Scalars and multipliers

The following parameters scale or multiply values set in other areas of the configuration file or other input files. This can be especially useful for understanding the sensitivities of disease dynamics to input data without requiring modifications to those base values. For example, one might set x_Birth to a value less than 1 to simulate a lower future birth rate due to increased economic prosperity and available medical technology.

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": {
        "aegypti": {
            "Acquire_Modifier": 1
        }
    }
}

Antibody_IRBC_Kill_Rate

double

NA

NA

2

The scale factor multiplied by antibody level to produce the rate of clearance of the infected red blood cell (IRBC) population.

 
{
    "Antibody_IRBC_Kill_Rate": 1.595
}

Aquatic_Arrhenius_1

float

0

1.00E+15

8.42E+10

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of fractional progression of mosquito aquatic development (egg-hatching through emergence). This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on development rate.

 
{
    "Vector_Species_Params": {
        "aegypti": {
            "Aquatic_Arrhenius_1": 9752291.727
        }
    }
}

Aquatic_Arrhenius_2

float

0

1.00E+15

8328

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of fractional progression of mosquito aquatic development (egg-hatching through emergence). This duration is a decreasing function of temperature. The variable a2 governs how quickly the rate changes with temperature.

 
{
    "Vector_Species_Params": {
        "arabiensis": {
            "Aquatic_Arrhenius_2": 8328
        }
    }
}

Birth_Rate_Time_Dependence

enum

NA

NA

NONE

A scale factor for BirthRate that allows it to be altered by time or season. Enable_Birth must be set to true (1). Possible values are:

NONE

Birth rate does not vary by time.

SINUSOIDAL_FUNCTION_OF_TIME

Allows birth rate to be time-dependent, following a sinusoidal shape defined by \(1 + \sin \text{Birth\_Rate\_Sinusoidal\_Forcing\_Amplitude} \times \sin(2 \pi \times (\text{day} - \sin \text{Birth\_Rate\_Sinusoidal\_Forcing\_Phase})/365)\). Set Birth_Rate_Sinusoidal_Forcing_Amplitude and Birth_Rate_Sinusoidal_Forcing_Phase.

ANNUAL_BOXCAR_FUNCTION

Allows birth rate to follow a boxcar function. The scale factor will be equal to 1 except for a single interval in which it is equal to a given constant equal to 1 + Birth_Rate_Boxcar_Forcing_Amplitude. Set Birth_Rate_Boxcar_Forcing_Amplitude, Birth_Rate_Boxcar_Forcing_End_Time, and Birth_Rate_Boxcar_Forcing_Start_Time.

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION"
}

Cycle_Arrhenius_1

float

0

1.00E+15

4.09E+10

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the mosquito feeding cycle rate. This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on feeding rate. Temperature_Dependent_Feeding_Cycle must be set to ARRHENIUS_DEPENDENCE.

 
{
    "Temperature_Dependent_Feeding_Cycle": "ARRHENIUS_DEPENDENCE",
    "Vector_Species_Params": {
        "arabiensis": {
            "Cycle_Arrhenius_1": 99,
            "Cycle_Arrhenius_2": 88
        }
    }
}

Cycle_Arrhenius_2

float

0

1.00E+15

7740

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the mosquito feeding cycle rate. This duration is a decreasing function of temperature. The variable a2 is a temperature-independent scale factor on feeding rate. Temperature_Dependent_Feeding_Cycle must be set to ARRHENIUS_DEPENDENCE.

 
{
    "Temperature_Dependent_Feeding_Cycle": "ARRHENIUS_DEPENDENCE",
    "Vector_Species_Params": {
        "arabiensis": {
            "Cycle_Arrhenius_1": 99,
            "Cycle_Arrhenius_2": 88
        }
    }
}

Cycle_Arrhenius_Reduction_Factor

float

0

1

1

The scale factor applied to cycle duration (from oviposition to oviposition) to reduce the duration when primary follicles are at stage II rather than I in the case of newly emerged females. Temperature_Dependent_Feeding_Cycle must be set to ARRHENIUS_DEPENDENCE.

 
{
    "Temperature_Dependent_Feeding_Cycle": "ARRHENIUS_DEPENDENCE",
    "Vector_Species_Params": {
        "funestus": {
            "Cycle_Arrhenius_Reduction_Factor": 0.44
        }
    }
}

Egg_Arrhenius1

float

0

1.00E+10

6.16E+07

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a1 is a temperature-independent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1.

