Commit 7dd8026
Initial Commit - HIV Release 2.0
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- Include
- Lib
- amd64
- i386
- License
- Eradication
- Regression
- 00_Default
- output
- 1000_TB_Namawala_SEAsia_HLfit
- output_IndivProperties_equal
- output_IndivProperties_none
- output_IndivProperties_privateinterv
- output_IndivProperties_public
- output_MDR_IndivProperties_noMDR
- output_MDR_IndivProperties
- output_default
- output
- 1001_TB_multinode_SEAsia_HLfit
- output
- 100_OneMalariaIndividual_SingleAntigen
- output
- 101_OneMalariaIndividual_MultipleAntigens
- output
- 102_OneMalariaIndividual_MultipleSwitchingAntigens
- output
- 103_OneMalariaIndividual_MultipleSwitchingAntigensSuperInfection
- output
- 10_Vector_Namawala_Oviposition
- output
- 110_Namawala_Production_Burnin
- output
- 111_Namawala_Immune_Initialization
- output
- 11_Vector_Namawala_Larvicides
- output
- 12_Malaria_Namawala_LargeVectorCampaign
- output
- 13_Generic_Seattle_SingleCore
- output
- 18_Vector_Namawala_Indoor_IRSOnly
- output
- 19_Vector_Namawala_Indoor_4Interventions
- output
- 1_Generic_Seattle_MultiNode
- output
- 20_Vector_Namawala_IRSOnly
- output
- 21_Vector_Namawala_4Interventions
- output
- 22_Malaria_Namawala_HousingModAt540
- output
- 23_Generic_Namawala
- output
- 24_Malaria_Garki
- output
- 25_Vector_Madagascar
- output
- 26_Vector_Garki
- output
- 27_Vector_Sandbox
- output
- 28_Malaria_Sandbox
- output
- 29_TB_Seattle_HTI_HSB_Drugs
- output
- 31_TB_Seattle_BirthTriggered_BCG_Calendar
- output
- 32_TB_Seattle_Diagnostic_Drugs
- output
- 34_Malaria_Namawala_Drugs
- output
- 36_Vector_Release_Wolbachia_Females_Individual
- output
- 37_Vector_Release_Sterile_Male_Cohort
- output
- 38_Malaria_Namawala_HousingModAt540_WithDeaths
- output
- 39_Vector_Namawala_HostSeekingTrap
- output
- 40_Malaria_Namawala_LargeVectorCampaign_StrainGenerator
- output
- 41_Malaria_Default_Geography
- output
- 43_Vector_Garki_MultiCore_VectorMigration
- output
- 44_Custom_Reporter_Demo
- output
- 45_Vector_An_farauti_IRS
- output
- 46_Vector_An_arabiensis_MultipleHabitats
- output
- 47_Vector_An_arabiensis_MultipleHabitats_Oviposition
- output
- 48_Generic_Seattle_SingleCore_Zoonosis
- output
- 50_Airborne_Namawala
- output
- 51_Vector_Namawala_SugarTrap_WeatherDependentFeed
- output
- 52_Vector_Namawala_Cohort_WeatherDependentFeed
- output
- 53_Vector_Release_HEGs
- output
- 54_Vector_Release_Wolbachia
- output
- 55_Malaria_Strain_Tracking
- output
- 56_Vector_InsectKillingFence
- output
- 57_Malaria_Namawala_Drugs_PkPd
- output
- 58_Vector_Release_HEGs_multipuddle
- output
- 59_Generic_Individual_Properties
- demog
- output
- 5_Vector_Namawala_SugarTrap_EveryFeedFeed
- output
- 61_TB_Simple
- output
- 62_TB_SmearNeg_And_SmearPos
- output
- 64_Vector_ScaleLarvalHabitat
- output
- 65_Generic_Seattle_CoverageByNode
- output
- 66_Malaria_InputEIR
- demographics
- output
- 67_Malaria_Namawala_AgeConcentrationDrugs
- 1_DRUG
- output
- DISABLE_NATURAL_MORTALITY
- output
- FULL
- output
- NO_CAMPAIGN_CONST_CLIMATE
- output
- NO_CAMPAIGN
- output
