Incubation#

The following parameters determine the characteristics of the incubation period.

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

Incubation_Period_Constant

float

0

3.40282E+38

-1

The incubation period, in days, to use for all individuals when Incubation_Period_Distribution is set to CONSTANT_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "CONSTANT_DISTRIBUTION",
    "Incubation_Period_Constant": 8
}

Incubation_Period_Distribution

enum

NA

NA

NOT_INITIALIZED

The distribution type to use for assigning the incubation period to each individual in the population. Each individual’s value is a random draw from the distribution.

Possible values are:

NOT_INITIALIZED

No distribution set.

CONSTANT_DISTRIBUTION

Use the same value for each individual. Set Incubation_Period_Constant.

UNIFORM_DISTRIBUTION

Use a uniform distribution with a given minimum and maximum. Set Incubation_Period_Max and Incubation_Period_Min.

GAUSSIAN_DISTRIBUTION

The distribution is Gaussian (or normal). Values are resampled to ensure >= 0. Set Incubation_Period_Gaussian_Mean and Incubation_Period_Gaussian_Std_Dev.

EXPONENTIAL_DISTRIBUTION

The distribution is exponential with a given mean. Set Incubation_Period_Exponential.

WEIBULL_DISTRIBUTION

Use a Weibull distribution with a given shape and scale. Set Incubation_Period_Kappa and Incubation_Period_Lambda.

LOG_NORMAL_DISTRIBUTION

Use a log-normal distribution with a given mean and standard deviation of the natural log. Set Incubation_Period_Log_Normal_Mu and Incubation_Period_Log_Normal_Sigma.

POISSON_DISTRIBUTION

Use a Poisson distribution with a given mean. Set Incubation_Period_Poisson_Mean.

DUAL_CONSTANT_DISTRIBUTION

Use a distribution where some individuals are set to a value of zero and the rest to a given value. Set Incubation_Period_Proportion_0 and Peak_2_Value. This distribution does not use the parameters set for CONSTANT_DISTRIBUTION.

DUAL_EXPONENTIAL_DISTRIBUTION

Use two exponential distributions with given means. Set Incubation_Period_Mean_1, Incubation_Period_Mean_2, and Incubation_Period_Proportion_1. This distribution does not use the parameters set for DUAL_EXPONENTIAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "GAUSSIAN_DISTRIBUTION",
    "Incubation_Period_Gaussian_Mean": 8,
    "Incubation_Period_Gaussian_Std_Dev": 1.5
}

Incubation_Period_Exponential

float

0

3.40282E+38

-1

The mean incubation period, in days, when Incubation_Period_Distribution is set to EXPONENTIAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "EXPONENTIAL_DISTRIBUTION",
    "Incubation_Period_Exponential": 4.25
}

Incubation_Period_Gaussian_Mean

float

0

3.40282E+38

-1

The mean of the incubation period, in days, when Incubation_Period_Distribution is set to GAUSSIAN_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "GAUSSIAN_DISTRIBUTION",
    "Incubation_Period_Gaussian_Mean": 8,
    "Incubation_Period_Gaussian_Std_Dev": 1.5
}

Incubation_Period_Gaussian_Std_Dev

float

1.17549E-38

3.40282E+38

-1

The standard deviation of the incubation period, in days, when Incubation_Period_Distribution is set to GAUSSIAN_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "GAUSSIAN_DISTRIBUTION",
    "Incubation_Period_Gaussian_Mean": 8,
    "Incubation_Period_Gaussian_Std_Dev": 1.5
}

Incubation_Period_Kappa

float

1.17549E-38

3.40282E+38

-1

The shape value for the incubation period, in days, when Incubation_Period_Distribution is set to WEIBULL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "WEIBULL_DISTRIBUTION",
    "Incubation_Period_Kappa": 0.9,
    "Incubation_Period_Lambda": 1.5
}

Incubation_Period_Lambda

float

1.17549E-38

3.40282E+38

-1

The scale value for the incubation period, in days, when Incubation_Period_Distribution is set to WEIBULL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "WEIBULL_DISTRIBUTION",
    "Incubation_Period_Kappa": 0.9,
    "Incubation_Period_Lambda": 1.5
}