 
{
    "Enable_Temperature_Dependent_Egg_Hatching": 1,
    "Egg_Arrhenius1": 61599956,
    "Egg_Arrhenius2": 5754
}

Egg_Arrhenius2

float

0

1.00E+10

5754.03

The Arrhenius equation, \(a_1^{-a_2/T}\), with T in degrees Kelvin, parameterizes the daily rate of mosquito egg hatching. This duration is a decreasing function of temperature. The variable a2 is a temperature-dependent scale factor on hatching rate. Enable_Temperature_Dependent_Egg_Hatching must be set to 1.

 
{
    "Enable_Temperature_Dependent_Egg_Hatching": 1,
    "Egg_Arrhenius1": 61599956,
    "Egg_Arrhenius2": 5754
}

Genome_Markers

array of strings

NA

NA

NA

A list of the names (strings) of genome marker(s) that represent the genetic components in a strain of an infection. To use this parameter, Vector_Sampling_Type must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS.

 
{
    "Genome_Markers": [
        "D6",
        "W2"
    ]
}

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": {
        "arabiensis": {
            "Acquire_Modifier": 0.2,
            "Adult_Life_Expectancy": 10,
            "Anthropophily": 0.95,
            "Aquatic_Arrhenius_1": 84200000000,
            "Aquatic_Arrhenius_2": 8328,
            "Aquatic_Mortality_Rate": 0.1,
            "Cycle_Arrhenius_1": 0,
            "Cycle_Arrhenius_2": 0,
            "Cycle_Arrhenius_Reduction_Factor": 0,
            "Days_Between_Feeds": 3,
            "Egg_Batch_Size": 100,
            "Immature_Duration": 4,
            "Indoor_Feeding_Fraction": 0.5,
            "Infected_Arrhenius_1": 117000000000,
            "Infected_Arrhenius_2": 8336,
            "Infected_Egg_Batch_Factor": 0.8,
            "Infectious_Human_Feed_Mortality_Factor": 1.5,
            "Larval_Habitat_Types": {
                "TEMPORARY_RAINFALL": 11250000000
            },
            "Nighttime_Feeding_Fraction": 1,
            "Transmission_Rate": 0.5
        }
    }
}

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": {
        "arabiensis": {
            "Acquire_Modifier": 0.2,
            "Adult_Life_Expectancy": 10,
            "Anthropophily": 0.95,
            "Aquatic_Arrhenius_1": 84200000000,
            "Aquatic_Arrhenius_2": 8328,
            "Aquatic_Mortality_Rate": 0.1,
            "Cycle_Arrhenius_1": 0,
            "Cycle_Arrhenius_2": 0,
            "Cycle_Arrhenius_Reduction_Factor": 0,
            "Days_Between_Feeds": 3,
            "Egg_Batch_Size": 100,
            "Immature_Duration": 4,
            "Indoor_Feeding_Fraction": 0.5,
            "Infected_Arrhenius_1": 117000000000,
            "Infected_Arrhenius_2": 8336,
            "Infected_Egg_Batch_Factor": 0.8,
            "Infectious_Human_Feed_Mortality_Factor": 1.5,
            "Larval_Habitat_Types": {
                "TEMPORARY_RAINFALL": 11250000000
            },
            "Nighttime_Feeding_Fraction": 1,
            "Transmission_Rate": 0.5
        }
    }
}

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": {
        "arabiensis": {
            "Acquire_Modifier": 0.2,
            "Adult_Life_Expectancy": 10,
            "Anthropophily": 0.95,
            "Aquatic_Arrhenius_1": 84200000000,
            "Aquatic_Arrhenius_2": 8328,
            "Aquatic_Mortality_Rate": 0.1,
            "Cycle_Arrhenius_1": 0,
            "Cycle_Arrhenius_2": 0,
            "Cycle_Arrhenius_Reduction_Factor": 0,
            "Days_Between_Feeds": 3,
            "Egg_Batch_Size": 100,
            "Immature_Duration": 4,
            "Indoor_Feeding_Fraction": 0.5,
            "Infected_Arrhenius_1": 117000000000,
            "Infected_Arrhenius_2": 8336,
            "Infected_Egg_Batch_Factor": 0.8,
            "Infectious_Human_Feed_Mortality_Factor": 1.5,
            "Larval_Habitat_Types": {
                "TEMPORARY_RAINFALL": 11250000000
            },
            "Nighttime_Feeding_Fraction": 1,
            "Transmission_Rate": 0.5
        }
    }
}

