Temperature dependent microsporidia

Eradication/MicrosporidiaParameters.cpp

@@ -82,13 +82,20 @@ namespace Kernel
         , m_StrainNames()
         , m_MortalityModifierMale()
         , m_MortalityModifierFemale()
+        , m_TemperatureDependentModifierModel()
     {
         m_Collection.push_back( MicrosporidiaParameters::CreateNoMicrosporidiaVersion() );
+
+        // makes pairs "time, value" for this it's "temperature C, modifier" 
+        m_TemperatureDependentModifierModel.add(10.0f, 0.1f);
+        m_TemperatureDependentModifierModel.add(24.0f, 1.0f);
+        m_TemperatureDependentModifierModel.add(30.0f, 2.0f);
+        m_TemperatureDependentModifierModel.add(47.0f, 0.1f);
     }
 
     MicrosporidiaCollection::~MicrosporidiaCollection()
     {
-    }  
+    }
 
     void MicrosporidiaCollection::CheckConfiguration()
     {
@@ -166,6 +173,12 @@ namespace Kernel
         return m_MortalityModifierFemale;
     }
 
+    float MicrosporidiaCollection::GetTemperatureDependentModifier( float temperature ) const
+    {
+        // using minimum value as default value, so if temperature below defined, we use the lowest-temp modifier
+        return m_TemperatureDependentModifierModel.getValueLinearInterpolation( temperature, 0.1f);
+    }
+
     MicrosporidiaParameters* MicrosporidiaCollection::CreateObject()
     {
         // this object should get added to the end of the collection

Eradication/MicrosporidiaParameters.h

@@ -61,13 +61,14 @@ namespace Kernel
         const MicrosporidiaParameters& GetStrain( const std::string& rStrainName ) const;
         const std::vector<float>& GetMortalityModifierListMale() const;
         const std::vector<float>& GetMortalityModifierListFemale() const;
+        float GetTemperatureDependentModifier(float temperature) const;
 
     protected:
         virtual MicrosporidiaParameters* CreateObject() override;
 
         jsonConfigurable::tDynamicStringSet m_StrainNames;
         std::vector<float> m_MortalityModifierMale;
         std::vector<float> m_MortalityModifierFemale;
-
+        InterpolatedValueMap m_TemperatureDependentModifierModel;
     };
 }

Eradication/SimulationConfig.cpp

@@ -257,6 +257,11 @@ void SimulationConfig::VectorInitConfig( const Configuration* inputJson )
     initConfigTypeMap( "Enable_Temperature_Dependent_Egg_Hatching", &(vector_params->temperature_dependent_egg_hatching), Enable_Temperature_Dependent_Egg_Hatching_DESC_TEXT, false );
     initConfigTypeMap( "Egg_Arrhenius1", &(vector_params->eggarrhenius1), Egg_Arrhenius1_DESC_TEXT, 0.0f, 10000000000.0f, 61599956.864f, "Enable_Temperature_Dependent_Egg_Hatching" );
     initConfigTypeMap( "Egg_Arrhenius2", &(vector_params->eggarrhenius2), Egg_Arrhenius2_DESC_TEXT, 0.0f, 10000000000.0f, 5754.033f, "Enable_Temperature_Dependent_Egg_Hatching" );
+    if( JsonConfigurable::_dryrun || inputJson->Exist( "Enable_Temperature_Dependent_Microsporidia" ) )
+    {
+        // make this optional for backwards compatibility
+        initConfigTypeMap( "Enable_Temperature_Dependent_Microsporidia", &(vector_params->temperature_dependent_microsporidia), Enable_Temperature_Dependent_Microsporidia_DESC_TEXT, false );
+    }
     initConfigTypeMap( "Enable_Egg_Mortality", &(vector_params->egg_mortality), Enable_Egg_Mortality_DESC_TEXT, false ); // not hooked up yet
     initConfigTypeMap( "Enable_Drought_Egg_Hatch_Delay", &(vector_params->delayed_hatching_when_habitat_dries_up), Enable_Drought_Egg_Hatch_Delay_DESC_TEXT, false );
     initConfigTypeMap( "Drought_Egg_Hatch_Delay", &(vector_params->droughtEggHatchDelay), Drought_Egg_Hatch_Delay_DESC_TEXT, 0.0f, 1.0f, 0.33f, "Enable_Drought_Egg_Hatch_Delay" );

