Configuration parameters

The parameters described in this reference section can be added to the JSON (JavaScript Object Notation) formatted configuration file to determine the core behavior of a simulation including the computing environment, functionality to enable, additional files to use, and characteristics of the disease being modeled. This file contains mostly a flat list of JSON key:value pairs.

For more information on the structure of these files, see Configuration file.

The tables below contain only parameters available when using the malaria simulation type. Some parameters may appear in multiple categories.

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 does not permit comments, but you can add “dummy” parameters to add contextual information to your files.

Drugs and treatments

The following parameters determine the efficacy of drugs and other treatments.

For more information on the drugs used to treat malaria, see Antimalarial drugs.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Bodyweight_Exponent

float

0

100000

0

The effect of bodyweight on maximum drug concentration in an individual patient. Drug_Cmax is divided by patient bodyweight raised to the power of Bodyweight_Exponent to account for the influence of body size on volume of distribution.

 
{
    "Malaria_Drug_Params": {
        "Artemether_Lumefantrine": {
            "Bodyweight_Exponent": 2
        }
    }
}

Drug_Cmax

float

0

100000

1000

The maximum drug concentration used.

Note

This parameter and the Drug_PKPD_C50 parameter must use the same units.

 
{
    "Malaria_Drug_Params": {
        "Artemether_Lumefantrine": {
            "Drug_Cmax": 1000,
            "Drug_PKPD_C50": 100
        }
    }
}

Drug_Decay_T1

float

0

100000

1

The primary drug decay rate, in days.

 
{
    "Malaria_Drug_Params": {
        "Artemisinin": {
            "Drug_Decay_T1": 1,
            "Drug_Decay_T2": 1
        }
    }
}

Drug_Decay_T2

float

0

100000

1

The secondary drug decay rate, in days.

 
{
    "Malaria_Drug_Params": {
        "Artemisinin": {
            "Drug_Decay_T1": 1,
            "Drug_Decay_T2": 1
        }
    }
}

Drug_Dose_Interval

float

0

100000

1

The interval between doses of drugs, in days.

 
{
    "Malaria_Drug_Params": {
        "Artemisinin": {
            "Drug_Dose_Interval": 1
        }
    }
}

Drug_Fulltreatment_Doses

float

1

100000

3

The number of doses for a full treatment of a drug.

 
{
    "Malaria_Drug_Params": {
        "Chloroquine": {
            "Drug_Fulltreatment_Doses": 3
        }
    }
}

Drug_Gametocyte02_Killrate

float

0

100000

0

The log reduction per day in early-stage gametocytes.

 
{
    "Malaria_Drug_Params": {
        "Chloroquine": {
            "Drug_Gametocyte02_Killrate": 0,
            "Drug_Gametocyte34_Killrate": 0,
            "Drug_GametocyteM_Killrate": 0
        }
    }
}

Drug_Gametocyte34_Killrate

float

0

100000

0

The log reduction per day in late-stage gametocytes.

 
{
    "Malaria_Drug_Params": {
        "Chloroquine": {
            "Drug_Gametocyte02_Killrate": 0,
            "Drug_Gametocyte34_Killrate": 0,
            "Drug_GametocyteM_Killrate": 0
        }
    }
}

Drug_GametocyteM_Killrate

float

0

100000

0

The log reduction per day in mature gametocyte numbers at saturated drug concentrations.

 
{
    "Malaria_Drug_Params": {
        "Chloroquine": {
            "Drug_Gametocyte02_Killrate": 0,
            "Drug_Gametocyte34_Killrate": 0,
            "Drug_GametocyteM_Killrate": 0
        }
    }
}

Drug_Hepatocyte_Killrate

float

0

100000

0

The log reduction in hepatocyte numbers per day.

 
{
    "Malaria_Drug_Params": {
        "Chloroquine": {
            "Drug_Hepatocyte_Killrate": 0
        }
    }
}

Drug_PKPD_C50

float

0

100000

100

The concentration at which drug killing rates are half of the maximum.

Note

This parameter and the Drug_Cmax parameter must use the same units.

 
{
    "Malaria_Drug_Params": {
        "Artemether_Lumefantrine": {
            "Drug_Cmax": 1000,
            "Drug_PKPD_C50": 100
        }
    }
}

Drug_Vd

float

0

100000

10

The volume of drug distribution in a pharmacokinetic two compartment model. The first compartment comprises central organs and tissues and the second compartment comprises peripheral tissues. This value is the ratio of the volume of the second compartment to that of the first.

 
{
    "Malaria_Drug_Params": {
        "Chloroquine": {
            "Drug_Vd": 3
        }
    }
}

Fractional_Dose_By_Upper_Age

array of JSON objects

NA

NA

NA

An array to specify the fraction of the adult dose to use for children at various ages. Contains Upper_Age_In_Years and Fraction_Of_Adult_Dose values.

 
{
    "Malaria_Drug_Params": {
        "Artemether": {
            "Fractional_Dose_By_Upper_Age": [
                {
                    "Fraction_Of_Adult_Dose": 0.25,
                    "Upper_Age_In_Years": 3
                },
                {
                    "Fraction_Of_Adult_Dose": 0.5,
                    "Upper_Age_In_Years": 6
                },
                {
                    "Fraction_Of_Adult_Dose": 0.75,
                    "Upper_Age_In_Years": 10
                }
            ]
        }
    }
}

Fraction_Of_Adult_Dose

float

0

1

NA

The fraction of the adult drug dose given to children below the age defined in Upper_Age_In_Years. Set in the Fractional_Dose_By_Upper_Age array.

 
{
    "Malaria_Drug_Params": {
        "Artemether": {
            "Fractional_Dose_By_Upper_Age": [
                {
                    "Fraction_Of_Adult_Dose": 0.25,
                    "Upper_Age_In_Years": 3
                },
                {
                    "Fraction_Of_Adult_Dose": 0.5,
                    "Upper_Age_In_Years": 6
                },
                {
                    "Fraction_Of_Adult_Dose": 0.75,
                    "Upper_Age_In_Years": 10
                }
            ]
        }
    }
}

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"
    ]
}

Malaria_Drug_Params

JSON object

NA

NA

NA

This JSON structure contains the names of anti-malarial drugs and the parameters that define them.

 
{
    "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": 4.6
        },
        "Artemisinin": {
            "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": 4.61
        }
    }
}

Max_Drug_IRBC_Kill

float

5

100000

5

The maximum log reduction in IRBCs per day due to treatment.

 
{
    "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": 4.61
        }
    }
}

PKPD_Model

enum

NA

NA

FIXED_DURATION_CONSTANT_EFFECT

Determines which pharmacokinetic pharmacodynamic model to use. Possible values are:

FIXED_DURATION_CONSTANT_EFFECT

This is the simplified model of drug action. Each dose of the drug has a constant effect for a fixed duration of time, after which the effect is zero.

CONCENTRATION_VERSUS_TIME

This model of drug action uses continuous pharmacokinetics with two-compartment decay. Effects of each drug depend on the concentration at that point in time.

 
{
    "PKPD_Model": "FIXED_DURATION_CONSTANT_EFFECT"
}

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
                    }
                }
            }
        }
    }
}

Upper_Age_In_Years

float

0

125

NA

The age, in years, below which children are given a fraction of the adult drug dose, as defined in Fraction_Of_Adult_Dose. Note that this parameter can be specified for each drug included in the configuration file, and different fractional doses may be used for different age groups.

 
{
    "Malaria_Drug_Params": {
        "Artemether": {
            "Fractional_Dose_By_Upper_Age": [
                {
                    "Fraction_Of_Adult_Dose": 0.25,
                    "Upper_Age_In_Years": 3
                },
                {
                    "Fraction_Of_Adult_Dose": 0.5,
                    "Upper_Age_In_Years": 6
                },
                {
                    "Fraction_Of_Adult_Dose": 0.75,
                    "Upper_Age_In_Years": 10
                }
            ]
        }
    }
}

Enable or disable features

The following parameters enable or disable features of the model, such as allowing births, deaths, or aging. Set to false (0) to disable; set to true (1) to enable.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Enable_Aging

boolean

0

1

1

Controls whether or not individuals in a population age during the simulation. Enable_Vital_Dynamics must be set to true (1).

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Aging": 1
}

Enable_Air_Migration

boolean

0

1

0

Controls whether or not migration by air travel will occur. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration": 1,
    "Air_Migration_Filename": "../inputs/air_migration.bin"
}

Enable_Birth

boolean

0

1

1

Controls whether or not individuals will be added to the simulation by birth. Enable_Vital_Dynamics must be set to true (1). If you want new individuals to have the same intervention coverage as existing individuals, you must add a BirthTriggeredIV to the campaign file.

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

Enable_Climate_Stochasticity

boolean

0

1

0

Controls whether or not the climate has stochasticity. Climate_Model must be set to CLIMATE_CONSTANT or CLIMATE_BY_DATA. Set the variance using the parameters Air_Temperature_Variance, Land_Temperature_Variance, Enable_Rainfall_Stochasticity, and Relative_Humidity_Variance.

 
{
    "Climate_Model": "CLIMATE_BY_DATA",
    "Enable_Climate_Stochasticity": 1,
    "Air_Temperature_Variance": 2,
    "Enable_Rainfall_Stochasticity": 1,
    "Land_Temperature_Variance": 2,
    "Relative_Humidity_Variance": 0.05
}

Enable_Default_Reporting

boolean

0

1

1

Controls whether or not the default InsetChart.json report is created.

 
{
    "Enable_Default_Reporting": 1
}

Enable_Demographics_Birth

boolean

0

1

0

Controls whether or not newborns have identical or heterogeneous characteristics. Set to false (0) to give all newborns identical characteristics; set to true (1) to allow for heterogeneity in traits such as sickle-cell status. Enable_Birth must be set to true (1).

 
{
    "Enable_Birth": 1,
    "Enable_Demographics_Birth": 1
}

Enable_Demographics_Builtin

boolean

0

1

0

Controls whether or not built-in demographics for default geography will be used. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing. Set to true (1) to define the initial population and number of nodes using Default_Geography_Initial_Node_Population and Default_Geography_Torus_Size. Set to false (0) to use demographics input files defined in Demographics_Filenames.

 
{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}

Enable_Demographics_Reporting

boolean

0

1

1

Controls whether or not demographic summary data and age-binned reports are outputted to file.

 
{
    "Enable_Demographics_Reporting": 1
}

Enable_Demographics_Risk

boolean

0

1

0

Controls whether or not the simulation includes the impact of disease risk in demographics.

