Infectivity and transmission

The following parameters determine aspects of infectivity and disease transmission. For example, how infectious individuals are and the length of time for which they remain infectious, whether the disease can be maternally transmitted, and how population density affects infectivity.

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

Acute_Duration_In_Months

float

0

5

2.9

The time since infection, in months, over which the Acute_Stage_Infectivity_Multiplier is applied to coital acts occurring in that time period.

 
{
    "Acute_Duration_In_Months": 2.9
}

AIDS_Stage_Infectivity_Multiplier

float

1

100

10

The multiplier acting on Base_Infectivity to determine the per-act transmission probability of an HIV+ individual during the AIDS stage.

 
{
    "AIDS_Stage_Infectivity_Multiplier": 8
}

ART_Reactivation_Factor

float

0

1

1

Factor for ART reducing reactivation in HIV+.

 
{
    "ART_Reactivation_Factor": 0.95
}

Base_Infectivity

float

0

1000

0.3

The base infectiousness of individuals before accounting for transmission-blocking effects of acquired immunity and/or campaign interventions.

For TB simulations, this is the base infectivity in smear-positive individuals. This value is modified by TB_Smear_Negative_Infectivity_Multiplier for smear-negative individuals.

 
{
    "Base_Infectivity": 0.5
}

CD4_Num_Steps

integer

1

2.15E+09

10

Number of time steps in CD4 forward vector for reactivation.

 
{
    "CD4_Num_Steps": 10
}

CD4_Time_Step

float

1

3.40282e+38

365

The length of steps in the CD4 longitudinal tracker.

 
{
    "CD4_Time_Step": 730
}

CoInfection_Mortality_Rate_Off_ART

float

0

3.40282e+38

0

The daily rate of death in excess to TB when coinfected with HIV off ART.

 
{
    "CoInfection_Mortality_Rate_On_ART": 0.01
}

CoInfection_Mortality_Rate_On_ART

float

0

3.40282e+38

0

The daily rate of death in excess to TB when coinfected with HIV on ART.

 
{
    "CoInfection_Mortality_Rate_On_ART": 0.003
}

Enable_Coinfection_Incidence

boolean

0

1

None

Controls whether or not coinfection incidence is enabled.

Enable_Coinfection_Mortality

boolean

0

1

None

Controls whether or not TB/HIV coinfection mortality is enabled.

Enable_Heterogeneous_Intranode_Transmission

boolean

0

1

0

Controls whether or not individuals experience heterogeneous disease transmission within a node. When set to true (1), individual property definitions and the \(\beta\) matrix must be specified in the demographics file (see NodeProperties and IndividualProperties parameters). The \(\beta\) values are multiplied with the \(\beta\) 0 value configured by Base_Infectivity.

This is used only in generic, environmental, and typhoid simulations, but must be set to false (0) for all other simulation types. Heterogeneous transmission for other diseases uses other mechanistic parameters included with the simulation type.

 
{
    "Enable_Heterogeneous_Intranode_Transmission": 1
}

Enable_Infectivity_Reservoir

boolean

0

1

0

Controls whether or not an exogeneous reservoir of infectivity will be included in the simulation and allows for the infectivity in a node to be increased additively. When set to 1 (true), the demographics parameter InfectivityReservoirSize is expected in NodeAtttributes for each node.

Warning

Do not set both Enable_Infectivity_Reservoir and Enable_Strain_Tracking to true (1) - as this combination will cause an exception error.

 
{
    "Enable_Infectivity_Reservoir": 1
}

Enable_Maternal_Infection_Transmission

boolean

0

1

0

Controls whether or not infectious mothers infect infants at birth. Enable_Birth must be set to 1 (true).

Warning

Do not set both Enable_Maternal_Infection_Transmission and Enable_Strain_Tracking to true (1) - as this combination will cause an exception error.

 
{
    "Enable_Birth": 1,
    "Enable_Maternal_Infection_Transmission": 1
}

Enable_Skipping

boolean

0

1

0

Controls whether or not the simulation uses an optimization that can increase performance by up to 50% in some cases by probabilistically exposing individuals rather than exposing every single person. Useful in low-prevalence, high-population scenarios.