Eradication/VectorContexts.h

@@ -169,6 +169,7 @@ namespace Kernel
         virtual float getSumAgeAtDeath( VectorStateEnum::Enum state ) const = 0;
         virtual float getSumAgeAtDeath( VectorStateEnum::Enum state, const VectorGenome& rGenome ) const = 0;
         virtual std::vector<std::string> GetMicrosporidiaStrainNames() const = 0;
+        virtual float getMicrosporidiaModifier() const = 0;
         virtual uint32_t getProgressFromLarvaeToImmatureNum() const = 0;
         virtual float    getProgressFromLarvaeToImmatureSumDuration() const = 0;
         virtual void visitVectors(vector_cohort_visit_function_t func, VectorGender::Enum gender) = 0;

Eradication/VectorParameters.h

@@ -36,6 +36,7 @@ namespace Kernel
         float human_feeding_mortality;
         float eggarrhenius1;
         float eggarrhenius2;
+        bool  temperature_dependent_microsporidia;
 
         // allows configuration of larval habitat decay time constants
         float tempHabitatDecayScalar;
@@ -72,8 +73,9 @@ namespace Kernel
         , HEGhomingRate(0.0f)
         , HEGfecundityLimiting(0.0f)
         , human_feeding_mortality(DEFAULT_HUMAN_FEEDING_MORTALITY)
-        , eggarrhenius1( 0.0f) 
-        , eggarrhenius2( 0.0f) 
+        , eggarrhenius1( 0.0f)
+        , eggarrhenius2( 0.0f)
+        , temperature_dependent_microsporidia(false)
         , tempHabitatDecayScalar(0.0f)
         , semipermanentHabitatDecayRate(0.0f)
         , mmRainfallToFillSwamp(1.0f)

Eradication/VectorPopulation.cpp

@@ -69,6 +69,7 @@ namespace Kernel
         , dryheatmortality(0.0f)
         , infectiouscorrection(0.0f)
         , infected_progress_this_timestep(0.0f)
+        , microsporidia_modifier_this_timestep(1.0f)
         , indoorinfectiousbites(0.0f)
         , outdoorinfectiousbites(0.0f)
         , indoorbites(0.0f)
@@ -653,6 +654,11 @@ namespace Kernel
         float temperature = m_context->GetLocalWeather()->airtemperature();
         infected_progress_this_timestep = (species()->infectedarrhenius1 * exp( -species()->infectedarrhenius2 / (temperature + float( CELSIUS_TO_KELVIN )) )) * dt;
 
+        if( params()->temperature_dependent_microsporidia )
+        {
+            microsporidia_modifier_this_timestep = species()->microsporidia_strains.GetTemperatureDependentModifier(temperature);
+        }
+
         // Over-ride some lifecycle probabilities with species-specific values
         Update_Lifecycle_Probabilities(dt);
 
@@ -1834,7 +1840,7 @@ namespace Kernel
             if( male_has_microsporidia && !female_has_microsporidia )
             {
                 // Male infecting Female
-                float prob_transmission = m_species_params->microsporidia_strains[ male_ms_strain_index ]->male_to_female_transmission_probability;
+                float prob_transmission = (std::min)( 1.0f, m_species_params->microsporidia_strains[ male_ms_strain_index ]->male_to_female_transmission_probability * microsporidia_modifier_this_timestep);
                 if( m_context->GetRng()->SmartDraw( prob_transmission ) )
                 {
                     female_has_microsporidia = true;
@@ -1845,7 +1851,7 @@ namespace Kernel
             else if( !male_has_microsporidia && female_has_microsporidia )
             {
                 // Female infecting Male
-                float prob_transmission = m_species_params->microsporidia_strains[ female_ms_strain_index ]->female_to_male_transmission_probability;
+                float prob_transmission = (std::min)( 1.0f, m_species_params->microsporidia_strains[ female_ms_strain_index ]->female_to_male_transmission_probability * microsporidia_modifier_this_timestep);
                 if( m_context->GetRng()->SmartDraw( prob_transmission ) )
                 {
                     if( microsporidia_infected_males[ female_ms_strain_index ].count( p_male_cohort->GetID() ) == 0 )
@@ -2396,6 +2402,12 @@ namespace Kernel
         int male_strain_index = rMaleGenome.GetMicrosporidiaStrainIndex();
         float male_to_egg_tran = m_species_params->microsporidia_strains[ male_strain_index ]->male_to_egg_transmission_probability;
 