 
{
    "Enable_Demographics_Risk": 1
}

Enable_Disease_Mortality

boolean

0

1

1

Controls whether or not individuals are removed from the simulation due to disease deaths.

 
{
    "Enable_Disease_Mortality": 1
}

Enable_Egg_Mortality

boolean

0

1

0

Controls whether or not to include a daily mortality rate on the egg population, which is independent of climatic factors.

 
{
    "Enable_Egg_Mortality": 1
}

Enable_Family_Migration

boolean

0

1

0

Controls whether or not all members of a household can migrate together when a MigrateFamily event occurs. All residents must be home before they can leave on the trip. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Enable_Migration": "FIXED_RATE_MIGRATION",
    "Enable_Family_Migration": 1,
    "Family_Migration_Filename": "../inputs/family_migration.bin"
}

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 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_Immune_Decay

boolean

0

1

1

Controls whether or not immunity decays after an infection clears. Set to true (1) if immunity decays; set to false (0) if recovery from the disease confers complete immunity for life. Enable_Immunity must be set to true (1).

This parameter should always be set to 1 (on) in this simulation type.

 
{
    "Enable_Immunity": 1,
    "Enable_Immune_Decay": 0
}

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_Initial_Susceptibility_Distribution

boolean

0

1

0

Controls whether or not individuals in the population have immunity at the beginning of the simulation. If set to 0, individuals are not initialized with immunity but may acquire immunity. If set to 1, you must indicate the type of distribution to use for immunity in the configuration parameter Immunity_Initialization_Distribution_Type and the distribution values in the demographics file. Enable_Immunity must be set to 1.

 
{
    "Enable_Immunity": 1,
    "Enable_Initial_Susceptibility_Distribution": 1,
    "Immunity_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE"
}

Enable_Interventions

boolean

0

1

0

Controls whether or not campaign interventions will be used in the simulation. Set Campaign_Filename to the path of the file that contains the campaign interventions.

 
{
    "Enable_Interventions": 1,
    "Campaign_Filename": "campaign.json"
}

Enable_Local_Migration

boolean

0

1

0

Controls whether or not local migration (the diffusion of people in and out of nearby nodes by foot travel) occurs. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Local_Migration": 1,
    "Local_Migration_Filename": "../inputs/local_migration.bin"
}

Enable_Maternal_Protection

boolean

0

1

0

Controls whether or not mothers pass immunity on to their infants. Setting to 1 (true) enables maternal protection as defined by Maternal_Protection_Type. Enable_Birth must be set to 1 (true).

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

Enable_Migration_Heterogeneity

boolean

0

1

1

Controls whether or not migration rate is heterogeneous among individuals within each group that has a migration rate setting. Set to true (1) to apply a migration rate distribution (see NodeAttributes demographics parameters); set to false (0) to use the same migration rate applied to all individuals in the group. For example, if you are using a migration file that sets different migration rates for each age group in a node, you could apply an Gaussian distribution around a mean value in each age group or you could assign the same value to each individual in each age group.

Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Migration_Heterogeneity": 1
}

Enable_Natural_Mortality

boolean

0

1

0

Controls whether or not individuals are removed from the simulation due to natural (non-disease) deaths. Enable_Vital_Dynamics must be set to 1 (true). Use Death_Rate_Dependence to set the natural death rate.

 
{
    "Enable_Natural_Mortality": 1,
    "Enable_Vital_Dynamics": 1
}

Enable_Property_Output

boolean

0

1

0

Controls whether or not to create property output reports, which detail groups as defined in IndividualProperties in the demographics file (see NodeProperties and IndividualProperties parameters). When there is more than one property type, the report will display the channel information for all combinations of the property type groups.

 
{
    "Enable_Property_Output": 1
}

Enable_Rainfall_Stochasticity

boolean

0

1

1

Controls whether or not there is stochastic variation in rainfall; set to true (1) for stochastic variation of rainfall that is drawn from an exponential distribution (with a mean value as the daily rainfall from the Climate_Model values CLIMATE_CONSTANT or CLIMATE_BY_DATA), or set to false (0) to disable rainfall stochasticity.

 
{
    "Enable_Climate_Stochasticity": 1,
    "Air_Temperature_Variance": 2,
    "Enable_Rainfall_Stochasticity": 1,
    "Land_Temperature_Variance": 2,
    "Relative_Humidity_Variance": 0.05
}

Enable_Regional_Migration

boolean

0

1

0

Controls whether or not there is migration by road or rail network into and out of nodes in the simulation. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Regional_Migration": 1,
    "Regional_Migration_Filename": "../inputs/regional_migration.bin"
}

Enable_Sea_Migration

boolean

0

1

0

Controls whether or not there is migration on ships into and out of coastal cities with seaports. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Sea_Migration": 1,
    "Sea_Migration_Filename": "../inputs/sea_migration.bin"
}

Enable_Sexual_Combination

boolean

0

1

0

Controls whether or not male and female gametocytes undergo sexual combination. Set to true (1) to allow for sexual combination; set to false (0) for transmission of each strain only.

Note

This parameter is currently not in use.

 
{
    "Enable_Sexual_Combination": 0
}

Enable_Spatial_Output

boolean

0

1

0

Controls whether or not spatial output reports are created. If set to true (1), spatial output reports include all channels listed in the parameter Spatial_Output_Channels.

Note

Spatial output files require significant processing time and disk space.

 
{
    "Enable_Spatial_Output": 1,
    "Spatial_Output_Channels": [
        "Prevalence",
        "New_Infections"
    ]
}

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_Susceptibility_Scaling

boolean

0

1

0

Controls whether or not susceptibility is scaled by time as defined by Susceptibility_Scaling_Type.

 
{
    "Enable_Susceptibility_Scaling": 1,
    "Susceptibility_Scaling_Type": "LOG_LINEAR_FUNCTION_OF_TIME"
}

Enable_Vector_Aging

boolean

0

1

0

Controls whether or not vectors undergo senescence as they age.

 
{
    "Enable_Vector_Aging": 1
}

Enable_Vector_Migration

boolean

0

1

0

Controls whether or not vectors can migrate. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS. Specific migration types must be enabled or disabled.

 
{
    "Vector_Sampling_Type": "TRACK_ALL_VECTORS",
    "Enable_Vector_Migration": 1,
    "Enable_Vector_Migration_Local": 1,
    "Vector_Migration_Filename_Local": "../inputs/vector_local.bin"
}

Enable_Vector_Migration_Local

boolean

0

1

0

Controls whether or not vectors may migrate to adjacent nodes. Enable_Vector_Migration must be set to true (1).

 
{
    "Vector_Sampling_Type": "TRACK_ALL_VECTORS",
    "Enable_Vector_Migration": 1,
    "Enable_Vector_Migration_Local": 1,
    "Vector_Migration_Filename_Local": "../inputs/vector_local.bin"
}

Enable_Vector_Migration_Regional

boolean

0

1

0

Controls whether or not vectors can migration to non-adjacent nodes. Enable_Vector_Migration must be set to true (1).

 
{
    "Vector_Sampling_Type": "TRACK_ALL_VECTORS",
    "Enable_Vector_Migration": 1,
    "Enable_Vector_Migration_Regional": 1,
    "Vector_Migration_Filename_Regional": "../inputs/vector_regional.bin"
}

Enable_Vector_Mortality

boolean

0

1

1

Controls whether or not vectors can die. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS.

 
{
    "Vector_Sampling_Type": "TRACK_ALL_VECTORS",
    "Enable_Vector_Mortality": 1
}

Enable_Vital_Dynamics

boolean

0

1

1

Controls whether or not births and deaths occur in the simulation. Births and deaths must be individually enabled and set.

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Death_Rate_Dependence": "NOT_INITIALIZED",
    "Base_Mortality": 0.002
}

General disease

The following parameters determine general disease characteristics.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Number_Basestrains

integer

1

10

1

The number of base strains in the simulation, such as antigenic variants. The specific base strain of an outbreak is specified using Antigen in the campaign file.

 
{
    "Number_Basestrains": 1
}

Number_Substrains

integer

1

16777216

256

The number of disease substrains for each base strain, such as genetic variants. The specific substrain of an outbreak is specified using Genome in the campaign file.

 
{
    "Number_Substrains": 256
}

Geography and environment

The following parameters determine characteristics of the geography and environment of the simulation. For example, how to use the temperature or rainfall data in the climate files and the size of the nodes in the simulation.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Air_Temperature_Filename

string

NA

NA

air_temp.json

The path to the input file that defines air temperature data measured two meters above ground. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.

 
{
    "Climate_Model": "CLIMATE_BY_DATA",
    "Air_Temperature_Filename": "Namawala_single_node_air_temperature_daily.bin"
}

Air_Temperature_Offset

float

-20

20

0

The linear shift of air temperature in degrees Celsius. Climate_Model must be set to CLIMATE_BY_DATA.

 
{
    "Air_Temperature_Offset": 1
}

Air_Temperature_Variance

float

0

5

2

The standard deviation (in degrees Celsius) for normally distributed noise applied to the daily air temperature values when Climate_Model is configured as CLIMATE_CONSTANT or CLIMATE_BY_DATA. Enable_Climate_Stochasticity must be set to true (1).

 
{
    "Enable_Climate_Stochasticity": 1,
    "Air_Temperature_Variance": 2
}

Base_Air_Temperature

float

-55

45

22

The air temperature, in degrees Celsius, where Climate_Model is set to CLIMATE_CONSTANT.

 
{
    "Climate_Model": "CLIMATE_CONSTANT",
    "Base_Air_Temperature": 30
}

Base_Land_Temperature

float

-55

60

26

The land temperature, in degrees Celsius, where Climate_Model is set to CLIMATE_CONSTANT.

 
{
    "Climate_Model": "CLIMATE_CONSTANT",
    "Base_Land_Temperature": 20
}

Base_Rainfall

float

0

150

10

The value of rainfall per day in millimeters when Climate_Model is set to CLIMATE_CONSTANT.

 
{
    "Climate_Model": "CLIMATE_CONSTANT",
    "Base_Rainfall": 20
}

Base_Relative_Humidity

float

0

1

0.75

The value of humidity where Climate_Model is set to CLIMATE_CONSTANT.

 
{
    "Base_Relative_Humidity": 0.1
}

Climate_Model

enum

NA

NA

CLIMATE_OFF

How and from what files the climate of a simulation is configured. The possible values are:

CLIMATE_OFF

No climate files used.

CLIMATE_CONSTANT

Uses the conditional parameters that give the fixed values of temperature or rain for land temperature, air temperature, rainfall, and humidity.

