OutbreakIndividual#
The OutbreakIndividual intervention class introduces contagious diseases that are compatible with the simulation type to existing individuals using the individual targeted features configured in the appropriate event coordinator. To instead add new infection individuals, use Outbreak.
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 |
---|---|---|---|---|---|---|
Antigen |
integer |
0 |
10 |
0 |
The antigenic base strain ID of the outbreak infection. |
{
"Antigen": 1
}
|
Genome |
integer |
-1 |
1.67E+07 |
0 |
The genome ID 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. Set this to -1 to create a random number generator. |
Intervention distribution example: {
"Enable_Strain_Tracking": 1,
"Events": [
{
"Event_Coordinator_Config": {
"Demographic_Coverage": 0.001,
"Intervention_Config": {
"Antigen": 1,
"Genome": 3,
"IgnoreImmunity": 1,
"class": "OutbreakIndividual"
},
"Target_Demographic": "Everyone",
"class": "StandardInterventionDistributionEventCoordinator"
},
"Event_Name": "Outbreak",
"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,
"Ignore_Immunity": 0,
"class": "OutbreakIndividual"
}
}
|
Incubation_Period_Override |
integer |
-1 |
2147480000.0 |
-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. Note for HIV simulations only: If set to 0, infection is assumed to be part of an outbreak event and a random duration until death is determined. For all other simulation types: Set to -1 to honor the configuration parameter settings. |
{
"Incubation_Period_Override": 0
}
|
{
"Events": [
{
"Event_Coordinator_Config": {
"Demographic_Coverage": 0.001,
"Intervention_Config": {
"Clade": 1,
"Genome": 3,
"IgnoreImmunity": 1,
"class": "OutbreakIndividual"
},
"Target_Demographic": "Everyone",
"class": "StandardInterventionDistributionEventCoordinator"
},
"Nodeset_Config": {
"class": "NodeSetAll"
},
"Start_Day": 30,
"class": "CampaignEvent"
}
]
}