mkdocs.yml

site_name: emodpy-hiv
site_url: https://emod.idmod.org/emodpy-hiv/
repo_name: EMOD-Hub/emodpy-hiv
repo_url: https://github.com/EMOD-Hub/emodpy-hiv/

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nav:
  - Home: index.md
  - Installation:
    - Installation: installation.md
    - Virtual environments: virtual_environments.md
  - Tutorials:
    - Overview: tutorials/overview.md
    - Setup: tutorials/setup.md
    - Input concepts: tutorials/concepts.md
    - Tutorial 1 - Run a simulation: tutorials/tutorial-1.md
    - Tutorial 2 - Add reports and plot results: tutorials/tutorial-2.md
    - Tutorial 3 - Customize with build functions: tutorials/tutorial-3.md
    - Tutorial 4 - Override the cascade of care: tutorials/tutorial-4.md
  - Software:
    - Overview: emod/software-overview.md
    - Inputs:
        - Overview: emod/software-inputs.md
        - Demographics: emod/software-demographics.md
        - Demographics overlay files: emod/software-demographics-overlay.md
        - Configuration: emod/software-configuration.md
        - Campaign: emod/software-campaign.md
        - Migration:
            - Overview: emod/software-migration.md
            - How to create migration files: emod/software-migration-creation.md
        - Load-balancing files: emod/software-load-balancing.md
    - Output reports:
        - Overview: emod/software-outputs.md
        - Plot simulation output: emod/software-plotting.md
    - Troubleshooting: emod/troubleshooting.md
    - Tips and tricks:
        - Speed up EMOD simulations: emod/software-simulation-performance.md
  - Model:
      - Overview: emod/model-overview.md
      - STI model:
          - Overview: emod/sti-model-overview.md
          - Relationships and contact networks: emod/sti-model-relationships.md
          - Transmission: emod/sti-model-transmission.md
      - HIV model:
          - Overview: emod/hiv-model-overview.md
          - Intrahost dynamics and HIV biology: emod/hiv-model-intrahost.md
          - Health care systems: emod/hiv-model-healthcare-systems.md
      - Disease outbreaks, reservoirs, and endemicity: emod/model-outbreak.md
      - Heterogeneity:
          - Overview: emod/model-heterogeneity.md
          - Population density and transmission scaling: emod/model-population-density.md
          - Individual and node properties: emod/model-properties.md
          - Geographic migration: emod/model-migration.md
      - Campaign:
          - Overview: emod/model-campaign.md
          - Targeting interventions to nodes or individuals: emod/model-targeted-interventions.md
          - Vaccination and herd immunity: emod/model-vaccination.md
          - Cascade of care: emod/model-care-cascade.md
  - HIV disease overview: emod/hiv-disease-overview.md
  - Parameters:
      - Overview: emod/parameter-overview.md
      - Demographics: emod/parameter-demographics.md
      - Configuration:
          - Overview: emod/parameter-configuration.md
          - Disease progression: emod/parameter-configuration-disease-progression.md
          - Drugs and treatments: emod/parameter-configuration-drugs.md
          - Enable or disable features: emod/parameter-configuration-enable.md
          - Geography and environment: emod/parameter-configuration-env.md
          - Immunity: emod/parameter-configuration-immunity.md
          - Incubation: emod/parameter-configuration-incubation.md
          - Infectivity and transmission: emod/parameter-configuration-infectivity.md
          - Input files: emod/parameter-configuration-input.md
          - Migration: emod/parameter-configuration-migration.md
          - Mortality and survival: emod/parameter-configuration-mortality.md
          - Output settings: emod/parameter-configuration-output.md
          - Population dynamics: emod/parameter-configuration-population.md
          - Relationships and pair formation: emod/parameter-configuration-pairs.md
          - Sampling: emod/parameter-configuration-sampling.md
          - Scalars and multipliers: emod/parameter-configuration-scalars.md
          - Simulation setup: emod/parameter-configuration-setup.md
          - Symptoms and diagnosis: emod/parameter-configuration-symptoms.md
          - Weibull distributions: emod/parameter-configuration-weibull.md
      - Campaign:
          - Overview: emod/parameter-campaign.md
          - Event coordinators:
              - Overview: emod/parameter-campaign-event-coordinators.md
              - BroadcastCoordinatorEvent: emod/parameter-campaign-event-broadcastcoordinatorevent.md
              - CalendarEventCoordinator: emod/parameter-campaign-event-calendareventcoordinator.md
              - CampaignEvent/CampaignEventByYear: emod/parameter-campaign-event-campaignevent.md
              - CommunityHealthWorkerEventCoordinator: emod/parameter-campaign-event-communityhealthworkereventcoordinator.md