CLIMATE_KOPPEN

Uses an input file that decodes Koppen codes by geographic location.

CLIMATE_BY_DATA

Reads everything out of several input files with additional parameters that allow the addition of stochasticity or scale offsets.

 
{
    "Climate_Model": "CLIMATE_CONSTANT"
}

Climate_Update_Resolution

enum

NA

NA

CLIMATE_UPDATE_YEAR

The resolution of data in climate files. Climate_Model must be set to CLIMATE_CONSTANT, CLIMATE_BY_DATA, or CLIMATE_KOPPEN. Possible values are:

CLIMATE_UPDATE_YEAR CLIMATE_UPDATE_MONTH CLIMATE_UPDATE_WEEK CLIMATE_UPDATE_DAY CLIMATE_UPDATE_HOUR

 
{
    "Climate_Update_Resolution": "CLIMATE_UPDATE_DAY"
}

Default_Geography_Initial_Node_Population

integer

0

1000000

1000

When using the built-in demographics for default geography, the initial number of individuals in each node. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing. Enable_Demographics_Builtin must be set to true (1).

 
{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}

Default_Geography_Torus_Size

integer

3

100

10

When using the built-in demographics for default geography, the square root of the number of nodes in the simulation. The simulation uses an N x N square grid of nodes with N specified by this parameter. If migration is enabled, the N x N nodes are assumed to be a torus and individuals can migrate from any node to all four adjacent nodes.

To enable migration, set Migration_Model to FIXED_RATE_MIGRATION. Built-in migration is a form of “local” migration where individuals only migrate to the adjacent nodes. You can use the x_Local_Migration parameter to control the rate of migration. The other migration parameters are ignored. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing.

Enable_Demographics_Builtin must be set to true (1).

 
{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}

Enable_Climate_Stochasticity

boolean

0

1

0

Controls whether or not the climate has stochasticity. Climate_Model must be set to CLIMATE_CONSTANT or CLIMATE_BY_DATA. Set the variance using the parameters Air_Temperature_Variance, Land_Temperature_Variance, Enable_Rainfall_Stochasticity, and Relative_Humidity_Variance.

 
{
    "Climate_Model": "CLIMATE_BY_DATA",
    "Enable_Climate_Stochasticity": 1,
    "Air_Temperature_Variance": 2,
    "Enable_Rainfall_Stochasticity": 1,
    "Land_Temperature_Variance": 2,
    "Relative_Humidity_Variance": 0.05
}

Enable_Rainfall_Stochasticity

boolean

0

1

1

Controls whether or not there is stochastic variation in rainfall; set to true (1) for stochastic variation of rainfall that is drawn from an exponential distribution (with a mean value as the daily rainfall from the Climate_Model values CLIMATE_CONSTANT or CLIMATE_BY_DATA), or set to false (0) to disable rainfall stochasticity.

 
{
    "Enable_Climate_Stochasticity": 1,
    "Air_Temperature_Variance": 2,
    "Enable_Rainfall_Stochasticity": 1,
    "Land_Temperature_Variance": 2,
    "Relative_Humidity_Variance": 0.05
}

Koppen_Filename

string

NA

NA

koppen_climate.json

The path to the input file used to specify Koppen climate classifications. Climate_Model must be set to CLIMATE_KOPPEN.

 
{
    "Koppen_Filename": "Mad_2_5arcminute_koppen.dat"
}

Land_Temperature_Filename

string

NA

NA

land_temp.json

The path of the input file defining temperature data measured at land surface; used only when Climate_Model is set to CLIMATE_BY_DATA. The file must be in .bin format.

 
{
    "Land_Temperature_Filename": "Namawala_single_node_land_temperature_daily.bin"
}

Land_Temperature_Offset

float

-20

20

0

The linear shift of land surface temperature in degrees Celsius; only used when Climate_Model is set to CLIMATE_BY_DATA.

 
{
    "Land_Temperature_Offset": 0
}

Land_Temperature_Variance

float

0

7

2

The standard deviation (in degrees Celsius) for normally distributed noise applied to the daily land temperature values when Climate_Model is configured to CLIMATE_CONSTANT or CLIMATE_BY_DATA; only used if the Enable_Climate_Stochasticity is set to true (1).

 
{
    "Land_Temperature_Variance": 1.5
}

Node_Grid_Size

float

0.00416

90

0.004167

The spatial resolution indicating the node grid size for a simulation in degrees.

 
{
    "Node_Grid_Size": 0.042
}

Rainfall_Filename

string

NA

NA

rainfall.json

The path of the input file which defines rainfall data. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.

 
{
    "Rainfall_Filename": "Namawala_single_node_rainfall_daily.bin"
}

Rainfall_In_mm_To_Fill_Swamp

float

1

10000

1000

Millimeters of rain to fill larval habitat to capacity. This is only used for vector species with Larval_Habitat_Types set to BRACKISH_SWAMP.

 
{
    "Rainfall_In_mm_To_Fill_Swamp": 1000.0
}

Rainfall_Scale_Factor

float

0.1

10

1

The scale factor used in multiplying rainfall value(s). Climate_Model must be set to CLIMATE_BY_DATA.

 
{
    "Rainfall_Scale_Factor": 1
}

Relative_Humidity_Filename

string

NA

NA

rel_hum.json

The path of the input file which defines relative humidity data measured 2 meters above ground. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.

 
{
    "Relative_Humidity_Filename": "Namawala_single_node_relative_humidity_daily.bin"
}

Relative_Humidity_Scale_Factor

float

0.1

10

1

The scale factor used in multiplying relative humidity values. Climate_Model must be set to CLIMATE_BY_DATA.

 
{
    "Relative_Humidity_Scale_Factor": 1
}

Relative_Humidity_Variance

float

0

0.12

0.05

The standard deviation (in percentage) for normally distributed noise applied to the daily relative humidity values when Climate_Model is configured as CLIMATE_CONSTANT or CLIMATE_BY_DATA. Enable_Climate_Stochasticity must be set to true (1).

 
{
    "Relative_Humidity_Variance": 0.05
}

Immunity

The following parameters determine the immune system response for the disease being modeled, including waning immunity after an infection clears.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Acquisition_Blocking_Immunity_Decay_Rate

float

0

1

0.001

The rate at which acquisition-blocking immunity decays after the initial period indicated by the base acquisition-blocking immunity offset. Only used when Enable_Immunity and Enable_Immune_Decay parameters are set to true (1).

 
{
    "Acquisition_Blocking_Immunity_Decay_Rate": 0.05
}

Acquisition_Blocking_Immunity_Duration_Before_Decay

float

0

45000

0

The number of days after infection until acquisition-blocking immunity begins to decay. Enable_Immunity and Enable_Immune_Decay must be set to true (1).

 
{
    "Acquisition_Blocking_Immunity_Duration_Before_Decay": 10
}

Antibody_Capacity_Growth_Rate

float

0

1

0.1

The maximum daily rate of specific antibody capacity increase. Antibody production begins at a capacity of 0.3., and hyperimmunity results at 0.4. The actual growth rate tends to be lower and is a function of antigen concentrations.

 
{
    "Antibody_Capacity_Growth_Rate": 0.09
}

Antibody_CSP_Decay_Days

float

1

3.40E+38

90

Exponential decay time for the circumsporozoite protein (CSP) antibody concentration (in days) when boosted above natural maximum concentrations.

 
{
    "Antibody_CSP_Decay_Days": 80
}

Antibody_CSP_Killing_Inverse_Width

float

1.00E-0

1000000

1.5

The inverse width of the sigmoidal sporozoite killing function of circumsporozoite protein (CSP) antibody concentration.

 
{
    "Antibody_CSP_Killing_Inverse_Width": 1.7
}

Antibody_CSP_Killing_Threshold

float

1.00E-0

1000000

10

The threshold value on circumsporozoite protein (CSP) antibody concentration for sporozoite killing.

 
{
    "Antibody_CSP_Killing_Threshold": 20
}

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
}

Antibody_Memory_Level

float

0

0.35

0.2

The limiting level of antibody capacity that remains after a prolonged absence of a specific antigen. The antibody capacity decays to this level gradually after infection is cleared. The decay rate in antibody capacity is set so that hyperimmunity is lost within 4 months, and capacity continues to decay to this level. The antibody memory level is relevant for year-scale dynamics, but not for long-term dynamics (10-20 years).

 
{
    "Antibody_Memory_Level": 0.3
}

Antibody_Stimulation_C50

float

0.1

10000

10

The concentration of an antigen, measured in IRBC/ul at which growth in antibody capacity against the antigen increases at half the maximum rate specified by Antibody_Capacity_Growth_Rate.

 
{
    "Antibody_Stimulation_C50": 30,
    "Antibody_Capacity_Growth_Rate": 0.09
}

Antigen_Switch_Rate

double

NA

NA

2.00E-09

The antigenic switching rate per infected red blood cell per asexual cycle. See Parasite_Switch_Type for different switching patterns.

 
{
    "Antigen_Switch_Rate": 5e-09
}

Cytokine_Gametocyte_Inactivation

float

0

1

0.02

The strength of inflammatory response inactivation of gametocytes.

 
{
    "Cytokine_Gametocyte_Inactivation": 0.0167
}

Enable_Immune_Decay

boolean

0

1

1

Controls whether or not immunity decays after an infection clears. Set to true (1) if immunity decays; set to false (0) if recovery from the disease confers complete immunity for life. Enable_Immunity must be set to true (1).

This parameter should always be set to 1 (on) in this simulation type.

 
{
    "Enable_Immunity": 1,
    "Enable_Immune_Decay": 0
}

Enable_Initial_Susceptibility_Distribution

boolean

0

1

0

Controls whether or not individuals in the population have immunity at the beginning of the simulation. If set to 0, individuals are not initialized with immunity but may acquire immunity. If set to 1, you must indicate the type of distribution to use for immunity in the configuration parameter Immunity_Initialization_Distribution_Type and the distribution values in the demographics file. Enable_Immunity must be set to 1.

 
{
    "Enable_Immunity": 1,
    "Enable_Initial_Susceptibility_Distribution": 1,
    "Immunity_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE"
}

Enable_Maternal_Antibodies_Transmission

boolean

0

1

0

Controls whether or not mothers pass antibodies to their infants. When enabled, you must set Maternal_Antibodies_Type,**Maternal_Antibody_Protection**, and Maternal_Antibody_Decay_Rate. Enable_Birth must be set to 1.