+        if( params()->temperature_dependent_microsporidia )
+        {
+            female_to_egg_tran = (std::min)( 1.0f, female_to_egg_tran * microsporidia_modifier_this_timestep );
+            male_to_egg_tran   = (std::min)( 1.0f, male_to_egg_tran   * microsporidia_modifier_this_timestep );
+        }
+
         float prob_transmission = 1.0 - (1.0 - female_to_egg_tran) * (1.0 - male_to_egg_tran);
         float fraction_female_strain = 1.0;
         if( (female_to_egg_tran + male_to_egg_tran) > 0.0 )
@@ -3294,6 +3306,11 @@ namespace Kernel
         return strain_name_list;
     }
 
+    float VectorPopulation::getMicrosporidiaModifier() const
+    {
+        return microsporidia_modifier_this_timestep;
+    }
+
     uint32_t VectorPopulation::getProgressFromLarvaeToImmatureNum() const
     {
         return m_ProgressedLarvaeToImmatureCount;

Eradication/VectorPopulation.h

@@ -132,6 +132,7 @@ namespace Kernel
         virtual float getSumAgeAtDeath( VectorStateEnum::Enum state ) const override;
         virtual float getSumAgeAtDeath( VectorStateEnum::Enum state, const VectorGenome& rGenome ) const override;
         virtual std::vector<std::string> GetMicrosporidiaStrainNames() const override;
+        virtual float getMicrosporidiaModifier() const override;
         virtual uint32_t getProgressFromLarvaeToImmatureNum() const override;
         virtual float    getProgressFromLarvaeToImmatureSumDuration() const override;
         virtual void visitVectors(vector_cohort_visit_function_t func, VectorGender::Enum gender) override;
@@ -473,6 +474,7 @@ namespace Kernel
         float dryheatmortality;
         float infectiouscorrection;
         float infected_progress_this_timestep;
+        float microsporidia_modifier_this_timestep;
 
         // intermediate counters
         float indoorinfectiousbites;

Eradication/VectorPopulationIndividual.cpp

@@ -616,7 +616,7 @@ namespace Kernel
             if( male_has_microsporidia && !female_has_microsporidia )
             {
                 // Male infecting Female
-                float prob_transmission = m_species_params->microsporidia_strains[ male_ms_strain_index ]->male_to_female_transmission_probability;
+                float prob_transmission = (std::min)( 1.0f, m_species_params->microsporidia_strains[ male_ms_strain_index ]->male_to_female_transmission_probability * microsporidia_modifier_this_timestep );
                 if( m_context->GetRng()->SmartDraw( prob_transmission ) )
                 {
                     pFemaleCohort->InfectWithMicrosporidia( male_ms_strain_index );
@@ -625,7 +625,7 @@ namespace Kernel
             else if( !male_has_microsporidia && female_has_microsporidia )
             {
                 // Female infecting Male
-                float prob_transmission = m_species_params->microsporidia_strains[ female_ms_strain_index ]->female_to_male_transmission_probability;
+                float prob_transmission = (std::min)( 1.0f, m_species_params->microsporidia_strains[ female_ms_strain_index ]->female_to_male_transmission_probability * microsporidia_modifier_this_timestep );
                 if( m_context->GetRng()->SmartDraw( prob_transmission ) )
                 {
                     uint32_t orig_unmated = p_male_cohort->GetUnmatedCount();

Regression/Malaria/119_Malaria_Microsporidia/campaign.json

@@ -0,0 +1,30 @@
+{
+    "Events": [
+        {
+            "class": "CampaignEvent",
+            "Comment": "Strain_A, 50% coverage, ALL_HABITATS, box infectivity 0.3 for 60 days",
+            "Start_Day": 20,
+            "Nodeset_Config": {
+                "class": "NodeSetAll"
+            },
+            "Event_Coordinator_Config": {
+                "class": "StandardInterventionDistributionEventCoordinator",
+                "Number_Repetitions": 1,
+                "Timesteps_Between_Repetitions": 1,
+                "Intervention_Config": {
+                    "class": "LarvalMicrosporidiaIntervention",
+                    "Cost_To_Consumer": 10,
+                    "Habitat_Target": "ALL_HABITATS",
+                    "Habitat_Coverage": 0.5,
+                    "Strain_Name": "Strain_A",
+                    "Infectivity_Config": {
+                        "class": "WaningEffectBox",
+                        "Initial_Effect": 0.3,
+                        "Box_Duration": 60
+                    }
+                }
+            }
+        }
+    ],
+    "Use_Defaults": 1
+}

Regression/Malaria/119_Malaria_Microsporidia/custom_reports.json

@@ -0,0 +1,8 @@
+{
+    "Reports": [
+        {
+            "class": "ReportMicrosporidia"
+        }
+    ],
+    "Use_Defaults": 1
+}

