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.
The malaria transmission model does not use many of the parameters provided by the generic simulation type. Instead, gametocyte abundances and cytokine mediated infectiousness are modeled explicitly. See Vector transmission model for more information.
Note
Parameters are casesensitive. 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 

Acquire_Modifier  float  0  1  1  Modifier of the probability of successful infection of a mosquito by an infected individual, given the individual’s infectiousness.  {
"Vector_Species_Params": [
{
"Name": "aegypti",
"Acquire_Modifier": 1
}
]
}

Age_Dependent_Biting_Risk_Type  enum  NA  NA  OFF  The type of functional form for agedependent biting risk. Possible values are:

{
"Age_Dependent_Biting_Risk_Type": "SURFACE_AREA_DEPENDENT"
}

Base_Infectivity  float  0  1000  0.3  The base infectiousness of individuals before accounting for transmissionblocking effects of acquired immunity and/or campaign interventions. For vector and malaria simulations, this is the probability of infecting a mosquito during a successful blood meal (modulated by the vector parameter Acquire_Modifier). The sum infectiousness of an individual is not allowed to exceed 100%. 
{
"Base_Infectivity": 0.5
}

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_Initial_Prevalence  boolean  0  1  0  Controls whether or not parameters in the demographics file are used to define a distribution for the number of infected people per node at the beginning of the simulation. Set the distribution under NodeAttributes using PrevalenceDistributionFlag, PrevalenceDistribution1, and PrevalenceDistribution2.  {
"Enable_Initial_Prevalence": 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 lowprevalence, highpopulation scenarios.  {
"Enable_Skipping": 0
}

Enable_Superinfection  boolean  0  1  0  Controls whether or not an individual can have multiple infections simultaneously. Set to true (1) to allow for multiple simultaneous infections; set to false (0) if multiple infections are not possible. Set the Max_Individual_Infections parameter.  {
"Enable_Superinfection": 1,
"Max_Individual_Infections": 2
}

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 singlenode simulations.  {
"Enable_Termination_On_Zero_Total_Infectivity": 1,
"Minimum_End_Time": 3650
}

Infected_Arrhenius_1  float  0  1.00E+15  1.17E+11  The Arrhenius equation, \(a_1^{a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of fractional progression of infected mosquitoes to an infectious state. The duration of sporogony is a decreasing function of temperature. The variable a1 is a temperatureindependent scale factor on the progression rate to infectiousness.  {
"Vector_Species_Params": [
{
"Name": "arabiensis",
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 20,
"Anthropophily": 0.65,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Habitats": [
{
"Habitat_Type": "TEMPORARY_RAINFALL",
"Max_Larval_Capacity": 11250000000.0
}
],
"Immature_Duration": 2,
"Indoor_Feeding_Fraction": 1,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Male_Life_Expectancy": 10,
"Temperature_Dependent_Feeding_Cycle": "NO_TEMPERATURE_DEPENDENCE",
"Transmission_Rate": 0.5,
"Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE"
}
]
}

Infected_Arrhenius_2  float  0  1.00E+15  8340  The Arrhenius equation, \(a_1^{a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of fractional progression of infected mosquitoes to an infectious state. The duration of sporogony is a decreasing function of temperature. The variable a2 is a temperaturedependent scale factor on the progression rate to infectiousness.  {
"Vector_Species_Params": [
{
"Name": "arabiensis",
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 20,
"Anthropophily": 0.65,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Habitats": [
{
"Habitat_Type": "TEMPORARY_RAINFALL",
"Max_Larval_Capacity": 11250000000.0
}
],
"Immature_Duration": 2,
"Indoor_Feeding_Fraction": 1,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Male_Life_Expectancy": 10,
"Temperature_Dependent_Feeding_Cycle": "NO_TEMPERATURE_DEPENDENCE",
"Transmission_Rate": 0.5,
"Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE"
}
]
}