 
{
    "Enable_Maternal_Antibodies_Transmission": 1,
    "Maternal_Antibodies_Type": "SIMPLE_WANING",
    "Maternal_Antibody_Protection": 0.23,
    "Maternal_Antibody_Decay_Rate": 0.03
}

Enable_Maternal_Protection

boolean

0

1

0

Controls whether or not mothers pass immunity on to their infants. Setting to 1 (true) enables maternal protection as defined by Maternal_Protection_Type. Enable_Birth must be set to 1 (true).

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

Erythropoiesis_Anemia_Effect

float

0

1000

3.5

The exponential rate of increased red-blood-cell production from reduced red-blood-cell availability.

 
{
    "Erythropoiesis_Anemia_Effect": 3
}

Falciparum_MSP_Variants

integer

0

1000

100

The number of distinct merozoite surface protein (MSP) variants for P. falciparum malaria in the overall parasite population in the simulation, not necessarily in an individual.

 
{
    "Falciparum_MSP_Variants": 4
}

Falciparum_Nonspecific_Types

integer

0

1000

20

The number of distinct non-specific types of P. falciparum malaria.

 
{
    "Falciparum_Nonspecific_Types": 92
}

Falciparum_PfEMP1_Variants

integer

0

100000

1000

The number of distinct Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) variants for P. falciparum malaria in the overall parasite population in the simulation.

 
{
    "Falciparum_PfEMP1_Variants": 300
}

Fever_IRBC_Kill_Rate

float

0

1000

0.15

The maximum kill rate for infected red blood cells due to the inflammatory innate immune response. As fever increases above 38.5 degrees Celsius, the kill rate becomes successively higher along a sigmoidal curve approaching this rate.

 
{
    "Fever_IRBC_Kill_Rate": 1.4
}

Immune_Threshold_For_Downsampling

float

0

1

0

The threshold on acquisition immunity at which to apply immunity-dependent downsampling; individuals who are more immune than this this threshold are downsampled. A value of 1 is equivalent to full susceptibility and 0 is equivalent to full immunity. If the acquisition immunity modifier is larger than the threshold, no downsampling occurs. Individual_Sampling_Type must set to ADAPTED_SAMPLING_BY_IMMUNE_STATE.

 
{
    "Relative_Sample_Rate_Immune": 0.1,
    "Immune_Threshold_For_Downsampling": 0.5,
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_IMMUNE_STATE"
}

Innate_Immune_Variation_Type

enum

NA

NA

NONE

The type of innate immunity on which to apply individual-level variation. Possible values are:

NONE

No variation in innate immunity between individuals.

PYROGENIC_THRESHOLD

Applies individual variation using the susceptibility distribution values set in SusceptibilityDistributionFlag, SusceptibilityDistribution1, and SusceptibilityDistribution2 in the demographics file to the average threshold for infected red blood cells resulting in fever, as set in Pyrogenic_Threshold.

PYROGENIC_THRESHOLD_VS_AGE

Ignores the demographic file settings and applies an age-dependent threshold for infected red blood cells resulting in fever.

CYTOKINE_KILLING

Applies individual variation using the susceptibility distribution values set in SusceptibilityDistributionFlag, SusceptibilityDistribution1, and SusceptibilityDistribution2 in the demographics file to the effectiveness of cytokines in killing infected red blood cells, as set in Fever_IRBC_Kill_Rate.

 
{
    "Innate_Immune_Variation_Type": "PYROGENIC_THRESHOLD"
}

Maternal_Antibodies_Type

enum

NA

NA

OFF

The type of maternal antibody protection. Enable_Maternal_Antibodies_Transmission must be set to 1 (true). Possible values are:

OFF

No maternal antibody protection provided.

SIMPLE_WANING

The protection from maternal antibodies is a function of the configured maximum fraction protection (Maternal_Antibody_Protection) and the age of the child (through Maternal_Antibody_Decay_Rate), but also of the transmission-intensity in the simulation. In particular, the protection is modified by a factor corresponding to the fraction of PfEMP1 antigenic variants to which possible mothers (14 to 45-year-old females) have been exposed in their lifetimes.

CONSTANT_INITIAL_IMMUNITY

Protection is independent of acquired immunity in possible mothers.

 
{
    "Maternal_Antibodies_Type": "CONSTANT_INITIAL_IMMUNITY"
}

Maternal_Antibody_Decay_Rate

float

0

3.40E+38

0.01

The decay rate per day in protection from maternal antibodies. Maternal_Antibodies_Type must be set to SIMPLE_WANING or CONSTANT_INITIAL_IMMUNITY.

 
{
    "Maternal_Antibodies_Type": "SIMPLE_WANING",
    "Maternal_Antibody_Decay_Rate": 0.01,
    "Maternal_Antibody_Protection": 0.1327
}

Maternal_Antibody_Protection

float

0

1

0.1

The strength of protection from maternal antibodies as a multiple of full antibody killing effect. Maternal_Antibodies_Type must be set to SIMPLE_WANING or CONSTANT_INITIAL_IMMUNITY.

 
{
    "Maternal_Antibodies_Type": "SIMPLE_WANING",
    "Maternal_Antibody_Decay_Rate": 0.01,
    "Maternal_Antibody_Protection": 0.1327
}

Maternal_Linear_Slope

float

0.0001

1

0.01

Slope parameter describing the rate of waning for maternal protection, must be positive. The per-day increase in susceptibility. Maternal_Protection_Type must be set to LINEAR_FRACTIONAL or LINEAR_BINARY.

 
{
    "Maternal_Protection_Type": "LINEAR_FRACTIONAL",
    "Maternal_Linear_SusZero": 0.45,
    "Maternal_Linear_Slope": 0.02
}

Maternal_Linear_SusZero

float

0

1

0.2

The initial level of maternal protection at age 0, given as susceptibility. A value of 0.0 implies total protection, a value of 1.0 implies no protection. Maternal_Protection_Type must be set to LINEAR_FRACTIONAL or LINEAR_BINARY.

 
{
    "Maternal_Protection_Type": "LINEAR_FRACTIONAL",
    "Maternal_Linear_SusZero": 0.45,
    "Maternal_Linear_Slope": 0.02
}

Maternal_Protection_Type

enum

NA

NA

NONE

The type of maternal protection afforded to infants. Enable_Maternal_Protection must be set to 1 (true). Possible values are:

NONE

No immune protection is passed on to infants.

LINEAR

Susceptibility is a function of age and governed by a linear equation. Susceptibility = Maternal_Linear_Slope * age + Maternal_Linear_SusZero

SIGMOID

Susceptibility is a function of age and governed by a sigmoidal equation. Susceptibility = Maternal_Sigmoid_SusInit + (1.0 - Maternal_Sigmoid_SusInit) / * (1.0 + EXP(( Maternal_Sigmoid_HalfMaxAge - age) / Maternal_Sigmoid_SteepFac))

You must set Susceptibility_Type to determine if susceptibility at a particular age is interpreted as a fractional value or the probability of complete immunity or susceptibility.

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

Maternal_Sigmoid_HalfMaxAge

float

-270

3650

180

The age in days that the level of maternal protection is half of its initial value. Maternal_Protection_Type must be set to SIGMOID_FRACTIONAL or SIGMOID_BINARY.

 
{
    "Maternal_Protection_Type": "SIGMOID_BINARY",
    "Maternal_Sigmoid_SteepFac": 30,
    "Maternal_Sigmoid_HalfMaxAge": 365,
    "Maternal_Sigmoid_SusInit": 0.0002
}

Maternal_Sigmoid_SteepFac

float

0.1

1000

30

The steepness factor describing the rate of waning for maternal protection, must be positive. Small values imply rapid waning.**Maternal_Protection_Type** must be set to SIGMOID_FRACTIONAL or SIGMOID_BINARY.

 
{
    "Maternal_Protection_Type": "SIGMOID_BINARY",
    "Maternal_Sigmoid_SteepFac": 30,
    "Maternal_Sigmoid_HalfMaxAge": 365,
    "Maternal_Sigmoid_SusInit": 0.0002
}

Maternal_Sigmoid_SusInit

float

0

1

0

The initial level of maternal protection at age -INF, given as susceptibility. A value of 0.0 implies total protection, a value of 1.0 implies no protection. Maternal_Protection_Type must be set to SIGMOID_FRACTIONAL or SIGMOID_BINARY.

 
{
    "Maternal_Protection_Type": "SIGMOID_BINARY",
    "Maternal_Sigmoid_SteepFac": 30,
    "Maternal_Sigmoid_HalfMaxAge": 365,
    "Maternal_Sigmoid_SusInit": 0.0002
}

Max_MSP1_Antibody_Growthrate

float

0

1

0.02

The maximum increase in MSP1 antibody capacity during each asexual cycle. The higher this value, the sooner early clearances are observed and the earlier the parasite density envelope decreases.

 
{
    "Max_MSP1_Antibody_Growthrate": 0.045
}

Min_Adapted_Response

float

0

1

0.02

The minimum level of antibody stimulation to a novel antigen. The value sets the low-range asymptote for antibody capacity growth, which is calculated from Antibody_Capacity_Growth_Rate and antigen density, in the presence of any nonzero antigen level.

 
{
    "Min_Adapted_Response": 0.01
}

Mortality_Blocking_Immunity_Decay_Rate

float

0

1

0.001

The rate at which mortality-blocking immunity decays after the mortality-blocking immunity offset period. Enable_Immune_Decay must be set to 1.

 
{
    "Mortality_Blocking_Immunity_Decay_Rate": 0.1
}

Mortality_Blocking_Immunity_Duration_Before_Decay

float

0

45000

0

The number of days after infection until mortality-blocking immunity begins to decay. Enable_Immunity and Enable_Immune_Decay must be set to 1.

 
{
    "Mortality_Blocking_Immunity_Duration_Before_Decay": 270
}

MSP1_Merozoite_Kill_Fraction

double

NA

NA

0.5

The fraction of merozoites inhibited from invading new erythrocytes when MSP1-specific antibody level is 1.

 
{
    "MSP1_Merozoite_Kill_Fraction": 0.4364623975644405
}

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
}

Nonspecific_Antigenicity_Factor

double

NA

NA

0.2

The nonspecific antigenicity factor that adjusts antibody IRBC kill rate to account for IRBCs caused by antibody responses to antigenically weak surface proteins.

 
{
    "Nonspecific_Antigenicity_Factor": 0.39192559432597257
}

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
}

RBC_Destruction_Multiplier

double

NA

NA

9.5

The number of total red blood cells destroyed per infected rupturing schizont.

