maximum fraction of a day that a

model/Transmission/Anopheles/PerHost.cpp → model/Transmission/Anopheles/PerHostAnoph.cpp

@@ -18,7 +18,7 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-#include "Transmission/Anopheles/PerHost.h"
+#include "Transmission/Anopheles/PerHostAnoph.h"
 #include "util/errors.h"
 
 namespace OM {
@@ -27,14 +27,14 @@ namespace Anopheles {
 
 // ----- Per host, per species, non-static -----
 
-void PerHost::initialise (const PerHostBase& base, double availabilityFactor)
+void PerHostAnoph::initialise (const PerHostAnophParams& base, double availabilityFactor)
 {
     entoAvailability = base.entoAvailability.sample() * availabilityFactor;
     probMosqBiting = base.probMosqBiting.sample();
     probMosqRest = base.probMosqFindRestSite.sample() * base.probMosqSurvivalResting.sample();
 }
 
-void PerHostBase::operator =(const scnXml::Mosq& mosq)
+void PerHostAnophParams::operator =(const scnXml::Mosq& mosq)
 {
     entoAvailability.setParams( numeric_limits<double>::quiet_NaN(),
                                 mosq.getAvailabilityVariance().getValue() );

model/Transmission/Anopheles/PerHost.h → model/Transmission/Anopheles/PerHostAnoph.h

@@ -32,7 +32,7 @@ namespace Anopheles {
  * mosquito species: intervention descriptions and model parameters.
  *
  * Parameters are read from XML, and the availability rate is adjusted. */
-class PerHostBase {
+class PerHostAnophParams {
 public:
     /** Set parameters from an XML element. */
     void operator= (const scnXml::Mosq& mosq);
@@ -68,12 +68,12 @@ class PerHostBase {
 };
 
 /** Data needed for each human which is per-mosquito species. */
-class PerHost
+class PerHostAnoph
 {
 public:
     /** In lieu of a constructor initialises elements, using the passed base to
      * get baseline parameters. */
-    void initialise (const PerHostBase& base, double availabilityFactor);
+    void initialise (const PerHostAnophParams& base, double availabilityFactor);
 
     /// Checkpointing
     template<class S>

model/Transmission/PerHost.cpp

@@ -20,14 +20,15 @@
 
 #include "Transmission/PerHost.h"
 #include "Transmission/VectorModel.h"
-#include "Transmission/Anopheles/PerHost.h"
+#include "Transmission/Anopheles/PerHostAnoph.h"
 #include "interventions/InterventionManager.hpp"
 #include "util/errors.h"
 #include "util/checkpoint.h"
 
 namespace OM {
 namespace Transmission {
 using namespace OM::util;
+using Anopheles::PerHostAnophParams;
 
 // -----  PerHost static  -----
 
@@ -80,22 +81,22 @@ void PerHost::deployComponent( const HumanVectorInterventionComponent& params ){
 // (easily large enough for conceivable Weibull params that the value is 0.0 when
 // rounded to a double. Performance-wise it's perhaps slightly slower than using
 // an if() when interventions aren't present.
-double PerHost::entoAvailabilityHetVecItv (const Anopheles::PerHostBase& base,
+double PerHost::entoAvailabilityHetVecItv (const PerHostAnophParams& base,
                                 size_t speciesIndex) const {
     double alpha_i = species[speciesIndex].getEntoAvailability();
     for( ListActiveComponents::const_iterator it = activeComponents.begin(); it != activeComponents.end(); ++it ){
         alpha_i *= it->relativeAttractiveness( speciesIndex );
     }
     return alpha_i;
 }
-double PerHost::probMosqBiting (const Anopheles::PerHostBase& base, size_t speciesIndex) const {
+double PerHost::probMosqBiting (const PerHostAnophParams& base, size_t speciesIndex) const {
     double P_B_i = species[speciesIndex].getProbMosqBiting();
     for( ListActiveComponents::const_iterator it = activeComponents.begin(); it != activeComponents.end(); ++it ){
         P_B_i *= it->preprandialSurvivalFactor( speciesIndex );
     }
     return P_B_i;
 }
-double PerHost::probMosqResting (const Anopheles::PerHostBase& base, size_t speciesIndex) const {
+double PerHost::probMosqResting (const PerHostAnophParams& base, size_t speciesIndex) const {
     double pRest = species[speciesIndex].getProbMosqRest();
     for( ListActiveComponents::const_iterator it = activeComponents.begin(); it != activeComponents.end(); ++it ){
         pRest *= it->postprandialSurvivalFactor( speciesIndex );

model/Transmission/PerHost.h

@@ -22,7 +22,7 @@
 #define Hmod_PerHost
 
 #include "Global.h"
-#include "Transmission/Anopheles/PerHost.h"
+#include "Transmission/Anopheles/PerHostAnoph.h"
 #include "interventions/Interfaces.hpp"
 #include "util/AgeGroupInterpolation.h"
 #include "util/DecayFunction.h"
@@ -33,6 +33,8 @@
 namespace OM {
 namespace Transmission {
 
+using Anopheles::PerHostAnophParams;
+using Anopheles::PerHostAnoph;
 using util::AgeGroupInterpolator;
 using util::DecayFunction;
 using util::DecayFuncHet;
@@ -200,7 +202,7 @@ class PerHost
      * rate factors.)
      * 
      * Assume mean is human-to-vector availability rate factor. */
-    double entoAvailabilityHetVecItv( const Anopheles::PerHostBase& base, size_t speciesIndex ) const;
+    double entoAvailabilityHetVecItv( const PerHostAnophParams& base, size_t speciesIndex ) const;
 