              - CoverageByNodeEventCoordinator: emod/parameter-campaign-event-coveragebynodeeventcoordinator.md
              - DelayEventCoordinator: emod/parameter-campaign-event-delayeventcoordinator.md
              - IncidenceEventCoordinator: emod/parameter-campaign-event-incidenceeventcoordinator.md
              - NChooserEventCoordinator: emod/parameter-campaign-event-nchoosereventcoordinator.md
              - NChooserEventCoordinatorHIV: emod/parameter-campaign-event-nchoosereventcoordinatorhiv.md
              - NChooserEventCoordinatorSTI: emod/parameter-campaign-event-nchoosereventcoordinatorsti.md
              - ReferenceTrackingEventCoordinator: emod/parameter-campaign-event-referencetrackingeventcoordinator.md
              - ReferenceTrackingEventCoordinatorHIV: emod/parameter-campaign-event-referencetrackingeventcoordinatorhiv.md
              - ReferenceTrackingEventCoordinatorTrackingConfig: emod/parameter-campaign-event-referencetrackingeventcoordinatortrackingconfig.md
              - StandardInterventionDistributionEventCoordinator: emod/parameter-campaign-event-standardinterventiondistributioneventcoordinator.md
              - SurveillanceEventCoordinator: emod/parameter-campaign-event-surveillanceeventcoordinator.md
              - TriggeredEventCoordinator: emod/parameter-campaign-event-triggeredeventcoordinator.md
          - Node IVs:
              - Overview: emod/parameter-campaign-node-interventions.md
              - BirthTriggeredIV: emod/parameter-campaign-node-birthtriggerediv.md
              - BroadcastCoordinatorEventFromNode: emod/parameter-campaign-node-broadcastcoordinatoreventfromnode.md
              - BroadcastNodeEvent: emod/parameter-campaign-node-broadcastnodeevent.md
              - CoitalActRateChanger: emod/parameter-campaign-node-coitalactratechanger.md
              - CondomUsageProbabilityChanger: emod/parameter-campaign-node-condomusageprobabilitychanger.md
              - FirstNodeWithNodePropertyEventCoordinator: emod/parameter-campaign-node-firstnodewithnodepropertyeventcoordinator.md
              - ImportPressure: emod/parameter-campaign-node-importpressure.md
              - MigrateFamily: emod/parameter-campaign-node-migratefamily.md
              - MultiNodeInterventionDistributor: emod/parameter-campaign-node-multinodeinterventiondistributor.md
              - NodeLevelHealthTriggeredIV: emod/parameter-campaign-node-nodelevelhealthtriggerediv.md
              - NodePropertyValueChanger: emod/parameter-campaign-node-nodepropertyvaluechanger.md
              - NLHTIVNode: emod/parameter-campaign-node-nlhtivnode.md
              - Outbreak: emod/parameter-campaign-node-outbreak.md
              - RelationshipDurationChanger: emod/parameter-campaign-node-relationshipdurationchanger.md
              - RelationshipFormationRateChanger: emod/parameter-campaign-node-relationshipformationratechanger.md
          - Individual IVs:
              - Overview: emod/parameter-campaign-individual-interventions.md
              - AgeDiagnostic: emod/parameter-campaign-individual-agediagnostic.md
              - AntiretroviralTherapy: emod/parameter-campaign-individual-antiretroviraltherapy.md
              - AntiretroviralTherapyFull: emod/parameter-campaign-individual-antiretroviraltherapyfull.md
              - ARTDropout: emod/parameter-campaign-individual-artdropout.md
              - ARTMortalityTable: emod/parameter-campaign-individual-artmortalitytable.md
              - BroadcastEvent: emod/parameter-campaign-individual-broadcastevent.md
              - BroadcastEventToOtherNodes: emod/parameter-campaign-individual-broadcasteventtoothernodes.md
              - CD4Diagnostic: emod/parameter-campaign-individual-cd4diagnostic.md
              - CoitalActRiskFactors: emod/parameter-campaign-individual-coitalactriskfactors.md
              - ControlledVaccine: emod/parameter-campaign-individual-controlledvaccine.md
              - DelayedIntervention: emod/parameter-campaign-individual-delayedintervention.md
              - FemaleContraceptive: emod/parameter-campaign-individual-femalecontraceptive.md
              - HIVARTStagingByCD4Diagnostic: emod/parameter-campaign-individual-hivartstagingbycd4diagnostic.md
              - HIVARTStagingCD4AgnosticDiagnostic: emod/parameter-campaign-individual-hivartstagingcd4agnosticdiagnostic.md
              - HIVDelayedIntervention: emod/parameter-campaign-individual-hivdelayedintervention.md
              - HIVDrawBlood: emod/parameter-campaign-individual-hivdrawblood.md
              - HIVMuxer: emod/parameter-campaign-individual-hivmuxer.md
              - HIVPiecewiseByYearandSexDiagnostic: emod/parameter-campaign-individual-hivpiecewisebyyearandsexdiagnostic.md
              - HIVRandomChoice: emod/parameter-campaign-individual-hivrandomchoice.md
              - HIVRapidHIVDiagnostic: emod/parameter-campaign-individual-hivrapidhivdiagnostic.md