- NO_CONC_BY_AGE
- output
- VAR_1
- output
- output
- 68_Malaria_Barcode_Genetics
- output
- 69_Vector_IRS_Ivermectin
- output
- 6_Vector_Namawala_SugarTrap_EveryDayFeed
- output
- 70_TB_Seattle_Multicore
- output
- 72_DistributionOverlay
- demog
- output
- 73_Vector_AnimalFeedKill
- output
- 74_Vector_ArtificialDiet
- output
- 75_Vector_ArtificialDietHousingModification
- output
- 76_Vector_DelayedIntervention_SimpleVaccine_SimpleDiagnostic
- 77_Vector_IRSHousingModification
- output
- 78_Vector_InsectKillingFenceHousingModification
- output
- 79_Vector_Ivermectin
- output
- 80_Vector_Larvicides
- output
- 81_Vector_OutdoorRestKill
- output
- 82_Vector_OvipositionTrap
- output
- 83_Vector_ScreeningHousingModification
- output
- 84_Vector_SimpleHousingModification
- output
- 85_Vector_SpaceSpraying
- output
- 86_Vector_SimpleIndividualRepellent
- output
- 87_Vector_SpatialRepellent
- output
- 88_Vector_SpatialRepellentHousingModification
- output
- 89_Generic_SimpleImmunoglobulin
- output
- 8_Vector_Namawala_SugarTrap_EmergeFeed
- output
- 90_Generic_Namawala_Climate_Constant
- output
- 91_Generic_Namawala_Climate_Data
- output
- 92_Generic_Namawala_Property_Restrictions_NLHTI
- output
- 93_Generic_Namawala_DelayedIntervention
- output
- 94_Generic_Intervention_SimpleDiagnostic
- output
- 95_Malaria_Intervention_RTSSVaccine
- output
- 96_Vector_DrivingYHEGs
- output
- 9_Vector_Namawala_SugarTrap_NoFeed
- output
- HIV
- 10_HIV_SigmoidByYearAndSex
- output
- 11_HIV_FixedDelayUptakeLoop
- output
- 12_HIV_CascadeOfCare
- output
- 13_HIV_Muxer
- output
- 14_HIV_Mortality
- output
- 15_HIV_StiCoInfection
- output
- 16_HIV_CD4_Diagnostic
- output
- 17_HIV_Age_Diagnostic
- output
- 18_PMTCT
- output
- 19_HIV_ViralSuppression
- output
- 1_HIV_ARTBasic
- output
- 26_HIV_All_Rel_Types_Assortivity_ReceivedResults
- output
- 27_HIV_All_Rel_Types_Assortivity_STI_CoInfection
- output
- 28_HIV_All_Rel_Types_Assortivity_TestedPositive
- output
- 29_HIV_All_Rel_Types_Assortivity_HIV
- output
- 2_HIV_Property_Dependent_ART
- output
- 30_HIV_DrawBlood
- output
- 31_HIV_IsPostDebut
- output
- 32_HIV_ARTStagingByCD4Diagnostic
- output
- 33_HIV_ARTStagingCD4AgnosticDiagnostic
- output
- 34_HIV_EighteenMonths
- output
- 35_HIV_Delayed_Intervention
- output
- 36_HIV_Risk_Groups
- output
- 37_HIV_Risk_Groups_Property_Changer
- output
- 38_HIV_Risk_Stratification
- output
- 39_HIV_CD4_ART_Dropout
- output
- 3_HIV_Relationship_Duration_Validation
- output
- 40_HIV_CD4_Heterogeneity
- output
- 41_HIV_HIVSimpleDiagnostic
- output
- 42_HIV_CoC_TriggerStrings
- output
- 4_HIV_Individuals
- output
- 5_HIV_Distributions
- output
- 6_HIV_Transmission
- output
- 7_HIV_RandomChoice
- output
- 9_HIV_PiecewiseByYearAndSex
- output
- input
- STI
- 101_MaleCircumcision
- output
- 102_STIBarrier
- output
- 103_STIBarrierLogistic
- output
- 10_STI_Transitory_Hi_Formation_Rate
- output
- 11_STI_Transitory_Concurrent
- output
- 12_STI_Transitory_Concurrent_JustMales
- output
- 13_STI_Marital_Only_No_Disease
- output
- 14_STI_Informal_Only_No_Disease
- output
- 15_STI_Transitory_Only_No_Disease
