emodpy_hiv package

Subpackages

• emodpy_hiv.campaign package
  • Submodules
    • emodpy_hiv.campaign.cascade_of_care module
      • CustomEvent
      • CascadeState
      • timestep_from_year()
      • convert_time_value_map()
      • seed_infections()
      • add_csw()
      • add_post_debut_coinfection()
      • add_pmtct()
      • add_traditional_male_circumcision()
      • add_vmmc_reference_tracking()
      • add_historical_vmmc_nchooser()
      • add_health_care_testing()
      • add_ART_cascade()
      • add_state_TestingOnANC()
      • add_state_TestingOnChild6w()
      • add_state_HCTUptakeAtDebut()
      • add_state_HCTUptakePostDebut()
      • add_state_HCTTestingLoop()
      • add_state_TestingOnSymptomatic()
      • add_state_ARTStagingDiagnosticTest()
      • add_state_ARTStaging()
      • add_state_LinkingToPreART()
      • add_state_OnPreART()
      • add_state_LinkingToART()
      • add_state_OnART()
      • add_state_LostForever()
    • emodpy_hiv.campaign.common module
      • CommonInterventionParameters
      • PropertyRestrictions
      • TargetGender
      • TargetDemographicsConfig
      • RepetitionConfig
      • ValueMap
      • NChooserTargetedDistributionHIV
    • emodpy_hiv.campaign.distributor module
      • add_intervention_scheduled()
      • add_intervention_triggered()
      • add_intervention_nchooser_df()
      • add_intervention_reference_tracking()
    • emodpy_hiv.campaign.event_coordinator module
      • StandardEventCoordinator
      • NChooserEventCoordinatorHIV
      • ReferenceTrackingEventCoordinatorTrackingConfig
    • emodpy_hiv.campaign.individual_intervention module
      • ARTDropout
      • AgeDiagnostic
      • AntiretroviralTherapy
      • AntiretroviralTherapyFull
      • CD4Diagnostic
      • CoitalActRiskFactors
      • FemaleContraceptive
      • HIVARTStagingByCD4Diagnostic
      • HIVARTStagingCD4AgnosticDiagnostic
      • HIVDrawBlood
      • HIVMuxer
      • HIVPiecewiseByYearAndSexDiagnostic
      • HIVRandomChoice
      • HIVRapidHIVDiagnostic
      • HIVSigmoidByYearAndSexDiagnostic
      • IVCalendar
      • InterventionForCurrentPartners
      • MaleCircumcision
      • ModifyStiCoInfectionStatus
      • PMTCT
      • RangeThreshold
      • STIBarrier
      • STIIsPostDebut
      • SetSexualDebutAge
      • Sigmoid
      • StartNewRelationship
      • BroadcastEvent
      • BroadcastEventToOtherNodes
      • ControlledVaccine
      • DelayedIntervention
      • IndividualImmunityChanger
      • IndividualNonDiseaseDeathRateModifier
      • MigrateIndividuals
      • MultiEffectBoosterVaccine
      • MultiEffectVaccine
      • MultiInterventionDistributor
      • OutbreakIndividual
      • PropertyValueChanger
      • SimpleBoosterVaccine
      • SimpleVaccine
      • StandardDiagnostic
    • emodpy_hiv.campaign.node_intervention module
      • MultiNodeInterventionDistributor
      • BroadcastNodeEvent
      • ImportPressure
      • MigrateFamily
      • NodePropertyValueChanger
      • Outbreak
    • emodpy_hiv.campaign.waning_config module
      • AbstractWaningConfig
      • BaseWaningConfig
      • Constant
      • MapLinear
      • MapPiecewise
      • RandomBox
      • MapLinearAge
      • MapLinearSeasonal
      • Box
      • BoxExponential
      • Exponential
      • Combo
• emodpy_hiv.countries package
  • Subpackages
    • emodpy_hiv.countries.converting package
      • Submodules
    • emodpy_hiv.countries.un_world_pop_data package
    • emodpy_hiv.countries.zambia package
      • Submodules
• emodpy_hiv.demographics package
  • Submodules
    • emodpy_hiv.demographics.DemographicsTemplates module
      • get_society_dict()
    • emodpy_hiv.demographics.assortivity module
      • Assortivity
    • emodpy_hiv.demographics.concurrency_parameters module