 
{
    "Enable_Skipping": 0
}

Enable_Termination_On_Zero_Total_Infectivity

boolean

0

1

0

Controls whether or not the simulation should be ended when total infectivity falls to zero. Supported only in single-node simulations.

 
{
    "Enable_Termination_On_Zero_Total_Infectivity": 1,
    "Minimum_End_Time": 3650
}

Infection_Updates_Per_Timestep

integer

0

144

1

The number of infection updates executed during each timestep; note that a timestep defaults to one day.

 
{
    "Infection_Updates_Per_Timestep": 1
}

Infectious_Period_Constant

float

0

3.40282E+38

-1

The infectious period to use for all individuals, in days, when Infectious_Period_Distribution is set to CONSTANT_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "CONSTANT_DISTRIBUTION",
    "Infectious_Period_Constant": 8
}

Infectious_Period_Distribution

enum

NA

NA

NOT_INITIALIZED

The distribution type to use for assigning the infectious 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 Infectious_Period_Constant.

UNIFORM_DISTRIBUTION

Use a uniform distribution with a given minimum and maximum. Set Infectious_Period_Max and Infectious_Period_Min.

GAUSSIAN_DISTRIBUTION

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

EXPONENTIAL_DISTRIBUTION

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

WEIBULL_DISTRIBUTION

Use a Weibull distribution with a given shape and scale. Set Infectious_Period_Kappa and Infectious_Period_Lambda.

LOG_NORMAL_DISTRIBUTION

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

POISSON_DISTRIBUTION

Use a Poisson distribution with a given mean. Set Infectious_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 Infectious_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 Infectious_Period_Mean_1, Infectious_Period_Mean_2, and Infectious_Period_Proportion_1. This distribution does not use the parameters set for EXPONENTIAL_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "GAUSSIAN_DISTRIBUTION",
    "Infectious_Period_Gaussian_Mean": 4,
    "Infectious_Period_Gaussian_Std_Dev": 1
}

Infectious_Period_Exponential

float

0

3.40282E+38

-1

The mean infectious period, in days, when Infectious_Period_Distribution is set to EXPONENTIAL_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "EXPONENTIAL_DISTRIBUTION",
    "Infectious_Period_Exponential": 4.25
}

Infectious_Period_Gaussian_Mean

float

0

3.40282E+38

-1

The mean infectious period, in days, when Infectious_Period_Distribution is set to GAUSSIAN_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "GAUSSIAN_DISTRIBUTION",
    "Infectious_Period_Gaussian_Mean": 4,
    "Infectious_Period_Gaussian_Std_Dev": 1
}

Infectious_Period_Gaussian_Std_Dev

float

1.17549E-38

3.40282E+38

-1

The standard deviation of the infectious period, in days, when Infectious_Period_Distribution is set to GAUSSIAN_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "GAUSSIAN_DISTRIBUTION",
    "Infectious_Period_Gaussian_Mean": 4,
    "Infectious_Period_Gaussian_Std_Dev": 1
}

Infectious_Period_Kappa

float

1.17549E-38

3.40282E+38

-1

The shape value for the infectious period, in days, when Infectious_Period_Distribution is set to WEIBULL_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "WEIBULL_DISTRIBUTION",
    "Infectious_Period_Kappa": 0.9,
    "Infectious_Period_Lambda": 1.5
}

Infectious_Period_Lambda

float

1.17549E-38

3.40282E+38

-1

The scale value for the infectious period, in days, when Infectious_Period_Distribution is set to WEIBULL_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "WEIBULL_DISTRIBUTION",
    "Infectious_Period_Kappa": 0.9,
    "Infectious_Period_Lambda": 1.5
}

Infectious_Period_Log_Normal_Mu

float

-3.40282e+38

1.70141e+38

3.40282e+38

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

 
{
    "Infectious_Period_Distribution": "LOG_NORMAL_DISTRIBUTION",
    "Infectious_Period_Log_Normal_Mu": 9,
    "Infectious_Period_Log_Normal_Sigma": 2
}