 
{
    "RBC_Destruction_Multiplier": 3.291048711
}

Susceptibility_Initialization_Distribution_Type

enum

NA

NA

DISTRIBUTION_OFF

The method for initializing the susceptibility distribution in the simulated population. Enable_Initial_Susceptibility_Distribution must be set to 1 (true). Possible values are:

DISTRIBUTION_OFF

All individuals default to no susceptibility.

DISTRIBUTION_SIMPLE

Individual susceptibilities are drawn from a distribution whose functional form and parameters are specified in the demographics file in IndividualAttributes using SusceptibilityDistributionFlag, SusceptibilityDistribution1, and SusceptibilityDistribution2 (see Simple distributions parameters).

DISTRIBUTION_COMPLEX

Individual susceptibilities are drawn from an age-dependent piecewise linear function for each specific antibody in the demographics file (see Complex distributions parameters).

 
{
    "Enable_Immunity": 1,
    "Enable_Initial_Susceptibility_Distribution": 1,
    "Susceptibility_Initialization_Distribution_Type": "DISTRIBUTION_COMPLEX"
}

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
}

Incubation

The following parameters determine the characteristics of the incubation period.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Incubation_Period_Constant

float

0

3.40282E+38

6

The incubation period to use for all individuals.

 
{
    "Incubation_Period_Distribution": "CONSTANT_DISTRIBUTION",
    "Incubation_Period_Constant": 8
}

Incubation_Period_Distribution

enum

NA

NA

NOT_INITIALIZED

The distribution type to use for assigning the incubation 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 Incubation_Period_Constant.

UNIFORM_DISTRIBUTION

Use a uniform distribution with a given minimum and maximum. Set Incubation_Period_Max and Incubation_Period_Min.

GAUSSIAN_DISTRIBUTION

The distribution is Gaussian (or normal). Set Incubation_Period_Gaussian_Mean and Incubation_Period_Gaussian_Std_Dev.

EXPONENTIAL_DISTRIBUTION

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

WEIBULL_DISTRIBUTION

Use a Weibull distribution with a given shape and scale. Set Incubation_Period_Kappa and Incubation_Period_Lambda.

LOG_NORMAL_DISTRIBUTION

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

POISSON_DISTRIBUTION

Use a Poisson distribution with a given mean. Set Incubation_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 Incubation_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 Incubation_Period_Mean_1, Incubation_Period_Mean_2, and Incubation_Period_Proportion_1. This distribution does not use the parameters set for DUAL_EXPONENTIAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "GAUSSIAN_DISTRIBUTION",
    "Incubation_Period_Gaussian_Mean": 8,
    "Incubation_Period_Gaussian_Std_Dev": 1.5
}

Incubation_Period_Exponential

float

0

3.40282E+38

6

The mean incubation period when Incubation_Period_Distribution is set to EXPONENTIAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "EXPONENTIAL_DISTRIBUTION",
    "Incubation_Period_Exponential": 4.25
}

Incubation_Period_Gaussian_Mean

float

0

3.40282E+38

6

The mean of the incubation period when Incubation_Period_Distribution is set to GAUSSIAN_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "GAUSSIAN_DISTRIBUTION",
    "Incubation_Period_Gaussian_Mean": 8,
    "Incubation_Period_Gaussian_Std_Dev": 1.5
}

Incubation_Period_Gaussian_Std_Dev

float

1.17549E-38

3.40282E+38

1

The standard deviation of the incubation period when Incubation_Period_Distribution is set to GAUSSIAN_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "GAUSSIAN_DISTRIBUTION",
    "Incubation_Period_Gaussian_Mean": 8,
    "Incubation_Period_Gaussian_Std_Dev": 1.5
}

Incubation_Period_Kappa

float

1.17549E-38

3.40282E+38

1

The shape value for the incubation period when Incubation_Period_Distribution is set to WEIBULL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "WEIBULL_DISTRIBUTION",
    "Incubation_Period_Kappa": 0.9,
    "Incubation_Period_Lambda": 1.5
}

Incubation_Period_Lambda

float

1.17549E-38

3.40282E+38

1

The scale value for the incubation period when Incubation_Period_Distribution is set to WEIBULL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "WEIBULL_DISTRIBUTION",
    "Incubation_Period_Kappa": 0.9,
    "Incubation_Period_Lambda": 1.5
}

Incubation_Period_Log_Normal_Mu

float

1.17549E-38

3.40282E+38

6

The mean of the natural log of the incubation period when Incubation_Period_Distribution is set to LOG_NORMAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "LOG_NORMAL_DISTRIBUTION",
    "Incubation_Period_Log_Normal_Mu": 4,
    "Incubation_Period_Log_Normal_Sigma": 1
}

Incubation_Period_Log_Normal_Sigma

float

1.17549E-38

3.40282E+38

1

The standard deviation of the natural log of the incubation period when Incubation_Period_Distribution is set to LOG_NORMAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "LOG_NORMAL_DISTRIBUTION",
    "Incubation_Period_Log_Normal_Mu": 4,
    "Incubation_Period_Log_Normal_Sigma": 1
}

Incubation_Period_Max

float

0

3.40282E+38

1

The maximum incubation period when Incubation_Period_Distribution is set to UNIFORM_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "UNIFORM_DISTRIBUTION",
    "Incubation_Period_Min": 2,
    "Incubation_Period_Max": 7
}

Incubation_Period_Mean_1

float

1.17549E-38

3.40282E+38

1

The mean of the first exponential distribution when Incubation_Period_Distribution is set to DUAL_EXPONENTIAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
    "Incubation_Period_Mean_1": 4,
    "Incubation_Period_Mean_2": 12,
    "Incubation_Period_Proportion_1": 0.2
}

Incubation_Period_Mean_2

float

1.17549E-38

3.40282E+38

1

The mean of the second exponential distribution when Incubation_Period_Distribution is set to DUAL_EXPONENTIAL_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
    "Incubation_Period_Mean_1": 4,
    "Incubation_Period_Mean_2": 12,
    "Incubation_Period_Proportion_1": 0.2
}

Incubation_Period_Min

float

0

3.40282E+38

0

The minimum incubation period when Incubation_Period_Distribution is set to UNIFORM_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "UNIFORM_DISTRIBUTION",
    "Incubation_Period_Min": 2,
    "Incubation_Period_Max": 7
}

Incubation_Period_Peak_2_Value

float

0

3.40282E+38

1

The incubation period value to assign to the remaining individuals when Incubation_Period_Distribution is set to DUAL_CONSTANT_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "DUAL_CONSTANT_DISTRIBUTION",
    "Incubation_Period_Proportion_0": 0.25,
    "Incubation_Period_Peak_2_Value": 5
}

Incubation_Period_Poisson_Mean

float

0

3.40282E+38

6

The mean of the incubation period when Incubation_Period_Distribution is set to POISSON_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "POISSON_DISTRIBUTION",
    "Incubation_Period_Poisson_Mean": 5
}

Incubation_Period_Proportion_0

float

0

1

1

The proportion of individuals to assign a value of zero days incubation when Incubation_Period_Distribution is set to DUAL_CONSTANT_DISTRIBUTION.

 
{
    "Incubation_Period_Distribution": "DUAL_CONSTANT_DISTRIBUTION",
    "Incubation_Period_Proportion_0": 0.25,
    "Incubation_Period_Peak_2_Value": 5
}

Incubation_Period_Proportion_1

float

0

1

1

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

 
{
    "Incubation_Period_Distribution": "DUAL_EXPONENTIAL_DISTRIBUTION",
    "Incubation_Period_Mean_1": 4,
    "Incubation_Period_Mean_2": 12,
    "Incubation_Period_Proportion_1": 0.2
}

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
}

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 vector 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.

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
        }
    }
}

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.

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 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_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 probablistically exposing individuals rather than exposing every single person. Useful in low-prevalence, high-population scenarios. Infectivity_Scale_Type must be set to CONSTANT_INFECTIVITY.

 
{
    "Exposure_Skipping": 1
}

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_Susceptibility_Scaling

boolean

0

1

0

Controls whether or not susceptibility is scaled by time as defined by Susceptibility_Scaling_Type.

 
{
    "Enable_Susceptibility_Scaling": 1,
    "Susceptibility_Scaling_Type": "LOG_LINEAR_FUNCTION_OF_TIME"
}

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": {
        "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
        }
    }
}

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": {
        "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_Period_Constant

float

0

3.40282E+38

6

The infectious period to use for all individuals.

 
{
    "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). 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

6

The mean infectious period 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

6

The mean of the infectious period 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 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 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 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

1.17549E-38

3.40282E+38

6

The mean of the natural log of the infectious period 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

1.17549E-38

3.40282E+38

1

The standard deviation of the natural log of the infectious period 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 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 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 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

0

The minimum infectious period 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 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

6

The mean of the infectious period with 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_Boxcar_Forcing_Amplitude

float

0

3.40E+38

0

The fractional increase in R0 during the high-infectivity season when Infectivity_Scale_Type is equal to ANNUAL_BOXCAR_FUNCTION.

 
{
    "Infectivity_Boxcar_Forcing_Amplitude": 0.25,
    "Infectivity_Boxcar_Forcing_End_Time": 270,
    "Infectivity_Boxcar_Forcing_Start_Time": 90,
    "Infectivity_Scale_Type": "ANNUAL_BOXCAR_FUNCTION"
}

Infectivity_Boxcar_Forcing_End_Time

float

0

365

0

The end of the high-infectivity season when Infectivity_Scale_Type is equal to ANNUAL_BOXCAR_FUNCTION.

 
{
    "Infectivity_Boxcar_Forcing_Amplitude": 0.25,
    "Infectivity_Boxcar_Forcing_End_Time": 270,
    "Infectivity_Boxcar_Forcing_Start_Time": 90,
    "Infectivity_Scale_Type": "ANNUAL_BOXCAR_FUNCTION"
}

Infectivity_Boxcar_Forcing_Start_Time

float

0

365

0

The beginning of the high-infectivity season, in days, when Infectivity_Scale_Type is equal to ANNUAL_BOXCAR_FUNCTION.

 
{
    "Infectivity_Boxcar_Forcing_Amplitude": 0.25,
    "Infectivity_Boxcar_Forcing_End_Time": 270,
    "Infectivity_Boxcar_Forcing_Start_Time": 90,
    "Infectivity_Scale_Type": "ANNUAL_BOXCAR_FUNCTION"
}

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"
}

Infectivity_Exponential_Delay

float

0

3.40E+38

0

The number of days before infectivity begins to ramp up 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"
}

Infectivity_Exponential_Rate

float

0

3.40E+38

0

The daily rate of exponential growth to approach to full infectivity after the delay set by Infectivity_Exponential_Delay has passed. Infectivity_Scale_Type must be set to EXPONENTIAL_FUNCTION_OF_TIME.