Incubation_Period_Log_Normal_Mu

float

-3.40282e+38

1.70141e+38

3.40282e+38

The mean of the natural log of the incubation period, in days, when Incubation_Period_Distribution is set to LOG_NORMAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "LOG_NORMAL_DISTRIBUTION",
    "Incubation_Period_Log_Normal_Mu": 4,
    "Incubation_Period_Log_Normal_Sigma": 1
}

Incubation_Period_Log_Normal_Sigma

float

1.17549E-38

3.40282E+38

1

The standard deviation of the natural log of the incubation period, in days, when Incubation_Period_Distribution is set to LOG_NORMAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "LOG_NORMAL_DISTRIBUTION",
    "Incubation_Period_Log_Normal_Mu": 4,
    "Incubation_Period_Log_Normal_Sigma": 1
}

Incubation_Period_Max

float

0

3.40282E+38

-1

The maximum incubation period, in days, when Incubation_Period_Distribution is set to UNIFORM_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "UNIFORM_DISTRIBUTION",
    "Incubation_Period_Min": 2,
    "Incubation_Period_Max": 7
}

Incubation_Period_Mean_1

float

1.17549E-38

3.40282E+38

-1

The mean of the first exponential distribution, in days, when Incubation_Period_Distribution is set to DUAL_EXPONENTIAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
    "Incubation_Period_Mean_1": 4,
    "Incubation_Period_Mean_2": 12,
    "Incubation_Period_Proportion_1": 0.2
}

Incubation_Period_Mean_2

float

1.17549E-38

3.40282E+38

-1

The mean of the second exponential distribution, in days, when Incubation_Period_Distribution is set to DUAL_EXPONENTIAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
    "Incubation_Period_Mean_1": 4,
    "Incubation_Period_Mean_2": 12,
    "Incubation_Period_Proportion_1": 0.2
}

Incubation_Period_Min

float

0

3.40282E+38

-1

The minimum incubation period, in days, when Incubation_Period_Distribution is set to UNIFORM_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "UNIFORM_DISTRIBUTION",
    "Incubation_Period_Min": 2,
    "Incubation_Period_Max": 7
}

Incubation_Period_Peak_2_Value

float

0

3.40282E+38

-1

The incubation period value, in days, to assign to the remaining individuals when Incubation_Period_Distribution is set to DUAL_CONSTANT_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "DUAL_CONSTANT_DISTRIBUTION",
    "Incubation_Period_Proportion_0": 0.25,
    "Incubation_Period_Peak_2_Value": 5
}

Incubation_Period_Poisson_Mean

float

0

3.40282E+38

-1

The mean of the incubation period, in days, when Incubation_Period_Distribution is set to POISSON_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "POISSON_DISTRIBUTION",
    "Incubation_Period_Poisson_Mean": 5
}

Incubation_Period_Proportion_0

float

0

1

-1

The proportion of individuals to assign a value of zero days incubation when Incubation_Period_Distribution is set to DUAL_CONSTANT_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "DUAL_CONSTANT_DISTRIBUTION",
    "Incubation_Period_Proportion_0": 0.25,
    "Incubation_Period_Peak_2_Value": 5
}

Incubation_Period_Proportion_1

float

0

1

-1

The proportion of individuals in the first exponential distribution when Incubation_Period_Distribution is set to DUAL_EXPONENTIAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
    "Incubation_Period_Mean_1": 4,
    "Incubation_Period_Mean_2": 12,
    "Incubation_Period_Proportion_1": 0.2
}

Symptomatic_Infectious_Offset

float

-3.40282e+38

3.40282e+38

3.40282e+38

Amount of time, in days, after the infectious period starts that symptoms appear. Negative values imply an individual is symptomatic before infectious. If this offset is greater than the infectious duration, the infection will not be symptomatic. For example, if Incubation_Period_Constant is set to 10 and Symptomatic_Infectious_Offset is set to 4, then an infected person would become symptomatic 14 days after transmission.

 
{
    "Infectious_Period_Distribution": "CONSTANT_DISTRIBUTION",
    "Symptomatic_Infectious_Offset": 4,
    "Incubation_Period_Constant": 10
}