- output
- 16_STI_Transitory_Concurrent_JustFemales
- output
- 17_STI_Transitory_Concurrent_Max
- output
- 18_STI_Marital_Concurrent
- output
- 19_STI_Marital_Concurrent_JustMales
- output
- 1_STI_Trivial
- output
- 20_STI_Marital_Concurrent_JustFemales
- output
- 21_STI_Marital_Concurrent_Max
- output
- 22_STI_Informal_Concurrent
- output
- 23_STI_Informal_Concurrent_JustMales
- output
- 24_STI_Informal_Concurrent_JustFemales
- output
- 25_STI_Informal_Concurrent_Max
- output
- 26_STI_Marital_Plus_Informal
- output
- 27_STI_Marital_Informal_Concurrent
- output
- 28_STI_Marital_Plus_Transitory
- output
- 29_STI_Marital_Transitory_Concurrent
- output
- 2_STI_Marital_Only
- output
- 30_STI_Informal_Plus_Transitory
- output
- 31_STI_Informal_Transitory_Concurrent
- output
- 32_Male_Female_Parity_Infectivity
- output
- 33_STI_Marital_Condoms
- output
- 34_STI_Informal_Condoms
- output
- 35_STI_Transitory_Condoms
- output
- 36_STI_Trivial_ReportRelationshipStart
- output
- 37_STI_Trivial_ReportRelationshipEnd
- output
- 38_STI_Trivial_ReportTransmission
- output
- 39_STI_Trivial_ReportCoitalActs
- output
- 3_STI_Informal_Only
- output
- 40_STI_Trivial_All_Reporters
- output
- 41_STI_Marital_Hi_Coinf_Factor
- output
- 42_STI_Marital_No_Coinf_Factor
- output
- 43_STI_Marital_Concurrent_Max_Mortality
- output
- 44_STI_PFA_Report
- output
- 45_STI_Cross_Report_Validation
- output
- 46_STI_All_Rel_Types_Plus_Births_Deaths_PFA_Freq
- output
- 47_STI_Condom_Intervention
- output
- 48_STI_Event_Lists
- output
- 49_STI_Transitory_Only_Assortivity_STI
- output
- 4_STI_Transitory_Only
- output
- 50_STI_Transitory_Only_Assortivity_Props
- output
- 51_STI_Transitory_Only_Assortivity_Prop_Locations
- output
- 52_STI_All_Rel_Types_Assortivity_Prop_Location_Matrix
- output
- 53_Simplified_PFA
- figs
- output
- 54_Non_Square_PFA
- output
- 55_STI_IsPostDebut
- output
- 56_STI_StiCoInfection
- output
- 5_STI_All_Rel_Types_Plus_Births_Deaths
- output
- 6_STI_Marital_Hi_CARM
- output
- 7_STI_Informal_Hi_CARI
- output
- 8_STI_Transitory_Hi_CART
- output
- 9_STI_Transitory_Hi_CART_Short_Lengths
- output
- Scenarios
- Generic
- 01_SIR
- output
- 02_SIR_Vaccinations
- A_BaselineOutbreak
- output
- B_Vaccinations
- output
- C_TargetedVaccinations
- output
- 03_SEIR
- output
- 04_SEIR_VitalDynamics
- output
- 05_SIRS
- output
- 06_SEIRS
- output
- 07_SI
- output
- 08_SIS
- output
- 09_DensityScaling
- output
- script
- 10_Zoonosis
- output
- HINT
- 01_RiskGroups
- output
- 02_SchoolClosure
- output
- 03_AgeAndAccess
- A_BaselineOutbreak
- output
- B_AgeTargetedVaccine
- output
- C_AccessTargetedVaccine
- output
- 04_WAPertussis
- A_BaselineOutbreak
- output
- B_TargetVaccineRefusers
- output
- plotting
- 05_SeattleCommuting
- output
- script
- InputFiles
- STIAndHIV
- 01_STI_Network
- A_Welcome_to_STI_SIM
- figs
- output
- B_Sexual_Debut
- figs
- output
- C_Choice_Of_Partner_Age
- figs
- output
- D_Relationship_Types_and_Durations
- figs
- output
- E_Concurrency_Independent
- RateRatio10
- output
- RateRatio1
- output
- SmallNetworkWithConcurrency