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": {
        "arabiensis": {
            "Acquire_Modifier": 0.2,
            "Adult_Life_Expectancy": 10,
            "Anthropophily": 0.95,
            "Aquatic_Arrhenius_1": 84200000000,
            "Aquatic_Arrhenius_2": 8328,
            "Aquatic_Mortality_Rate": 0.1,
            "Cycle_Arrhenius_1": 0,
            "Cycle_Arrhenius_2": 0,
            "Cycle_Arrhenius_Reduction_Factor": 0,
            "Days_Between_Feeds": 3,
            "Egg_Batch_Size": 100,
            "Immature_Duration": 4,
            "Indoor_Feeding_Fraction": 0.5,
            "Infected_Arrhenius_1": 117000000000,
            "Infected_Arrhenius_2": 8336,
            "Infected_Egg_Batch_Factor": 0.8,
            "Infectious_Human_Feed_Mortality_Factor": 1.5,
            "Larval_Habitat_Types": {
                "TEMPORARY_RAINFALL": 11250000000
            },
            "Nighttime_Feeding_Fraction": 1,
            "Transmission_Rate": 0.5
        }
    }
}

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"
}

Larval_Density_Mortality_Scalar

float

0.01

1000

10

A scale factor in the formula determining the larval-age-dependent mortality for the GRADUAL_INSTAR_SPECIFIC and LARVAL_AGE_DENSITY_DEPENDENT_MORTALITY_ONLY models.

 
{
    "Larval_Density_Mortality_Scalar": 1.0
}

Newborn_Biting_Risk_Multiplier

float

0

1

0.2

The scale factor that defines the y-intercept of the linear portion of the biting risk curve when Age_Dependent_Biting_Risk_Type is set to LINEAR.

 
{
    "Newborn_Biting_Risk_Multiplier": 0.2
}

Nonspecific_Antibody_Growth_Rate_Factor

float

0

1000

0.5

The factor that adjusts Antibody_Capacity_Growth_Rate for less immunogenic surface proteins, called minor epitopes.

 
{
    "Nonspecific_Antibody_Growth_Rate_Factor": 0.5
}

Population_Scale_Type

enum

NA

NA

USE_INPUT_FILE

The method to use for scaling the initial population specified in the demographics input file. Possible values are:

USE_INPUT_FILE

Turns off population scaling and uses InitialPopulation in the demographics file (see NodeAttributes parameters).

FIXED_SCALING

Enables Base_Population_Scale_Factor.

 
{
    "Population_Scale_Type": "FIXED_SCALING"
}

Post_Infection_Acquisition_Multiplier

float

0

1

0

The multiplicative reduction in the probability of reacquiring disease. At the time of recovery, the immunity against acquisition is multiplied by Acquisition_Blocking_Immunity_Decay_Rate x (1 - Post_Infection_Acquisition_Multiplier). Enable_Immunity must be set to 1 (true).

 
{
    "Enable_Immunity": 1,
    "Enable_Immune_Decay": 1,
    "Post_Infection_Acquisition_Multiplier": 0.9
}

Post_Infection_Mortality_Multiplier

float

0

1

0

The multiplicative reduction in the probability of dying from infection after getting reinfected. At the time of recovery, the immunity against mortality is multiplied by Mortality_Blocking_Immunity_Decay_Rate x (1 - Post_Infection_Mortality_Multiplier). Enable_Immunity must be set to 1 (true).

 
{
    "Enable_Immunity": 1,
    "Enable_Immune_Decay": 1,
    "Post_Infection_Mortality_Multiplier": 0.5
}

Post_Infection_Transmission_Multiplier

float

0

1

0

The multiplicative reduction in the probability of transmitting infection after getting reinfected. At the time of recovery, the immunity against transmission is multiplied by Transmission_Blocking_Immunity_Decay_Rate x (1 - Post_Infection_Transmission_Multiplier). Enable_Immunity must be set to 1 (true).

 
{
    "Enable_Immunity": 1,
    "Enable_Immunity_Decay": 1,
    "Post_Infection_Transmission_Multiplier": 0.9
}

Resistance

JSON object

NA

NA

NA

Specifies the drug resistance multiplier. This parameter is used with the infection strain indicated in the Genome_Markers parameter. The value specified for the parameter modifier, which is part of the Resistance JSON object, is multiplied with associated parameter. If the infection strain contains different markers, then the same modifiers for each marker are multiplied together before being multiplied with the associated parameter.