     /** Availability rate of human to mosquitoes (α_i). Equals 
      * entoAvailabilityHetVecItv()*getRelativeAvailability().
@@ -210,7 +212,7 @@ class PerHost
      * by the average availability of the population, which was incorrectly done
      * in the past. */
     inline double entoAvailabilityFull (
-        const Anopheles::PerHostBase& base,
+        const PerHostAnophParams& base,
         size_t speciesIndex,
         double ageYears
     ) const {
@@ -222,10 +224,10 @@ class PerHost
     ///@brief Get effects of interventions pre/post biting
     //@{
     /** Probability of a mosquito succesfully biting a host (P_B_i). */
-    double probMosqBiting (const Anopheles::PerHostBase& base, size_t speciesIndex) const;
+    double probMosqBiting (const PerHostAnophParams& base, size_t speciesIndex) const;
     /** Probability of a mosquito succesfully finding a resting
      * place after biting and then resting (P_C_i * P_D_i). */
-    double probMosqResting (const Anopheles::PerHostBase& base, size_t speciesIndex) const;
+    double probMosqResting (const PerHostAnophParams& base, size_t speciesIndex) const;
     /** Multiplicative factor for the number of fertile eggs laid by mosquitoes
      * after feeding on this host. Should be 1 normally, less than 1 to reduce
      * fertility, greater than 1 to increase. */
@@ -235,7 +237,7 @@ class PerHost
     ///@brief Convenience wrappers around several functions
     //@{
     /// entoAvailabilityHetVecItv * probMosqBiting
-    inline double availBite (const Anopheles::PerHostBase& base, size_t speciesIndex) const{
+    inline double availBite (const PerHostAnophParams& base, size_t speciesIndex) const{
         return entoAvailabilityHetVecItv(base, speciesIndex) *
                 probMosqBiting(base, speciesIndex);
     }
@@ -269,7 +271,7 @@ class PerHost
     void checkpointIntervs( ostream& stream );
     void checkpointIntervs( istream& stream );
 
-    vector<Anopheles::PerHost> species;
+    vector<PerHostAnoph> species;
 
     // Determines whether human is outside transmission
     bool outsideTransmission;

model/Transmission/VectorModel.cpp

@@ -36,6 +36,7 @@
 namespace OM {
 namespace Transmission {
 using namespace OM::util;
+using Anopheles::PerHostAnophParams;
 
 void VectorModel::ctsCbN_v0 (ostream& stream) {
     for(size_t i = 0; i < numSpecies; ++i)
@@ -67,7 +68,7 @@ void VectorModel::ctsCbS_v (ostream& stream) {
 }
 void VectorModel::ctsCbAlpha (const Population& population, ostream& stream){
     for( size_t i = 0; i < numSpecies; ++i){
-        const Anopheles::PerHostBase& params = species[i].getHumanBaseParams();
+        const PerHostAnophParams& params = species[i].getHumanBaseParams();
         double total = 0.0;
         for(Population::ConstIter iter = population.cbegin(); iter != population.cend(); ++iter) {
             total += iter->perHostTransmission.entoAvailabilityFull( params, i, iter->age(sim::now()).inYears() );
@@ -77,7 +78,7 @@ void VectorModel::ctsCbAlpha (const Population& population, ostream& stream){
 }
 void VectorModel::ctsCbP_B (const Population& population, ostream& stream){
     for( size_t i = 0; i < numSpecies; ++i){
-	const Anopheles::PerHostBase& params = species[i].getHumanBaseParams();
+	const PerHostAnophParams& params = species[i].getHumanBaseParams();
         double total = 0.0;
         for(Population::ConstIter iter = population.cbegin(); iter != population.cend(); ++iter) {
             total += iter->perHostTransmission.probMosqBiting( params, i );
@@ -87,7 +88,7 @@ void VectorModel::ctsCbP_B (const Population& population, ostream& stream){
 }
 void VectorModel::ctsCbP_CD (const Population& population, ostream& stream){
     for( size_t i = 0; i < numSpecies; ++i){
-	const Anopheles::PerHostBase& params = species[i].getHumanBaseParams();
+	const PerHostAnophParams& params = species[i].getHumanBaseParams();
         double total = 0.0;
         for(Population::ConstIter iter = population.cbegin(); iter != population.cend(); ++iter) {
             total += iter->perHostTransmission.probMosqResting( params, i );
@@ -270,7 +271,7 @@ void VectorModel::init2 () {
         double sigma_df = 0.0;
         double sigma_dff = 0.0;
 
-        const Anopheles::PerHostBase& humanBase = species[i].getHumanBaseParams();
+        const PerHostAnophParams& humanBase = species[i].getHumanBaseParams();
         foreach(const Host::Human& human, sim::humanPop().crange()) {
             const OM::Transmission::PerHost& host = human.perHostTransmission;
             double prod = host.entoAvailabilityFull (humanBase, i, human.age(sim::now()).inYears());
@@ -458,7 +459,7 @@ void VectorModel::vectorUpdate () {
     saved_sigma_dif.assign_at1(popDataInd, 0.0);
     vector<double> sigma_dff(numSpecies, 0.0);
 
-    vector<const Anopheles::PerHostBase*> humanBases;
+    vector<const PerHostAnophParams*> humanBases;
     humanBases.reserve( numSpecies );
     for(size_t s = 0; s < numSpecies; ++s){
         humanBases.push_back( &species[s].getHumanBaseParams() );