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 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

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 age-dependent biting risk. Possible values are:

OFF

This is the default value.

LINEAR

The biting risk is 20% of the adult exposure rising linearly until age 20.

SURFACE_AREA_DEPENDENT

The biting risk rises linearly from 7% to 23% over the first two years of life and then rises with a shallower linear slope to the adult value at age 20.

 
{
    "Age_Dependent_Biting_Risk_Type": "SURFACE_AREA_DEPENDENT"
}

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.

 
{
    "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 low-prevalence, high-population 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 single-node 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 temperature-independent 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
                }
            ],
            "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 temperature-dependent 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
                }
            ],
            "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
                }
            ],
            "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
                }
            ],
            "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:

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"
}

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:

FALCIPARUM_NONRANDOM_STRAIN

The strain created uses the exact same MSP variant, non-specific PfEMP1 variant, and ordered repertoire of PfEMP1 major epitopes. Minor surface protein epitopes are randomly drawn from a set of 5.

FALCIPARUM_RANDOM50_STRAIN

Strain creation extends the logic used for FALCIPARUM_NONRANDOM_STRAIN, but increases variation by randomly drawing PfEMP1 variants from a population of 50, and allowing the variants to have a random switching order. Random draws are done with replacement.

FALCIPARUM_RANDOM_STRAIN

The MSP variant is drawn from the population set by the parameter Falciparum_MSP_Variants, a repertoire of 50 PfEMP1 variants is drawn from the population set by the parameter Falciparum_PfEMP1_Variants, and the set of five minor surface protein epitope variants is drawn from the population set by the parameter Falciparum_Nonspecific_Types.

FALCIPARUM_STRAIN_GENERATOR

This is an exploratory effort created to provide a pseudo-random generation of strains similar to FALCIPARUM_RANDOM_STRAIN, but with variant indices deterministically assigned according to the strain ID.

 
{
    "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 2.5-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"
}

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:

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
}

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
}

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 pre-erythrocytic 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
                }
            ],
            "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"
        }
    ]
}