OutbreakIndividualMalaria

The OutbreakIndividualMalaria class extends OutbreakIndividual class and allows for specifying a specific strain of infection.

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 does not permit comments, but you can add “dummy” parameters to add contextual information to your files.

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

Antigen

integer

0

10

0

The antigenic base strain ID of the outbreak infection. This must not exceed the number specified in the configuration parameter Number_Basestrains.

 
{
    "Intervention_Config": {
        "Antigen": 0,
        "Genome": 0,
        "Outbreak_Source": "PrevalenceIncrease",
        "class": "OutbreakIndividual"
    }
}

Create_Random_Genome

boolean

0

1

0

If set to true (1), then a random genome is created for the infection and the Genome_Markers parameter is not used. If set to false (0), then you must define the Genome_Markers parameter which allows you to then specify genetic components in a strain of infection.

 
{
    "OIM_Create_Random_Genome": 1
}

Genome_Markers

array of strings

NA

NA

NA

A list of the names of genome marker(s) that represent the genetic components in a strain of an infection.

 
{
    "Intervention_Config": {
        "class": "OutbreakIndividualMalaria",
        "Antigen": 0,
        "Genome_Markers": [
            "D6",
            "W2"
        ]
    }
}

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,
        "class": "OutbreakIndividual",
        "Ignore_Immunity": 0
    }
}

Incubation_Period_Override

integer

-1

2.15E+0

-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.

 
{
    "Incubation_Period_Override": 0
}

{
    "Intervention_Config": {
        "class": "OutbreakIndividualMalaria",
        "Antigen": 0,
        "Genome_Markers": [ "D6", "W2" ]
        }
}