Infectious_Period_Log_Normal_Sigma

float

-3.40282e+38

1.70141e+38

3.40282e+38

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

 
{
    "Infectious_Period_Distribution": "LOG_NORMAL_DISTRIBUTION",
    "Infectious_Period_Log_Normal_Mu": 9,
    "Infectious_Period_Log_Normal_Sigma": 2
}

Infectious_Period_Max

float

0

3.40282E+38

-1

The maximum infectious period, in days, when Infectious_Period_Distribution is set to UNIFORM_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "UNIFORM_DISTRIBUTION",
    "Infectious_Period_Min": 2,
    "Infectious_Period_Max": 7
}

Infectious_Period_Mean_1

float

1.17549E-38

3.4E+38

-1

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

 
{
    "Infectious_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
    "Infectious_Period_Mean_1": 4,
    "Infectious_Period_Mean_2": 12,
    "Infectious_Period_Proportion_1": 0.2
}

Infectious_Period_Mean_2

float

1.17549E-38

3.40282E+38

-1

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

 
{
    "Infectious_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
    "Infectious_Period_Mean_1": 4,
    "Infectious_Period_Mean_2": 12,
    "Infectious_Period_Proportion_1": 0.2
}

Infectious_Period_Min

float

0

3.40282E+38

-1

The minimum infectious period, in days, when Infectious_Period_Distribution is set to UNIFORM_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "UNIFORM_DISTRIBUTION",
    "Infectious_Period_Min": 2,
    "Infectious_Period_Max": 7
}

Infectious_Period_Peak_2_Value

float

0

3.40282E+38

-1

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

 
{
    "Infectious_Period_Distribution": "DUAL_CONSTANT_DISTRIBUTION",
    "Infectious_Period_Proportion_0": 0.25,
    "Infectious_Period_Peak_2_Value": 5
}

Infectious_Period_Poisson_Mean

float

0

3.40282E+38

-1

The mean of the infectious period, in days, when Infectious_Period_Distribution is set to POISSON_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "POISSON_DISTRIBUTION",
    "Infectious_Period_Poisson_Mean": 5
}

Infectious_Period_Proportion_0

float

0

1

-1

The proportion of individuals to assign a value of zero days infectiousness when Infectious_Period_Distribution is set to DUAL_CONSTANT_DISTRIBUTION.

 
{
    "Infectious_Period_Distribution": "DUAL_CONSTANT_DISTRIBUTION",
    "Infectious_Period_Proportion_0": 0.25,
    "Infectious_Period_Peak_2_Value": 5
}

Infectious_Period_Proportion_1

float

0

1

-1

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

 
{
    "Infectious_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
    "Infectious_Period_Mean_1": 4,
    "Infectious_Period_Mean_2": 12,
    "Infectious_Period_Proportion_1": 0.2
}

Infectivity_Exponential_Baseline

float

0

1

0

The scale factor applied to Base_Infectivity at the beginning of a simulation, before the infectivity begins to grow exponentially. Infectivity_Scale_Type must be set to EXPONENTIAL_FUNCTION_OF_TIME.

 
{
    "Infectivity_Exponential_Baseline": 0.1,
    "Infectivity_Exponential_Delay": 90,
    "Infectivity_Exponential_Rate": 45,
    "Infectivity_Scale_Type": "EXPONENTIAL_FUNCTION_OF_TIME"
}

Maternal_Infection_Transmission_Probability

float

0

1

0

The probability of transmission of infection from mother to infant at birth. Enable_Maternal_Infection_Transmission must be set to 1.

Note

For malaria and vector simulations, set this to 0. Instead, use the Maternal_Antibody_Protection, Maternal_Antibody_Decay_Rate, and Maternal_Antibodies_Type parameters.

 
{
    "Maternal_Infection_Transmission_Probability": 0.3
}

Population_Density_C50

float

0

3.40E+38

10

The population density at which R0 for a 2.5-arc minute square reaches half of its initial value. Population_Density_Infectivity_Correction must be set to SATURATING_FUNCTION_OF_DENSITY.