 
{
    "parameters": {
        "Genome_Markers": [
            "A",
            "B"
        ],
        "Malaria_Drug_Params": {
            "Artemether_Lumefantrine": {
                "Bodyweight_Exponent": 0,
                "Drug_Cmax": 1000,
                "Drug_Decay_T1": 1,
                "Drug_Decay_T2": 1,
                "Drug_Dose_Interval": 1,
                "Drug_Fulltreatment_Doses": 3,
                "Drug_Gametocyte02_Killrate": 2.3,
                "Drug_Gametocyte34_Killrate": 2.3,
                "Drug_GametocyteM_Killrate": 0,
                "Drug_Hepatocyte_Killrate": 0,
                "Drug_PKPD_C50": 100,
                "Drug_Vd": 10,
                "Max_Drug_IRBC_Kill": 3.45,
                "Resistance": {
                    "A": {
                        "Max_IRBC_Kill_Modifier": 0.05,
                        "PKPD_C50_Modifier": 1.0
                    },
                    "B": {
                        "Max_IRBC_Kill_Modifier": 0.25,
                        "PKPD_C50_Modifier": 1.0
                    }
                }
            }
        }
    }
}

Vector_Migration_Food_Modifier

float

0

3.40E+38

0

The preference of a vector to migrate toward a node currently occupied by humans, independent of the number of humans in the node. Used only when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1.

 
{
    "Vector_Migration_Food_Modifier": 1.0
}

Vector_Migration_Habitat_Modifier

float

0

3.40E+38

0

The preference of a vector to migrate toward a node with more habitat. Only used when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1.

 
{
    "Vector_Migration_Habitat_Modifier": 1.0
}

Vector_Migration_Modifier_Equation

enum

NA

NA

LINEAR

The functional form of vector migration modifiers. Enable_Vector_Migration must be set to 1. Possible values are: LINEAR EXPONENTIAL

 
{
    "Vector_Migration_Modifier_Equation": "EXPONENTIAL"
}

Vector_Migration_Stay_Put_Modifier

float

0

3.40E+38

0

The preference of a vector to remain in its current node rather than migrate to another node. Used only when Vector_Sampling_Type is set to TRACK_ALL_VECTORS. Enable_Vector_Migration must be set to 1.

 
{
    "Vector_Migration_Stay_Put_Modifier": 1.0
}

x_Air_Migration

float

0

3.40E+38

1

Scale factor for the rate of migration by air, as provided by the migration file. Enable_Air_Migration must be set to 1.

 
{
    "Scale_Factor_Air_Migration": 1
}

x_Base_Population

float

0

3.40E+38

1

Scale factor for InitialPopulation in the demographics file (see NodeAttributes parameters). If Population_Scale_Type is set to FIXED_SCALING, the initial simulation population is uniformly scaled over the entire area to adjust for historical or future population density.

 
{
    "x_Base_Population": 0.0001
}

x_Birth

float

0

3.40E+38

1

Scale factor for birth rate, as provided by the demographics file (see NodeAttributes parameters). Enable_Birth must be set to 1.

 
{
    "x_Birth": 1
}

x_Family_Migration

float

0

3.40E+38

1

Scale factor for the rate of migration by families, as provided by the migration file. Enable_Family_Migration must be set to true (1).

 
{
    "x_Family_Migration": 1
}

x_Larval_Habitats

float

0

10000

1

Scale factor for the habitat size for all mosquito populations.

 
{
    "x_Larval_Habitats": 1
}

x_Local_Migration

float

0

3.40E+38

1

Scale factor for rate of migration by foot travel, as provided by the migration file. Enable_Local_Migration must be set to 1.

 
{
    "x_Local_Migration": 1
}

x_Other_Mortality

float

0

3.40E+38

1

Scale factor for mortality from causes other than the disease being simulated. Base mortality is provided by the demographics file (see Complex distributions parameters). Enable_Natural_Mortality must be set to 1.

 
{
    "x_Other_Mortality": 1
}

x_Regional_Migration

float

0

3.40E+38

1

Scale factor for the rate of migration by road vehicle, as provided by the migration file. Enable_Regional_Migration must be set to 1.

 
{
    "x_Regional_Migration": 1
}

x_Sea_Migration

float

0

3.40E+38

1

Scale factor for the rate of migration by sea, as provided by the migration file. Enable_Sea_Migration must be set to 1.

 
{
    "x_Sea_Migration": 1
}

x_Vector_Migration_Local

float

0

3.40E+38

1

Scale factor for the rate of vector migration to adjacent nodes, as provided by the vector migration file. Enable_Vector_Migration must be set to 1.

 
{
    "x_Vector_Migration_Local": 1.0
}

x_Vector_Migration_Regional

float

0

3.40E+38

1

Scale factor for the rate of vector migration to non-adjacent nodes, as provided by the vector migration file. Enable_Vector_Migration must be set to 1.

 
{
    "x_Vector_Migration_Regional": 1.0
}