              - HIVSigmoidByYearAndSexDiagnostic: emod/parameter-campaign-individual-hivsigmoidbyyearandsexdiagnostic.md
              - HIVSimpleDiagnostic: emod/parameter-campaign-individual-hivsimplediagnostic.md
              - ImmunityBloodTest: emod/parameter-campaign-individual-immunitybloodtest.md
              - IndividualImmunityChanger: emod/parameter-campaign-individual-individualimmunitychanger.md
              - IndividualNonDiseaseDeathRateModifier: emod/parameter-campaign-individual-individualnondiseasedeathratemodifier.md
              - InterventionForCurrentPartners: emod/parameter-campaign-individual-interventionforcurrentpartners.md
              - IVCalendar: emod/parameter-campaign-individual-ivcalendar.md
              - MaleCircumcision: emod/parameter-campaign-individual-malecircumcision.md
              - MigrateIndividuals: emod/parameter-campaign-individual-migrateindividuals.md
              - ModifyStiCoInfectionStatus: emod/parameter-campaign-individual-modifysticoinfectionstatus.md
              - MultiEffectBoosterVaccine: emod/parameter-campaign-individual-multieffectboostervaccine.md
              - MultiEffectVaccine: emod/parameter-campaign-individual-multieffectvaccine.md
              - MultiInterventionDistributor: emod/parameter-campaign-individual-multiinterventiondistributor.md
              - OutbreakIndividual: emod/parameter-campaign-individual-outbreakindividual.md
              - PMTCT: emod/parameter-campaign-individual-pmtct.md
              - PropertyValueChanger: emod/parameter-campaign-individual-propertyvaluechanger.md
              - SetSexualDebutAge: emod/parameter-campaign-individual-setsexualdebutage.md
              - SimpleBoosterVaccine: emod/parameter-campaign-individual-simpleboostervaccine.md
              - SimpleDiagnostic: emod/parameter-campaign-individual-simplediagnostic.md
              - SimpleHealthSeekingBehavior: emod/parameter-campaign-individual-simplehealthseekingbehavior.md
              - SimpleVaccine: emod/parameter-campaign-individual-simplevaccine.md
              - StandardDiagnostic: emod/parameter-campaign-individual-standarddiagnostic.md
              - StartNewRelationship: emod/parameter-campaign-individual-startnewrelationship.md
              - STIBarrier: emod/parameter-campaign-individual-stibarrier.md
              - StiCoInfectionDiagnostic: emod/parameter-campaign-individual-sticoinfectiondiagnostic.md
              - STIIsPostDebut: emod/parameter-campaign-individual-stiispostdebut.md
          - Waning effect classes: emod/parameter-campaign-waningeffects.md
          - Targeting_Config classes: emod/parameter-campaign-targeting-config.md
          - Nodeset_Config classes: emod/parameter-campaign-nodeset-config.md
          - Builtin events: emod/parameter-campaign-event-list.md
      - Reports:
          - Overview: emod/parameter-reports-overview.md
          - General reports:
            - BinnedReport: emod/software-report-binned.md
            - DemographicsSummary: emod/software-report-demographic-summary.md
            - InsetChart: emod/software-report-inset-chart.md
            - PropertyReport: emod/software-report-property.md
            - ReportEventCounter: emod/software-report-event-counter.md
            - ReportEventRecorder: emod/software-report-event-recorder.md
            - ReportHumanMigrationTracking: emod/software-report-human-migration.md
            - ReportInfectionDuration: emod/software-report-infection-duration.md
            - ReportNodeDemographics: emod/software-report-node-demographics.md
            - ReportSimulationStats: emod/software-report-simulation-stats.md
            - SpatialReport: emod/software-report-spatial.md
            - SqlReport: emod/software-report-sql.md
          - HIV reports:
            - HIVMortality: emod/software-report-hivmort.md
            - ReportHIVART: emod/software-report-hivart.md
            - ReportHIVByAgeAndGender: emod/software-report-age-gender.md
            - ReportHIVInfection: emod/software-report-hivinfection.md
            - TransmissionReport: emod/software-report-transmission.md
          - Relationship reports:
            - RelationshipConsummated: emod/software-report-relationship-consummated.md
            - RelationshipEnd: emod/software-report-relationship-end.md
            - RelationshipStart: emod/software-report-relationship-start.md
            - ReportRelationshipCensus: emod/software-report-relationship-census.md
            - ReportRelationshipMigrationTracking: emod/software-report-relationship-migration-tracking.md
          - Error and logging files: emod/software-error-logging.md
      - Schema: emod/parameter-schema.md
  - Glossary: glossary.md
  - API reference: autoapi/
  - Related projects: https://emod.idmod.org/

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