Infected_Egg_Batch_Factor  float  0  10  0.8  The dimensionless factor used to modify mosquito egg batch size in order to account for reduced fertility effects arising due to infection (e.g. when females undergo sporogony).  {
"Vector_Species_Params": [
{
"Name": "arabiensis",
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 20,
"Anthropophily": 0.65,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Habitats": [
{
"Habitat_Type": "TEMPORARY_RAINFALL",
"Max_Larval_Capacity": 11250000000.0
}
],
"Immature_Duration": 2,
"Indoor_Feeding_Fraction": 1,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Male_Life_Expectancy": 10,
"Temperature_Dependent_Feeding_Cycle": "NO_TEMPERATURE_DEPENDENCE",
"Transmission_Rate": 0.5,
"Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE"
}
]
}

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_Human_Feed_Mortality_Factor  float  0  1000  1.5  The (dimensionless) factor used to modify the death rate of mosquitoes when feeding on humans, to account for the higher mortality rate infected mosquitoes experience during human feeds versus uninfected mosquitoes.  {
"Vector_Species_Params": [
{
"Name": "arabiensis",
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 20,
"Anthropophily": 0.65,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Habitats": [
{
"Habitat_Type": "TEMPORARY_RAINFALL",
"Max_Larval_Capacity": 11250000000.0
}
],
"Immature_Duration": 2,
"Indoor_Feeding_Fraction": 1,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Male_Life_Expectancy": 10,
"Temperature_Dependent_Feeding_Cycle": "NO_TEMPERATURE_DEPENDENCE",
"Transmission_Rate": 0.5,
"Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE"
}
]
}

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  1.17549E38  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  1.17549E38  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  1.17549E38  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  1.17549E38  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  1.17549E38  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"
}

Malaria_Strain_Model  enum  NA  NA  FALCIPARUM_NONRANDOM_STRAIN  The generator that is used to construct the antigenic repertoire of a malaria infection. To create parasite diversity, various antigenic strains are created by conducting draws for merozoite surface protein (MSP) variants, Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) variants, and minor surface epitopes, out of available populations. Each possible value for this parameter utilizes different settings for the available population draws. Possible values are:

{
"Malaria_Strain_Model": "FALCIPARUM_STRAIN_GENERATOR"
}

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
}

Max_Individual_Infections  integer  0  1000  1  The limit on the number of infections that an individual can have simultaneously. Enable_Superinfection must be set to 1.  {
"Max_Individual_Infections": 5
}

Population_Density_C50  float  0  3.40E+38  10  The population density at which R0 for a 2.5arc 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"
}

Pyrogenic_Threshold  float  0.1  20000  1000  The level of bloodstream infection, measured in IRBC per microliter, at which stimulation of the innate inflammatory immune response is half its maximum value.  {
"Pyrogenic_Threshold": 15000
}

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:

{
"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
}

Transmission_Blocking_Immunity_Decay_Rate  float  0  1000  0.001  The rate at which transmissionblocking immunity decays after the base transmissionblocking 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 transmissionblocking 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
}

Transmission_Rate  float  0  1  0.5  The probability that the bite of an infected mosquito establishes a new infection in an immunologically naive and uninfected individual, or the modifier of the probability of success for an individual with preerythrocytic immunity. Note that each mosquito species will have their own Transmission_Rate parameter.  {
"Vector_Species_Params": [
{
"Name": "arabiensis",
"Acquire_Modifier": 0.2,
"Adult_Life_Expectancy": 20,
"Anthropophily": 0.65,
"Aquatic_Arrhenius_1": 84200000000,
"Aquatic_Arrhenius_2": 8328,
"Aquatic_Mortality_Rate": 0.1,
"Days_Between_Feeds": 3,
"Egg_Batch_Size": 100,
"Habitats": [
{
"Habitat_Type": "TEMPORARY_RAINFALL",
"Max_Larval_Capacity": 11250000000.0
}
],
"Immature_Duration": 2,
"Indoor_Feeding_Fraction": 1,
"Infected_Arrhenius_1": 117000000000,
"Infected_Arrhenius_2": 8336,
"Infected_Egg_Batch_Factor": 0.8,
"Infectious_Human_Feed_Mortality_Factor": 1.5,
"Male_Life_Expectancy": 10,
"Temperature_Dependent_Feeding_Cycle": "NO_TEMPERATURE_DEPENDENCE",
"Transmission_Rate": 0.5,
"Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE"
}
]
}