      • ConcurrencyParameters
    • emodpy_hiv.demographics.condom_usage_parameters module
      • CondomUsageParameters
    • emodpy_hiv.demographics.hiv_demographics module
      • HIVDemographics
    • emodpy_hiv.demographics.hiv_node module
      • HIVNode
    • emodpy_hiv.demographics.infer_natural_mortality module
      • infer_natural_mortality()
      • mortality_read_infer_plot()
      • mortality_read_infer_plot_app()
    • emodpy_hiv.demographics.library module
      • set_concurrency_parameters()
      • set_pair_formation_parameters()
      • set_relationship_parameters()
      • set_initial_risk_distribution()
      • set_initial_cascade_state_distribution()
      • set_initial_health_care_accessibility_distribution()
    • emodpy_hiv.demographics.pair_formation_parameters module
      • PairFormationParameters
    • emodpy_hiv.demographics.relationship_parameters module
      • RelationshipParameters
    • emodpy_hiv.demographics.relationship_types module
      • RelationshipTypes
    • emodpy_hiv.demographics.risk_groups module
      • RiskGroups
    • emodpy_hiv.demographics.society module
      • Society
    • emodpy_hiv.demographics.un_world_pop module
      • extract_population_by_age()
      • extract_population_by_age_for_ingest_form()
      • extract_population_by_age_and_distribution()
      • extract_fertility()
      • extract_mortality()
    • emodpy_hiv.demographics.year_age_rate module
      • YearAgeRate
      • plot()
• emodpy_hiv.plotting package
  • Submodules
    • emodpy_hiv.plotting.channel_report module
      • ChannelReport
    • emodpy_hiv.plotting.helpers module
      • get_filenames()
    • emodpy_hiv.plotting.plot_a_vs_b module
      • plot_csv_a_vs_b()
    • emodpy_hiv.plotting.plot_hiv_by_age_and_gender module
      • create_title()
      • create_y_axis_name()
      • extract_population_data()
      • extract_population_data_multiple_ages()
      • extract_population_data_by_stratification()
      • extract_population_data_by_stratification_for_dir()
      • create_df_for_plot_by_stratification()
      • plot_population_for_dir()
      • plot_population_by_gender()
      • plot_population_by_ip()
      • plot_columns()
      • plot_circumcision_by_age()
      • extract_population_data_multiple_ages_for_dir()
      • create_df_for_plot_by_age()
      • base_plot_by_age()
      • plot_onART_by_age()
      • plot_population_by_age()
      • plot_vmmc_by_age()
      • plot_population_by_age_vs_unworld_pop()
      • plot_risk()
      • plot_vmmc_for_dir()
      • plot_prevalence_for_dir()
      • plot_risk_zambia()
    • emodpy_hiv.plotting.plot_inset_chart module
      • get_raw_color()
      • get_color_name()
      • get_list_of_channels()
      • create_title_string()
      • get_data_from_directory()
      • plot_subplot()
      • plot_data()
      • plot_inset_chart()
    • emodpy_hiv.plotting.plot_inset_chart_mean_compare module
      • calculate_mean()
      • plot_mean()
    • emodpy_hiv.plotting.plot_relationship_end module
      • extract_data_for_relationship()
      • plot_relationship_duration_histogram()
      • plot_relationship_duration_histogram_with_expected()
    • emodpy_hiv.plotting.plot_relationship_start module
      • extract_assortivity_risk()
      • plot_relationship_assortivity_risk()
      • plot_relationship_assortivity_risk_all()
    • emodpy_hiv.plotting.xy_plot module
      • create_common_x_values()
      • fill_in_y_values()
      • get_color_name()
      • get_line_style()
      • get_marker_style()
      • xy_plot()
• emodpy_hiv.reporters package
  • Submodules
    • emodpy_hiv.reporters.reporters module
      • ReportNodeDemographics
      • ReportSimulationStats
      • ReportHumanMigrationTracking
      • ReportEventCounter
      • ReportEventRecorder
