OutbreakIndividualTBorHIV

The OutbreakIndividualTBorHIV class extends OutbreakIndividual class and allows for specifying HIV or a specific strain of infection for TB.

Note

Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false. Minimum, maximum, or default values of “NA” indicate that those values are not applicable for that parameter.

EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.

JSON format does not permit comments, but you can add “dummy” parameters to add contextual information to your files. Any keys that are not EMOD parameter names will be ignored by the model.

The table below describes all possible parameters with which this class can be configured. The JSON example that follows shows one potential configuration.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Clade

integer

0

9

0

The clade ID (Clade) of the outbreak infection. Together with the genome ID (Genome) they are a unitary object representing a strain of infection, which allows for differentiation among infections. Values for Clade may range from 0 to Number_of_Clades-1.

Intervention distribution example:

{
    "Enable_Strain_Tracking": 1,
    "Events": [
        {
            "Event_Coordinator_Config": {
                "Demographic_Coverage": 0.001,
                "Intervention_Config": {
                    "Clade": 1,
                    "Genome": 3,
                    "IgnoreImmunity": 1,
                    "class": "Outbreak"
                },
                "Target_Demographic": "Everyone",
                "class": "StandardInterventionDistributionEventCoordinator"
            },
            "Event_Name": "Outbreak",
            "Nodeset_Config": {
                "class": "NodeSetAll"
            },
            "Start_Day": 30,
            "class": "CampaignEvent"
        }
    ]
}

Genome

integer

0

16777215

0

The genome ID (Genome) of the outbreak infection. Together with the clade ID (Clade) they represent an infection as a unitary object. Values for Genome may range from -1 to 2Log2_Number_of_Genomes_per_Clade-1

Intervention distribution example:

{
    "Enable_Strain_Tracking": 1,
    "Events": [
        {
            "Event_Coordinator_Config": {
                "Demographic_Coverage": 0.001,
                "Intervention_Config": {
                    "Clade": 1,
                    "Genome": 3,
                    "IgnoreImmunity": 1,
                    "class": "OutbreakIndividualTBorHIV"
                },
                "Target_Demographic": "Everyone",
                "class": "StandardInterventionDistributionEventCoordinator"
            },
            "Event_Name": "OutbreakIndividualTBorHIV",
            "Nodeset_Config": {
                "class": "NodeSetAll"
            },
            "Start_Day": 30,
            "class": "CampaignEvent"
        }
    ]
}

Ignore_Immunity

boolean

0

1

1

Individuals will be force-infected (with a specific strain) regardless of actual immunity level when set to true (1).

 
{
    "Intervention_Config": {
        "Antigen": 0,
        "Genome": 0,
        "Infection_Type": "TB",
        "Outbreak_Source": "PrevalenceIncrease",
        "Ignore_Immunity": 0,
        "class": "OutbreakIndividualTBorHIV"
    }
}

Incubation_Period_Override

integer

-1

2147480000

-1

The incubation period, in days, that infected individuals will go through before becoming infectious. This value overrides the incubation period set in the configuration file. Set to -1 to honor the configuration parameter settings.

 
{
    "Intervention_Config": {
        "Antigen": 0,
        "Genome": 0,
        "Ignore_Immunity": 0,
        "Incubation_Period_Override": -1,
        "Infection_Type": "TB",
        "Outbreak_Source": "PrevalenceIncrease",
        "class": "OutbreakIndividualTBorHIV"
    }
}

Infection_Type

enum

NA

NA

HIV

Infection type. Possible values are:

HIV

HIV infection.

TB

TB infection.

 
{
    "Intervention_Config": {
        "Antigen": 0,
        "Genome": 0,
        "Ignore_Immunity": 0,
        "Incubation_Period_Override": -1,
        "Infection_Type": "TB",
        "Outbreak_Source": "PrevalenceIncrease",
        "class": "OutbreakIndividualTBorHIV"
    }
}

{
  "Campaign_Name": "Outbreak",
  "Events": [
    {
      "Event_Coordinator_Config": {
        "Demographic_Coverage": 0.2,
        "Intervention_Config": {
          "Infection_Type": "TB",
          "class": "OutbreakIndividualTBorHIV"
        },
        "Target_Group": "Everyone",
        "class": "StandardInterventionDistributionEventCoordinator"
      },
      "Event_Name": "Seeding the TB epidemic at time 2",
      "Nodeset_Config": {
        "class": "NodeSetAll"
      },
      "Start_Day": 2,
      "class": "CampaignEvent"
    }
  ],
  "Use_Defaults": 1
}