General disease#

The following parameters determine general disease characteristics.

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.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Enable_Strain_Tracking

boolean

0

1

0

Enable an association of an infection with a specified strain, defined by unique integers for a clade and a genome.

For infections distributed through interventions, you specify clade and genome values using the Clade and Genome parameters with the Outbreak and OutbreakIndividual intervention classes in the campaign file.

When using an initial prevalence distribution, you specify clade and genome values using the InitialPrevalenceStrains parameter as part of IndividualAttributes in the demographics file.

When Enable_Strain_Tracking is set to false (0) or absent, all infections are associated with a single strain that has clade and genome identity (0, 0).

When Enable_Strain_Tracking is set to true (1) then both Number_of_Clades and Log2_Number_of_Genomes_per_Clade parameters must be specified.

Warning

Do not set both Enable_Strain_Tracking and Enable_Infectivity_Reservoir to true (1) or Enable_Strain_Tracking and Enable_Maternal_Infection_Transmission to true (1) - as these combinations will cause an exception error.

 
{
    "Enable_Strain_Tracking": 1,
    "Log2_Number_of_Genomes_per_Clade": 8,
    "Number_of_Clades": 2
}

Log2_Number_of_Genomes_per_Clade

integer

0

24

0

The maximum number of genome combinations per clades. Used with Number_of_Clades and dependent upon Enable_Strain_Tracking enabled, set to 1.

Note

Log2_Number_of_Genomes_per_Clade is internally fixed to 0 when using Typhoid and Malaria simulations.

 
{
    "Enable_Strain_Tracking": 1,
    "Log2_Number_of_Genomes_per_Clade": 8,
    "Number_of_Clades": 2
}

Number_of_Clades

integer

1

10

1

The maximum number of distinct clades in the simulation. Used with Log2_Number_of_Genomes_per_Clade to define the strain associated with an infection. Dependent upon Enable_Strain_Tracking enabled, set to 1.

 
{
    "Enable_Strain_Tracking": 1,
    "Log2_Number_of_Genomes_per_Clade": 8,
    "Number_of_Clades": 2
}