- output
- SmallNetworkWithoutConcurrency
- output
- figs
- G_Partner_Choice_By_Age
- figs
- output
- H_Risk_Groups
- figs
- output
- I_Coital_Dilution
- figs
- output
- 02_HIV_Specific_Biology
- A_Baseline_Disease_Progression
- figures
- output
- B_Survival_Time_for_Children
- figures
- output
- C_Survival_Time_for_Adults
- figures
- output
- D_CD4_Count_and_WHO_Stage
- figures
- output
- E_CD4_Count_at_Seroconversion
- figures
- output
- F_Survival_Time_on_ART
- figures
- output
- G_Reconstitution_of_CD4
- Heterogeneous
- output
- Homogeneous
- output
- figures
- H_CD4_During_Treatment_Interruption
- Heterogeneous
- output
- Homogeneous
- output
- figures
- helper_functions_for_Matlab_plots
- 03_Transmission
- A_Base_Infectivity_and_Coital_Rate
- figs
- output
- B_Effect_of_VMMC
- figs
- output
- C_Effect_of_ART
- figs
- output
- D_Effect_of_Condoms
- figs
- output
- E_Effect_of_STI_CoInfection
- figs
- output
- F_PrEP_and_Vaccines
- figs
- output
- G_Vertical_Transmission
- figs
- output
- 04_Health_Care
- 4_1_b_and_c_Property_Restriction
- RestrictAtEventCoordinator
- output
- RestrictAtNodeLevelHealthTriggeredIV
- output
- 4_1_e_CascadeState_and_AbortState
- output
- 4_2_2_c_ART_Eligibility
- figs
- output
- 4_2_4_c_HIVMuxer
- output
- 4_3_Health_Care_Model_Baseline
- PMTCT
- figures
- output
- 05_Intervention_Examples
- 1a_MaleCircumcision_at_2020
- output
- 1b_MaleCircumcision_at_2020_AgeTargeted
- output
- 1c_MaleCircumcision_Continuous
- output
- 1d_MaleCircumcision_at_Age_18
- output
- 1e_MaleCircumcision_After_Negative_HIV_Test_Post2020
- output
- 1f_IncreasedTesting_and_MaleCircumcision_Starting_2020
- output
- 2a_UniversalART
- output
- 2b_UniversalART_Increased_LTFU_6mo_CD4_500
- output
- 2c_UniversalART_Increased_LTFU_CD4_500
- output
- 2d_UniversalART_for_F35_M40
- output
- 3a_TestingDay_at_2020
- output
- 3b_HCTExpansion_at_2020
- output
- 3c_AnnualCommunityTest_Starting_2020
- output
- 3d_AnnualCommunityTest_WithStaging_Starting_2020
- output
- 3e_AnnualCommunityTest_WithStaging_DelayToPresentation_Starting_2020
- output
- 4a_ARTRetention_Depends_on_Time_CD4_Demographics
- output
- 4b_ImprovedRetention_To_BloodDraw
- output
- 4c_ImprovedRetention_To_BloodDraw_TimeVarying
- output
- 4d_ImprovedRetention_PreART_and_ART
- output
- 5a_ImprovedRetention_OnART
- output
- 5b_ImprovedReinitiation_FindPreviouslyLost
- output
- 6a_ReduceDelays_Lossy
- output
- 6b_ReduceDelays_Lossless
- output
- 7a_HIVProphylaxis_Uniform_Lifelong_Protection_F_15to49
- output
- 7b_HIVProphylaxis_Heterogeneous_Adherence_or_Efficacy_F_15to49
- output
- 7c_HIVProphylaxis_LongActingInjectable_F_15to49
- output
- Scripts
- HIV
- figs
- TB
- 01_BasicModel
- A_SEIR
- output
- B_Presentation
- output
- C_Presymptomatic
- output
- D_Progression
- output
- 02_AgeDependentImmunity
- A_Lifelong
- output
- B_Waning
- output
- C_Vaccines
- output
- 03_HealthSystems
- A_MultipleSystems
- output
- B_NoneToPublic
- output
- C_PrivateToPublic
- output
- D_SystemImprovement
- output
- 04_CascadeOfCare
- A_PassiveCaseFinding
- output
- B_ACF
- output
- 05_MDR