 
{
    "Population_Density_C50": 30
}

Population_Density_Infectivity_Correction

enum

NA

NA

CONSTANT_INFECTIVITY

Correction to alter infectivity by population density set in the Population_Density_C50 parameter. Measured in people per square kilometer. Possible values are:

  • CONSTANT_INFECTIVITY

  • SATURATING_FUNCTION_OF_DENSITY

Note

Sparsely populated areas have a lower infectivity, while densely populated areas have a higher infectivity, which rises to saturate at the Base_Infectivity value.

 
{
    "Population_Density_Infectivity_Correction": "SATURATING_FUNCTION_OF_DENSITY"
}

Relative_Sample_Rate_Immune

float

0.001

1

0.1

The relative sampling rate for people who have acquired immunity through recovery or vaccination. The immune threshold at which to downsample is set by Immune_Threshold_For_Downsampling. If set to 1, this will have no effect, even if the individual’s immunity modifier is below threshold. This can be a useful sanity check while learning this feature. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_IMMUNE_STATE.

 
{
    "Relative_Sample_Rate_Immune": 0.1,
    "Immune_Threshold_For_Downsampling": 0.8,
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_IMMUNE_STATE"
}

Susceptibility_Type

enum

NA

NA

FRACTIONAL

Controls implementation of an individual’s susceptibility. Currently only relevant to Maternal_Protection_Type parameter. Possible values are:

FRACTIONAL

All agents are assigned equal values between 0 and 1 according to a governing equation as specified by Maternal_Protection_Type.

BINARY

Agents receive a value of either 0 or 1 (complete immunity or susceptibility) with the probability determined by a governing equation as specified by Maternal_Protection_Type.

 
{
    "Susceptibility_Type": "FRACTIONAL",
    "Enable_Maternal_Protection": 1,
    "Maternal_Protection_Type": "LINEAR_FRACTIONAL"
}

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
}

TB_CD4_Infectiousness

array of floats

0

1

1

Relative multiplicative increase in TB Infectiousness due to HIV positivity/CD4 decline.

 
{
    "TB_CD4_Infectiousness": [
        1,
        1,
        0.9,
        0.5
    ]
}

TB_CD4_Strata_Infectiousness_Susceptibility

array of floats

0

3.40282e+38

0

The CD4 strata defining increases and decreases in TB infectiousness and susceptibility.

 
{
    "TB_CD4_Strata_Infectiousness_Susceptibility": [
        1e-09,
        250,
        300,
        350,
        500,
        2000,
        20000
    ]
}

TB_CD4_Susceptibility

array of floats

1

3.40282e+38

1

The relative increase in TB susceptibility due to HIV/CD4 decline

 
{
    "TB_CD4_Susceptibility": [
        5,
        5,
        5,
        5,
        1,
        1,
        1
    ]
}

TB_Enable_Exogenous

boolean

0

1

0

Controls whether or not exogenous reinfection of latent TB can occur.

 
{
    "TB_Enable_Exogenous": 1
}

TB_MDR_Fitness_Multiplier

float

0

1

1

The scale factor for Base_Infectivity to give the infectiousness of MDR-TB strains.

 
{
    "TB_MDR_Fitness_Multiplier": 0.65
}

TB_Smear_Negative_Infectivity_Multiplier

float

0

1

0.25

The scale factor for Base_Infectivity to give the infectiousness of active smear-negative individuals.

 
{
    "TB_Smear_Negative_Infectivity_Multiplier": 1
}

Transmission_Blocking_Immunity_Decay_Rate

float

0

1000

0.001

The rate at which transmission-blocking immunity decays after the base transmission-blocking immunity offset period. Used only when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).

 
{
    "Transmission_Blocking_Immunity_Decay_Rate": 0.01
}

Transmission_Blocking_Immunity_Duration_Before_Decay

float

0

45000

0

The number of days after infection until transmission-blocking immunity begins to decay. Only used when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).

 
{
    "Transmission_Blocking_Immunity_Duration_Before_Decay": 90
}