      • ReportPluginAgeAtInfection
      • ReportPluginAgeAtInfectionHistogram
      • SqlReport
      • ReportNodeEventRecorder
      • ReportCoordinatorEventRecorder
      • ReportSurveillanceEventRecorder
      • InsetChart
      • SpatialReport
      • ReportHIVByAgeAndGender
      • ReportRelationshipStart
      • ReportCoitalActs
      • ReportRelationshipEnd
      • ReportTransmission
      • ReportHIVART
      • ReportHIVInfection
      • ReportHIVMortality
      • ReportRelationshipMigrationTracking
      • ReportPfaQueues
      • ReportRelationshipCensus
      • ReportFilter
      • DemographicsReport
      • PropertyReport
      • ReportInfectionDuration
      • SpatialReportChannels
      • RelationshipType
• emodpy_hiv.utils package
  • Submodules
    • emodpy_hiv.utils.config_utils module
      • non_schema_checks()
    • emodpy_hiv.utils.distributions module
      • BaseDistribution
      • ConstantDistribution
      • ExponentialDistribution
      • UniformDistribution
      • GaussianDistribution
      • PoissonDistribution
      • LogNormalDistribution
      • WeibullDistribution
      • DualConstantDistribution
      • DualExponentialDistribution
      • BimodalDistribution
    • emodpy_hiv.utils.emod_enum module
      • StrEnum
      • DistributionType
      • NodeSelectionType
      • VaccineType
      • SensitivityType
      • EventOrConfig
      • SettingType
      • PrioritizePartnersBy
      • RelationshipType
      • CondomUsageParametersType
      • TargetDiseaseState
    • emodpy_hiv.utils.targeting_config module
      • AbstractTargetingConfig
      • BaseTargetingConfig
      • HasIP
      • HasIntervention
      • IsPregnant
      • YesNoNa
      • MoreOrLess
      • OfRelationshipType
      • NumMonthsType
      • RecentlyType
      • RelationshipTerminationReasonType
      • IsCircumcised
      • IsHivPositive
      • IsOnART
      • IsPostDebut
      • HasBeenOnArtMoreOrLessThanNumMonths
      • HasMoreOrLessThanNumPartners
      • HasHadMultiplePartnersInLastNumMonths
      • HasCd4BetweenMinAndMax
      • HasRelationship

Submodules

• emodpy_hiv.country_model module
  • get_country_class()
  • Country
    • Country.country_name
    • Country.base_year
    • Country.generate_label()
    • Country.get_config_parameterized_calls()
    • Country.get_demographics_parameterized_calls()
    • Country.get_campaign_parameterized_calls()
    • Country.initialize_config()
    • Country.initialize_demographics()
    • Country.initialize_campaign()
    • Country.build_reports()
    • Country.build_config()
    • Country.build_demographics()
    • Country.build_campaign()
    • Country.load_nchooser_distribution_data()
    • Country.add_historical_vmmc_nchooser()
    • Country.add_traditional_male_circumcision()
    • Country.add_vmmc_reference_tracking()
    • Country.seed_infections()
    • Country.add_csw()
    • Country.add_post_debut_coinfection()
    • Country.add_pmtct()
    • Country.add_health_care_testing()
    • Country.add_ART_cascade()
    • Country.add_state_TestingOnANC()
    • Country.add_state_TestingOnChild6w()
    • Country.add_state_HCTUptakeAtDebut()
    • Country.add_state_HCTUptakePostDebut()
    • Country.add_state_HCTTestingLoop()
    • Country.add_state_TestingOnSymptomatic()
    • Country.add_state_ARTStagingDiagnosticTest()
    • Country.add_state_ARTStaging()
    • Country.add_state_LinkingToPreART()
    • Country.add_state_OnPreART()
    • Country.add_state_LinkingToART()
    • Country.add_state_OnART()
    • Country.add_state_LostForever()
• emodpy_hiv.download module
  • download()
• emodpy_hiv.parameterized_call module
  • ParameterizedCall
    • ParameterizedCall.labeled_hyperparameters
    • ParameterizedCall.set_labeled_hyperparameter()
    • ParameterizedCall.prepare_call()