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
}
|
Acute_Stage_Infectivity_Multiplier |
float |
1 |
100 |
26 |
The multiplier acting on Base_Infectivity to determine the per-act transmission probability of an HIV+ individual during the acute stage. |
{
"Acute_Stage_Infectivity_Multiplier": 3
}
|
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 STI or HIV simulations, this is the probability of transmission when none of the transmission multipliers apply to a particular coital act (or when all multipliers are set to 1). |
{
"Base_Infectivity": 0.5
}
|
CD4_At_Death_LogLogistic_Heterogeneity |
float |
0 |
100 |
0 |
The inverse shape parameter of a Weibull distribution that represents the at-death CD4 cell count. |
{
"CD4_At_Death_LogLogistic_Heterogeneity": 0.7
}
|
Condom_Transmission_Blocking_Probability |
float |
0 |
1 |
0.9 |
The per-act multiplier of the transmission probability when a condom is used. |
{
"Condom_Transmission_Blocking_Probability": 0.99
}
|
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
}
|
Heterogeneous_Infectiousness_LogNormal_Scale |
float |
0 |
10 |
0 |
Scale parameter of a log normal distribution that governs an infectiousness multiplier. The multiplier represents heterogeneity in infectivity and adjusts Base_Infectivity. |
{
"Heterogeneous_Infectiousness_LogNormal_Scale": 1
}
|
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:
|
{
"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"
}
|
Male_To_Female_Relative_Infectivity_Ages |
array of floats |
NA |
NA |
0 |
The vector of ages governing the susceptibility of females relative to males, by age. Used with Male_To_Female_Relative_Infectivity_Multipliers. |
{
"Male_To_Female_Relative_Infectivity_Ages": [
15,
25,
35
]
}
|
Male_To_Female_Relative_Infectivity_Multipliers |
array of floats |
NA |
NA |
1 |
An array of scale factors governing the susceptibility of females relative to males, by age. Used with Male_To_Female_Relative_Infectivity_Ages. Scaling is linearly interpolated between ages. The first value is used for individuals younger than the first age in Male_To_Female_Relative_Infectivity_Ages and the last value is used for individuals older than the last age. |
{
"Male_To_Female_Relative_Infectivity_Multipliers": [
5,
1,
0.5
]
}
|
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
}
|
Maternal_Transmission_ART_Multiplier |
float |
0 |
1 |
0.1 |
The maternal transmission multiplier for on-ART mothers. |
{
"Maternal_Transmission_ART_Multiplier": 0.03
}
|
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:
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"
}
|
STI_Coinfection_Acquisition_Multiplier |
float |
0 |
100 |
10 |
The per-act HIV acquisition probability multiplier for individuals with the STI coinfection flag. |
{
"STI_Coinfection_Transmission_Multiplier": 13.4,
"STI_Coinfection_Acquisition_Multiplier": 10
}
|
STI_Coinfection_Transmission_Multiplier |
float |
0 |
100 |
10 |
The per-act HIV transmission probability multiplier for individuals with the STI coinfection flag. |
{
"STI_Coinfection_Transmission_Multiplier": 13.4,
"STI_Coinfection_Acquisition_Multiplier": 10
}
|
Susceptibility_Type |
enum |
NA |
NA |
FRACTIONAL |
Controls implementation of an individual’s susceptibility. Currently only relevant to Maternal_Protection_Type parameter. Possible values are:
|
{
"Susceptibility_Type": "FRACTIONAL",
"Enable_Maternal_Protection": 1,
"Maternal_Protection_Type": "LINEAR_FRACTIONAL"
}
|