 
{
    "Infectivity_Exponential_Rate": 45
}

Infectivity_Scale_Type

enum

NA

NA

CONSTANT_INFECTIVITY

A scale factor that allows infectivity to be altered by time or season. Possible values are:

CONSTANT_INFECTIVITY

No infectivity correction is applied.

FUNCTION_OF_TIME_AND_LATITUDE

Infectivity is corrected for approximate seasonal forcing. The use of a seasonal infectivity correction is a proxy for the effects of varying climate. From October through March, infectivity increases in the Northern Hemisphere and decreases in the Southern Hemisphere. From April through September, the trend reverses: regions closer to the equator have reduced forcing compared to temperate regions.

This is not a substitute for the weather-driven vector dynamics of vector-borne and malaria simulations.

FUNCTION_OF_CLIMATE

Allows infectivity to be modulated by weather directly, for example, relative humidity in airborne simulations or rainfall in waterborne simulations. There is no default climate dependence enabled for generic simulations.

EXPONENTIAL_FUNCTION_OF_TIME

To facilitate certain burn-in scenarios, infectivity ramps up from zero at the beginning of the simulation according to the functional form, 1-exp(-rate*time), where the rate is specified by the parameter Infectivity_Scaling_Rate.

SINUSOIDAL_FUNCTION_OF_TIME

Allows infectivity to be time-dependent, following a sinusoidal shape defined by \(1 + \sin \text{Infectivity\_Sinusoidal\_Forcing\_Amplitude} \times \sin(2 \pi \times (\text{day} - \sin \text{Infectivity\_Sinusoidal\_Forcing\_Phase})/365)\). Set Infectivity_Sinusoidal_Forcing_Amplitude and Infectivity_Sinusoidal_Forcing_Phase.

ANNUAL_BOXCAR_FUNCTION

Allows infectivity 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 + Infectivity_Boxcar_Forcing_Amplitude. Set Infectivity_Boxcar_Forcing_Amplitude, Infectivity_Boxcar_Forcing_End_Time, and Infectivity_Boxcar_Forcing_Start_Time.

 
{
    "Infectivity_Scale_Type": "FUNCTION_OF_CLIMATE"
}

Infectivity_Sinusoidal_Forcing_Amplitude

float

0

1

0

Sets the amplitude of sinusoidal variations in Base_Infectivity. Only used when Infectivity_Scale_Type is set to SINUSOIDAL_FUNCTION_OF_TIME.

 
{
    "Infectivity_Scale_Type": "SINUSOIDAL_FUNCTION_OF_TIME",
    "Infectivity_Sinusoidal_Forcing_Amplitude": 0.1,
    "Infectivity_Sinusoidal_Forcing_Phase": 0
}

Infectivity_Sinusoidal_Forcing_Phase

float

0

365

0

Sets the phase of sinusoidal variations in Base_Infectivity. Only used when Infectivity_Scale_Type is set to SINUSOIDAL_FUNCTION_OF_TIME.

 
{
    "Infectivity_Scale_Type": "SINUSOIDAL_FUNCTION_OF_TIME",
    "Infectivity_Sinusoidal_Forcing_Amplitude": 0.1,
    "Infectivity_Sinusoidal_Forcing_Phase": 0
}

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_Scaling_Rate

float

0

3.40282e+38

0

The scaling rate for the variation in time of the log-linear susceptibility scaling. Susceptibility_Scaling_Type must be set to LOG_LINEAR_FUNCTION_OF_TIME.

 
{
    "Susceptibility_Scaling_Type": "LOG_LINEAR_FUNCTION_OF_TIME",
    "Susceptibility_Scaling_Rate": 1.58
}

Susceptibility_Scaling_Type

enum

NA

NA

CONSTANT_SUSCEPTIBILITY

The effect of time on susceptibility. Possible values are:

  • CONSTANT_SUSCEPTIBILITY

  • LOG_LINEAR_FUNCTION_OF_TIME

 
{
    "Susceptibility_Scaling_Type": "CONSTANT_SUSCEPTIBILITY"
}

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": {
        "arabiensis": {
            "Cycle_Arrhenius_1": 99.0,
            "Cycle_Arrhenius_2": 88.0,
            "Cycle_Arrhenius_Reduction_Factor": 0.77,
            "Nighttime_Feeding_Fraction": 1.0,
            "Acquire_Modifier": 0.2,
            "Adult_Life_Expectancy": 10,
            "Anthropophily": 0.95,
            "Aquatic_Arrhenius_1": 84200000000,
            "Aquatic_Arrhenius_2": 8328,
            "Aquatic_Mortality_Rate": 0.1,
            "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,
                "BRACKISH_SWAMP": 10000000000
            },
            "Transmission_Rate": 0.5
        }
    }
}

Input files

The following parameters set the paths to the the campaign file and the input files for climate, migration, demographics, and load-balancing.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Air_Migration_Filename

string

NA

NA

The path to the input file that defines patterns of migration by airplane. Enable_Air_Migration must be set to true (1). The file must be in .bin format.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration": 1,
    "Air_Migration_Filename": "../Global_1degree_air_migration.bin"
}

Air_Temperature_Filename

string

NA

NA

air_temp.json

The path to the input file that defines air temperature data measured two meters above ground. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.

 
{
    "Climate_Model": "CLIMATE_BY_DATA",
    "Air_Temperature_Filename": "Namawala_single_node_air_temperature_daily.bin"
}

Campaign_Filename

string

NA

NA

The path to the campaign file. It is required when interventions are part of the simulation and Enable_Interventions is set to true (1). The file must be in .json format.

 
{
    "Enable_Interventions": 1,
    "Campaign_Filename": "campaign.json"
}

Demographics_Filenames

array of strings

NA

NA

An array of the paths to demographics files containing information on the identity and demographics of the region to simulate. The files must be in .json format. Note that this parameter is only required when Enable_Demographics_Builtin is set to 0.

 
{
    "Demographics_Filenames": [
        "Namawala_single_node_demographics.json",
        "Namawala_demographics_overlay.json"
    ]
}

Family_Migration_Filename

string

NA

NA

The name of the binary file to use to configure family migration. Enable_Family_Migration must be set to true (1). The file must be in .bin format.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Family_Migration": 1,
    "Family_Migration_Filename": "../inputs/family_migration.bin"
}

Koppen_Filename

string

NA

NA

koppen_climate.json

The path to the input file used to specify Koppen climate classifications. Climate_Model must be set to CLIMATE_KOPPEN.

 
{
    "Koppen_Filename": "Mad_2_5arcminute_koppen.dat"
}

Land_Temperature_Filename

string

NA

NA

land_temp.json

The path of the input file defining temperature data measured at land surface; used only when Climate_Model is set to CLIMATE_BY_DATA. The file must be in .bin format.

 
{
    "Land_Temperature_Filename": "Namawala_single_node_land_temperature_daily.bin"
}

Load_Balance_Filename

string

NA

NA

UNINITIALIZED STRING

The path to the input file used when a static load balancing scheme is selected. The file must be in .json format.

 
{
    "Load_Balance_Filename": "GitHub_426_LoadBalance.json"
}

Local_Migration_Filename

string

NA

NA

The path of the input file which defines patterns of migration to adjacent nodes by foot travel. The file must be in .bin format.

 
{
    "Local_Migration_Filename": "Local_Migration.bin"
}

Rainfall_Filename

string

NA

NA

rainfall.json

The path of the input file which defines rainfall data. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.

 
{
    "Rainfall_Filename": "Namawala_single_node_rainfall_daily.bin"
}

Regional_Migration_Filename

string

NA

NA

The path of the input file which defines patterns of migration by vehicle via road or rail network. If the node is not on a road or rail network, regional migration focuses on the closest hub city in the network. The file must be in .bin format.

 
{
    "Regional_Migration_Filename": "Regional_Migration.bin"
}

Relative_Humidity_Filename

string

NA

NA

rel_hum.json

The path of the input file which defines relative humidity data measured 2 meters above ground. Climate_Model must be set to CLIMATE_BY_DATA. The file must be in .bin format.

 
{
    "Relative_Humidity_Filename": "Namawala_single_node_relative_humidity_daily.bin"
}

Sea_Migration_Filename

string

NA

NA

The path of the input file which defines patterns of migration by ship. Only used when Enable_Sea_Migration is set to true (1). The file must be in .bin format.

 
{
    "Sea_Migration_Filename": "5x5_Households_Work_Migration.bin"
}

Serialized_Population_Filenames

array of strings

NA

NA

NA

An array of filenames with serialized population data. The number of filenames must match the number of cores used for the simulation. The files must be in .dtk format. Serialized population files are created using Serialization_Time_Steps.

 
{
    "Serialized_Population_Filenames": [
        "state-00010.dtk"
    ]
}

Serialized_Population_Path

string

NA

NA

.

The root path for the serialized population files. Serialized population files are created using Serialization_Time_Steps.

 
{
    "Serialized_Population_Path": "../00_Generic_Version_1_save/output"
}

Vector_Migration_Filename_Local

string

NA

NA

UNSPECIFIED_FILE

The path to the vector migration file which defines patterns of vector migration to adjacent nodes. Enable_Vector_Migration must be set to 1. The file must be in .bin format.

 
{
    "Vector_Migration_Filename_Local": "5x5_Households_Local_Vector_Migration.bin"
}

Vector_Migration_Filename_Regional

string

NA

NA

UNSPECIFIED_FILE

The path to the vector migration file which defines patterns of vector migration to non-adjacent nodes. Enable_Vector_Migration must be set to 1. The file must be in .bin format.

 
{
    "Vector_Migration_Filename_Regional": "5x5_Households_Regional_Vector_Migration.bin"
}

Larval habitat

The following parameters determine mosquito larval development related to habitat and climate. For more information, see Larval habitat. Parameters for the vector life cycle more broadly are described in Vector life cycle.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

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
        }
    }
}

Aquatic_Mortality_Rate

float

0

1

0.1

The base aquatic mortality per day for the species before adjusting for effects of overpopulation and drying out of aquatic habitat.

 
{
    "Vector_Species_Params": {
        "arabiensis": {
            "Aquatic_Mortality_Rate": 0.1
        }
    }
}

Drought_Egg_Hatch_Delay

float

0

1

0.33

Proportion of regular egg hatching that still occurs when habitat dries up. Enable_Drought_Egg_Hatch_Delay must be set to 1.