Regression/Malaria/119_Malaria_Microsporidia/param_overrides.json

@@ -0,0 +1,109 @@
+{
+    "Default_Config_Path": "../../defaults/malaria_default_config.json",
+    "parameters": {
+        "CLIMATE": {
+            "AIR": {
+                "Air_Temperature_Filename": "Namawala_single_node_air_temperature_daily.bin"
+            },
+            "HUMIDITY": {
+                "Relative_Humidity_Filename": "Namawala_single_node_relative_humidity_daily.bin"
+            },
+            "LAND_TEMP": {
+                "Land_Temperature_Filename": "Namawala_single_node_land_temperature_daily.bin"
+            },
+            "RAINFALL": {
+                "Rainfall_Filename": "Namawala_single_node_rainfall_daily.bin"
+            }
+        },
+        "DEMOGRAPHICS": {
+            "Demographics_Filenames": [
+                "Namawala_single_node_demographics.json"
+            ],
+            "Enable_Initial_Prevalence": 1
+        },
+        "PRIMARY": {
+            "Config_Name": "119_Malaria_Microsporidia",
+            "Enable_Temperature_Dependent_Microsporidia": 1,
+            "x_Temporary_Larval_Habitat": 0.5,
+            "Custom_Reports_Filename": "custom_reports.json",
+            "Enable_Demographics_Reporting": 0,
+            "Geography": "Namawala",
+            "Run_Number": 1,
+            "Simulation_Duration": 180
+
+        },
+        "Vector_Species_Params": [
+            {
+                "Name": "arabiensis",
+                "Microsporidia": [
+                    {
+                        "Strain_Name": "Strain_A",
+                        "Female_To_Egg_Transmission_Probability": 0.3,
+                        "Male_To_Egg_Transmission_Probability": 0.3,
+                        "Female_To_Male_Transmission_Probability": 0.4,
+                        "Male_To_Female_Transmission_Probability": 0.4,
+                        "Larval_Growth_Modifier": 1.0,
+                        "Female_Mortality_Modifier": 1.0,
+                        "Male_Mortality_Modifier": 1.0,
+                        "Duration_To_Disease_Acquisition_Modification": {
+                            "Times":  [ 0, 3 ],
+                            "Values": [ 1.0, 0.1 ]
+                        },
+                        "Duration_To_Disease_Transmission_Modification": {
+                            "Times":  [ 0, 3 ],
+                            "Values": [ 1.0, 0.1 ]
+                        }
+                    }
+                ],
+                "Acquire_Modifier": 1,
+                "Adult_Life_Expectancy": 10,
+                "Male_Life_Expectancy": 10,
+                "Anthropophily": 0.95,
+                "Aquatic_Arrhenius_1": 84200000000,
+                "Aquatic_Arrhenius_2": 8328,
+                "Aquatic_Mortality_Rate": 0.1,
+                "Days_Between_Feeds": 3,
+                "Egg_Batch_Size": 100,
+                "Immature_Duration": 4,
+                "Indoor_Feeding_Fraction": 0.5,
+                "Infected_Arrhenius_1": 117000000000,
+                "Infected_Arrhenius_2": 8336,
+                "Infected_Egg_Batch_Factor": 0.8,
+                "Infectious_Human_Feed_Mortality_Factor": 1.5,
+                "Habitats": [
+                    {
+                        "Habitat_Type": "TEMPORARY_RAINFALL",
+                        "Max_Larval_Capacity": 11250000000.0
+                    }
+                ],
+                "Temperature_Dependent_Feeding_Cycle": "NO_TEMPERATURE_DEPENDENCE",
+                "Transmission_Rate": 0.5,
+                "Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE",
+                "Vector_Migration_Filename": "",
+                "x_Vector_Migration": 1,
+                "Vector_Migration_Food_Modifier": 0.0,
+                "Vector_Migration_Habitat_Modifier": 0.0,
+                "Vector_Migration_Modifier_Equation": "LINEAR",
+                "Vector_Migration_Stay_Put_Modifier": 0.0
+            },
+                {
+                "Habitats": [
+                    {
+                        "Habitat_Type": "TEMPORARY_RAINFALL",
+                        "Max_Larval_Capacity": 0.0
+                    }
+                ],
+                "Name": "gambiae"
+            },
+                            {
+                "Habitats": [
+                    {
+                        "Habitat_Type": "TEMPORARY_RAINFALL",
+                        "Max_Larval_Capacity": 0.0
+                    }
+                ],
+                "Name": "funestus"
+            }
+        ]
+    }
+}