- A_Acquired
- output
- B_Transmitted
- output
- C_IneffectiveTreatment
- output
- D_SecondLineDrugs
- output
- 06_PopulationBurnIn
- A_SteadyState
- output
- B_PrivateToPublic
- output
- VectorAndMalaria
- 01_A_Namawala3Vectors_lowEIR
- output
- 01_B_Namawala3Vectors_highEIR
- output
- 02_Namawala_Full_Malaria_Model
- output
- 03_A_Namawala_Vector
- output
- 03_B_Muheza_Vector
- output
- 03_C_Garki_single_node_Vector
- output
- 04_Madagascar_Vector
- 05_Namawala_Vector_ITNs
- output
- 06_Namawala_Vector_ITNsPEV
- output
- 07_Namawala_Vector_SSV
- output
- 08_Garki_IRSMDA
- output
- 09_Namawala_Vector_SugarBaitedTraps
- output
- 10_InsectKillingFence
- output
- 11_MultipleLarvalHabitats
- output
- TB_10_LatentFast_SmearPos
- output
- TB_11_LatentFast_SmearNeg
- output
- TB_12_LatentFast_Extrapulm
- output
- TB_13_LatentFast_ActivePresymptomatic
- output
- TB_14_LatentSlow_SmearPos_Relapse
- output
- TB_14b_LatentSlow_SmearPos_Relapse_NodeHTIPostRelapse
- output
- TB_15_LatentSlow_SmearNeg_Inactivation
- output
- TB_16_LatentSlow_Extrapulm_Clearance
- output
- TB_17_LatentSlow_ActivePresymptomatic
- output
- TB_18_LatentFast_NaturalCure
- output
- TB_19_LatentFast_ActivePresymp_NaturalCure
- output
- TB_1_MDR_evolution
- output
- TB_20_LatentFast_ActiveSmearpos_NaturalCure
- output
- TB_21_LatentFast_SmearPos_NaturalInactivation
- output
- TB_22_LatentFast_SmearPos_DiseaseMortality
- output
- TB_23_LatentFast_SmearPos_ImmuneLoss
- output
- TB_27_nodeHTI_ActiveSymptomatic
- output
- TB_28_nodeHTI_ActivePresymptomatic
- output
- TB_29_nodeHTI_PendingRelapse
- output
- TB_2_MDR_transmission_only
- output
- TB_2b_MDR_transmission_mixed
- output
- TB_2c_MDR_transmission_mixed_reducedfitness
- output
- TB_30_HSB
- output
- TB_32_HSBUpdate
- output
- TB_33_DiagnosticTreatNeg
- output
- TB_34_GroupCoordinator
- output
- TB_35_NodeHTIScaleUpSwitch_PhaseInOnly
- output
- TB_35b_NodeHTIScaleUpSwitch_PhaseOutandIn
- output
- TB_3_Relapse_after_tx
- output
- TB_40_SEIR_Presymptomatic_Exposed
- output
- TB_41_SEIR_Presymptomatic_Infectious
- output
- TB_4_PropertyChanger_Hospital2CDC
- output
- TB_50_scenariotutorial
- ActivePresymptomatic
- output
- ActiveSymptomaticExtrapulm
- output
- ActiveSymptomaticSmearNegReducedR0
- output
- ActiveSymptomaticSmearNeg
- output
- DiseaseDuration
- output
- LatentFastAndSlow
- output
- baseline
- output
- TB_55_scenariotutorial_MDR
- AcquiredMDR
- output
- AcquiredandTransmittedMDR
- output
- IneffectiveRetreatmentforMDRTB
- output
- MDRDiagnosticandSecondLineDrugsforMDRTB
- output
- TransmittedMDR
- output
- TB_5a_CalendarIV_delayedTreatment
- output
- TB_5b_BirthTriggeredIV_BCG
- output
- TB_6_OutbreakIndividual
- output
- TB_7b_Diagnostic_smearPositive
- output
- TB_7c_Diagnostic_MDR
- TB
- ActiveDiagnostic
- output-one-day-latent
- HTIV-Scaleup
- output_scaleup_property
- MDRDiagnostic
- output_mdr-fiveProperty
- output_mdr
- SLDDiagnostic
- output-sld-fiveProperty
- output-sld-neg-config
- SmearDiagnostic
- output-smear-diagnostic
- demographics
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