 
{
    "Enable_Drought_Egg_Hatch_Delay": 1,
    "Drought_Egg_Hatch_Delay": 0.33
}

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
}

Egg_Hatch_Density_Dependence

enum

NA

NA

NO_DENSITY_DEPENDENCE

The effect of larval density on egg hatching rate. Possible values are:

DENSITY_DEPENDENCE

Egg hatching is reduced when the habitat is nearing its carrying capacity.

NO_DENSITY_DEPENDENCE

Egg hatching is not dependent upon larval density.

 
{
    "Egg_Hatch_Density_Dependence": "NO_DENSITY_DEPENDENCE"
}

Egg_Saturation_At_Oviposition

enum

NA

NA

NO_SATURATION

If laying all eggs from ovipositing females would overflow the larval habitat capacity on a given day, the means by which the viable eggs become saturated. Possible values are:

NO_SATURATION

Egg number does not saturate; all eggs are laid.

SATURATION_AT_OVIPOSITION

Eggs are saturated at oviposition; habitat is filled to capacity and excess eggs are discarded.

SIGMOIDAL_SATURATION

Eggs are saturated along a sigmoidal curve; proportionately fewer eggs are laid depending on how oversubscribed the habitat would be.

 
{
    "Egg_Saturation_At_Oviposition": "SATURATION_AT_OVIPOSITION"
}

Enable_Drought_Egg_Hatch_Delay

boolean

0

1

0

Controls whether or not eggs hatch at delayed rates, set by Drought_Egg_Hatch_Delay, when the habitat dries up completely.

 
{
    "Enable_Drought_Egg_Hatch_Delay": 1,
    "Drought_Egg_Hatch_Delay": 0.33
}

Enable_Egg_Mortality

boolean

0

1

0

Controls whether or not to include a daily mortality rate on the egg population, which is independent of climatic factors.

 
{
    "Enable_Egg_Mortality": 1
}

Enable_Temperature_Dependent_Egg_Hatching

boolean

0

1

0

Controls whether or not temperature has an effect on egg hatching, defined by Egg_Arrhenius_1 and Egg_Arrhenius_2.

 
{
    "Enable_Temperature_Dependent_Egg_Hatching": 1,
    "Egg_Arrhenius1": 61599956.864,
    "Egg_Arrhenius2": 5754.033
}

Larval_Density_Dependence

enum

NA

NA

UNIFORM_WHEN_OVERPOPULATION

The functional form of mortality and growth delay for mosquito larvae based on population density. Possible values are:

UNIFORM_WHEN_OVERPOPULATION

Mortality is uniformly applied to all larvae when the population exceeds the specified carrying capacity for that habitat.

GRADUAL_INSTAR_SPECIFIC

Mortality and delayed growth are instar-specific, where the younger larvae are more susceptible to predation and competition from older larvae.

LARVAL_AGE_DENSITY_DEPENDENT_MORTALITY_ONLY

Mortality is based only on larval age.

DENSITY_DELAYED_GROWTH_NOT_MORTALITY

There is no mortality, only delayed growth in larvae.

NO_DENSITY_DEPENDENCE

There is no additional larval density-dependent mortality factor.

 
{
    "Larval_Density_Dependence": "GRADUAL_INSTAR_SPECIFIC"
}

Larval_Habitat_Types

JSON object

NA

NA

NA

A measure of the habitat type and scale factors used to estimate larval population. This parameter is a dictionary that specifies habitat type with a simple numeric scale factor or, for LINEAR_SPLINE, with a more detailed configuration for scaling. The numeric scaling value represents larval density with the number of larvae in a 1x1-degree area. The factor multiplicatively scales the resulting weather or population-dependent functional form. See Larval habitat for more information. Possible habitat values are:

CONSTANT

Larval carrying capacity is constant throughout the year and does not depend on weather. However, mosquito abundance will exhibit a seasonal signal due to the effects of temperature on aquatic developmental rates.

TEMPORARY_RAINFALL

This habitat type corresponds to temporary puddles which are replenished by rainfall and drained through evaporation and infiltration. Habitat availability is proportional to temperature and humidity, and decays over time as configured by the parameter Temporary_Habitat_Decay_Factor.

WATER_VEGATATION

This habitat type corresponds to semi-permanent habitats, such as developing vegetation on the edges of small water sources such as swamps or rice cultivation settings. Development of habitat lags behind rainfall, and typically peaks near the end of the rainy season. Habitat decays daily, as specified by the parameter Semipermanent_Habitat_Decay_Rate.

HUMAN_POPULATION

This habitat type scales with correlates of human development, such as available water in pots in urban areas. It is configured by multiplying the number of people in a node’s population times the capacity value set for this parameter, and is not climate-dependent.

BRACKISH_SWAMP

This habitat type deals with the dynamics of how rain fills brackish swamps, how this habitat availability decays, and includes a rainfall-driven mortality threshold. Habitat decay rate is specified by the parameter Semipermanent_Habitat_Decay_Rate.

LINEAR_SPLINE

The LINEAR_SPLINE configuration specifies the day of year, larval value, and larval capacity scaling number. The model linearly interpolates the values to estimate the habitat availability for each vector species without requiring climatological data.

The values set here can be scaled per node using LarvalHabitatMultiplier in the demographics file (see NodeAttributes) or per intervention using Larval_Habitat_Multiplier in the campaign file (see ScaleLarvalHabitat).

The following example shows how to specify larval habitat using LINEAR_SPLINE.

{
    "Vector_Species_Params": {
        "arabiensis": {
            "Larval_Habitat_Types": {
                "LINEAR_SPLINE": {
                    "Capacity_Distribution_Per_Year": {
                        "Times": [
                            0.0,
                            60.833,
                            121.667,
                            182.5,
                            243.333,
                            204.167
                        ],
                        "Values": [
                            0.0,
                            0.0,
                            0.2,
                            1.0,
                            0.5,
                            0.0
                        ]
                    },
                    "Max_Larval_Capacity": 10000000000.0
                }
            }
        }
    }
}

The following example shows how to specify the larval habitat using climatological habitat types (you may use one or more for each vector species).

{
    "arabiensis": {
        "Larval_Habitat_Types": {
            "TEMPORARY_RAINFALL": 11250000000,
            "WATER_VEGETATION": 6000000000,
            "BRACKISH_SWAMP": 30000000
        }
    }
}

Larval_Rainfall_Mortality_Threshold

float

0.01

1000

100

The threshold value on daily rainfall in millimeters, above which larval mortality is applied when Vector_Larval_Rainfall_Mortality is set to either SIGMOID or SIGMOID_HABITAT_SHIFTING.

 
{
    "Larval_Rainfall_Mortality_Threshold": 30.0
}

Rainfall_In_mm_To_Fill_Swamp

float

1

10000

1000

Millimeters of rain to fill larval habitat to capacity. This is only used for vector species with Larval_Habitat_Types set to BRACKISH_SWAMP.

 
{
    "Rainfall_In_mm_To_Fill_Swamp": 1000.0
}

Semipermanent_Habitat_Decay_Rate

float

0.0001

100

0.01

Daily rate of larval habitat loss for semi-permanent habitats with Larval_Habitat_Types parameter value of WATER_VEGETATION or BRACKISH_SWAMP.

 
{
    "Semipermanent_Habitat_Decay_Rate": 0.01
}

Temporary_Habitat_Decay_Factor

float

0.001

100

0.05

The factor to convert raw evaporation rate (ignoring boundary layer effects) to the daily rate of larval habitat loss for temporary habitats (Larval_Habitat_Types set to TEMPORARY_RAINFALL). Units are (larval carrying capacity per day) / (kg per square meter per second).

 
{
    "Temporary_Habitat_Decay_Factor": 0.05
}

Vector_Larval_Rainfall_Mortality

enum

NA

NA

NONE

The type of vector larval mortality function due to rainfall. Possible values are:

NONE

No larval mortality due to rainfall.

SIGMOID

The mortality rate grows linearly from 0 at the threshold to 1 at twice the threshold value.

SIGMOID_HABITAT_SHIFTING

The threshold value is reduced by a factor proportional to how full the larval habitat is.

 
{
    "Vector_Larval_Rainfall_Mortality": "SIGMOID"
}

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
}

x_Temporary_Larval_Habitat

double

NA

NA

1

Scale factor for the habitat size for all mosquito populations.

 
{
    "x_Temporary_Larval_Habitat": 1
}

Migration

The following parameters determine aspects of population migration into and outside of a node, including daily commutes, seasonal migration, and one-way moves. Modes of transport includes travel by foot, automobile, sea, or air. Migration can also be configured to move all individuals in a family at the same time.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Air_Migration_Filename

string

NA

NA

The path to the input file that defines patterns of migration by airplane. Enable_Air_Migration must be set to true (1). The file must be in .bin format.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration": 1,
    "Air_Migration_Filename": "../Global_1degree_air_migration.bin"
}

Air_Migration_Roundtrip_Duration

float

0

10000

1

The average time spent (in days) at the destination node during a round-trip migration by airplane. Migration_Pattern must be set to SINGLE_ROUND_TRIPS.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration": 1,
    "Migration_Pattern": "SINGLE_ROUND_TRIPS",
    "Air_Migration_Roundtrip_Duration": 2
}

Air_Migration_Roundtrip_Probability

float

0

1

0.8

The likelihood that an individual who flies to another node will return to the node of origin during the next migration. Enable_Air_Migration must be set to true (1).

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration": 1,
    "Air_Migration_Roundtrip_Probability": 0.9
}

Enable_Air_Migration

boolean

0

1

0

Controls whether or not migration by air travel will occur. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Air_Migration": 1,
    "Air_Migration_Filename": "../inputs/air_migration.bin"
}

Enable_Family_Migration

boolean

0

1

0

Controls whether or not all members of a household can migrate together when a MigrateFamily event occurs. All residents must be home before they can leave on the trip. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Enable_Migration": "FIXED_RATE_MIGRATION",
    "Enable_Family_Migration": 1,
    "Family_Migration_Filename": "../inputs/family_migration.bin"
}

Enable_Local_Migration

boolean

0

1

0

Controls whether or not local migration (the diffusion of people in and out of nearby nodes by foot travel) occurs. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Local_Migration": 1,
    "Local_Migration_Filename": "../inputs/local_migration.bin"
}

Enable_Migration_Heterogeneity

boolean

0

1

1

Controls whether or not migration rate is heterogeneous among individuals within each group that has a migration rate setting. Set to true (1) to apply a migration rate distribution (see NodeAttributes demographics parameters); set to false (0) to use the same migration rate applied to all individuals in the group. For example, if you are using a migration file that sets different migration rates for each age group in a node, you could apply an Gaussian distribution around a mean value in each age group or you could assign the same value to each individual in each age group.

Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Migration_Heterogeneity": 1
}

Enable_Regional_Migration

boolean

0

1

0

Controls whether or not there is migration by road or rail network into and out of nodes in the simulation. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Regional_Migration": 1,
    "Regional_Migration_Filename": "../inputs/regional_migration.bin"
}

Enable_Sea_Migration

boolean

0

1

0

Controls whether or not there is migration on ships into and out of coastal cities with seaports. Migration_Model must be set to FIXED_RATE_MIGRATION.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Sea_Migration": 1,
    "Sea_Migration_Filename": "../inputs/sea_migration.bin"
}

Enable_Vector_Migration

boolean

0

1

0

Controls whether or not vectors can migrate. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS. Specific migration types must be enabled or disabled.

 
{
    "Vector_Sampling_Type": "TRACK_ALL_VECTORS",
    "Enable_Vector_Migration": 1,
    "Enable_Vector_Migration_Local": 1,
    "Vector_Migration_Filename_Local": "../inputs/vector_local.bin"
}

Enable_Vector_Migration_Local

boolean

0

1

0

Controls whether or not vectors may migrate to adjacent nodes. Enable_Vector_Migration must be set to true (1).

 
{
    "Vector_Sampling_Type": "TRACK_ALL_VECTORS",
    "Enable_Vector_Migration": 1,
    "Enable_Vector_Migration_Local": 1,
    "Vector_Migration_Filename_Local": "../inputs/vector_local.bin"
}

Enable_Vector_Migration_Regional

boolean

0

1

0

Controls whether or not vectors can migration to non-adjacent nodes. Enable_Vector_Migration must be set to true (1).

 
{
    "Vector_Sampling_Type": "TRACK_ALL_VECTORS",
    "Enable_Vector_Migration": 1,
    "Enable_Vector_Migration_Regional": 1,
    "Vector_Migration_Filename_Regional": "../inputs/vector_regional.bin"
}

Family_Migration_Filename

string

NA

NA

The name of the binary file to use to configure family migration. Enable_Family_Migration must be set to true (1). The file must be in .bin format.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Enable_Family_Migration": 1,
    "Family_Migration_Filename": "../inputs/family_migration.bin"
}

Family_Migration_Roundtrip_Duration

float

0

10000

1

The number of days to complete the trip and return to the original node. Migration_Pattern must be set to SINGLE_ROUND_TRIPS.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Migration_Pattern": "SINGLE_ROUND_TRIPS",
    "Enable_Family_Migration": 1,
    "Family_Migration_Roundtrip_Duration": 100
}

Local_Migration_Filename

string

NA

NA

The path of the input file which defines patterns of migration to adjacent nodes by foot travel. The file must be in .bin format.

 
{
    "Local_Migration_Filename": "Local_Migration.bin"
}

Local_Migration_Roundtrip_Duration

float

0

10000

1

The average time spent (in days) at the destination node during a round-trip migration by foot travel. Migration_Pattern must be set to SINGLE_ROUND_TRIPS.

 
{
    "Enable_Local_Migration": 1,
    "Migration_Pattern": "SINGLE_ROUND_TRIPS",
    "Local_Migration_Roundtrip_Duration": 1.0
}

Local_Migration_Roundtrip_Probability

float

0

1

0.95

The likelihood that an individual who walks into a neighboring node will return to the node of origin during the next migration. Only used when Enable_Local_Migration is set to true (1).

 
{
    "Local_Migration_Roundtrip_Probability": 1.0
}

Migration_Model

enum

NA

NA

NO_MIGRATION

Model to use for migration. Possible values are:

NO_MIGRATION

Migration into and out of nodes will not occur.

FIXED_RATE_MIGRATION

Migration into and out of nodes will occur at a fixed rate as defined in the migration files. At the beginning of the simulation or whenever an individual has just moved, they pick their next destination and the time and type of the migration. If an individual is on an outbound leg of their journey, they will query the node’s MigrationInfo object and, through probability, pick a new destination; if the individual is inbound, they will travel back to their previous location.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Local_Migration_Filename": "../inputs/local_migration.bin",
    "Enable_Local_Migration": 1
}

Migration_Pattern

enum

NA

NA

RANDOM_WALK_DIFFUSION

Describes the pattern of travel used during migration. Migration_Model must be set to FIXED_RATE_MIGRATION. Possible values are:

RANDOM_WALK_DIFFUSION

Individuals retain no memory of where they came from; every move is to a new destination with no thought of returning home.

SINGLE_ROUND_TRIPS

Individuals have a probability (determined Local_Migration_Roundtrip_Probability, Air_Migration_Roundtrip_Probability, etc.) that they will return to their original location after some duration of time. If they do not, the current location is the new departure point for migration, but their original location remains their home node.

WAYPOINTS_HOME

Individuals go on a multi-step journey along several waypoints and then retrace their steps back along their path once they have reached a maximum number of waypoints from their home node. For example, the path of travel would be 1 -> 2 -> 3 -> 4 -> 3 -> 2 -> 1 if their home is node 1. On the outbound journey, the duration at each waypoint is not set explicitly but is determined by each node’s migration rate; on the return journey, one timestep is spent at each waypoint.

 
{
    "Migration_Model": "FIXED_RATE_MIGRATION",
    "Migration_Pattern": "SINGLE_ROUND_TRIPS",
    "Enable_Local_Migration": 1,
    "Local_Migration_Roundtrip_Probability": 0.05,
    "Local_Migration_Roundtrip_Duration": 10
}

Regional_Migration_Filename

string

NA

NA

The path of the input file which defines patterns of migration by vehicle via road or rail network. If the node is not on a road or rail network, regional migration focuses on the closest hub city in the network. The file must be in .bin format.

 
{
    "Regional_Migration_Filename": "Regional_Migration.bin"
}

Regional_Migration_Roundtrip_Duration

float

0

10000

1

The average time spent (in days) at the destination node during a round-trip migration by road network. Migration_Pattern must be set to SINGLE_ROUND_TRIPS.

 
{
    "Enable_Regional_Migration": 1,
    "Migration_Pattern": "SINGLE_ROUND_TRIPS",
    "Regional_Migration_Roundtrip_Duration": 1.0
}

Regional_Migration_Roundtrip_Probability

float

0

1

0.1

The likelihood that an individual who travels by vehicle to another node will return to the node of origin during the next migration. Migration_Pattern must be set to SINGLE_ROUND_TRIPS.

 
{
    "Regional_Migration_Roundtrip_Probability": 1.0
}

Roundtrip_Waypoints

integer

0

1000

10

The maximum number of points reached during a trip before steps are retraced on the return trip home. Migration_Pattern must be set to WAYPOINTS_HOME.

 
{
    "Roundtrip_Waypoints": 5
}

Sea_Migration_Filename

string

NA

NA

The path of the input file which defines patterns of migration by ship. Only used when Enable_Sea_Migration is set to true (1). The file must be in .bin format.

 
{
    "Sea_Migration_Filename": "5x5_Households_Work_Migration.bin"
}

Sea_Migration_Roundtrip_Duration

float

0

10000

1

The average time spent at the destination node during a round-trip migration by ship. Used only when Migration_Pattern must be set to SINGLE_ROUND_TRIPS.

 
{
    "Enable_Sea_Migration": 1,
    "Migration_Pattern": "SINGLE_ROUND_TRIPS",
    "Sea_Migration_Roundtrip_Duration": 10000
}

Sea_Migration_Roundtrip_Probability

float

0

1

0.25

The likelihood that an individual who travels by ship into a neighboring node will return to the node of origin during the next migration. Used only when Enable_Sea_Migration is set to true (1).

 
{
    "Sea_Migration_Roundtrip_Probability": 0
}

Vector_Migration_Filename_Local

string

NA

NA

UNSPECIFIED_FILE

The path to the vector migration file which defines patterns of vector migration to adjacent nodes. Enable_Vector_Migration must be set to 1. The file must be in .bin format.

 
{
    "Vector_Migration_Filename_Local": "5x5_Households_Local_Vector_Migration.bin"
}

Vector_Migration_Filename_Regional

string

NA

NA

UNSPECIFIED_FILE

The path to the vector migration file which defines patterns of vector migration to non-adjacent nodes. Enable_Vector_Migration must be set to 1. The file must be in .bin format.

 
{
    "Vector_Migration_Filename_Regional": "5x5_Households_Regional_Vector_Migration.bin"
}

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_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_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_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
}

Mortality and survival

The following parameter determine mortality and survival characteristics of the disease being modeled and the population in general (non-disease mortality).

See Severe disease and mortality for more information about how fever, anemia, and parasite counts lead to severe malaria and mortality.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Anemia_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia.

 
{
    "Anemia_Mortality_Inverse_Width": 150
}

Anemia_Mortality_Threshold

double

NA

NA

3

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for hemoglobin count in grams per deciliter (g/dL) at which 50% of individuals die per day.

 
{
    "Anemia_Mortality_Threshold": 1.5
}

Anemia_Severe_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia.

 
{
    "Anemia_Severe_Inverse_Width": 20
}

Anemia_Severe_Threshold

float

0

100

5

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the severe disease threshold level for anemia. Threshold units are in grams per deciliter (g/dL).

 
{
    "Anemia_Severe_Threshold": 3.0
}

Death_Rate_Dependence

enum

NA

NA

NOT_INITIALIZED

Determines how likely individuals are to die from natural, non-disease causes. Enable_Natural_Mortality must be set to 1. Possible values are:

NOT_INITIALIZED

The daily mortality rate is 0, and no one dies from non-disease related causes.

NONDISEASE_MORTALITY_BY_AGE_AND_GENDER

The individual’s age and gender are taken into account to determine the daily mortality rate.

NONDISEASE_MORTALITY_BY_YEAR_AND_AGE_FOR_EACH_GENDER

Gender, age, and year, are all taken into account to determine the daily mortality rate.

Properties, rates, and bin sizes can be set for non-disease mortality for each gender in the demographics file (see Complex distributions parameters).

 
{
    "Death_Rate_Dependence": "NONDISEASE_MORTALITY_BY_AGE_AND_GENDER"
}

Enable_Disease_Mortality

boolean

0

1

1

Controls whether or not individuals are removed from the simulation due to disease deaths.

 
{
    "Enable_Disease_Mortality": 1
}

Enable_Natural_Mortality

boolean

0

1

0

Controls whether or not individuals are removed from the simulation due to natural (non-disease) deaths. Enable_Vital_Dynamics must be set to 1 (true). Use Death_Rate_Dependence to set the natural death rate.

 
{
    "Enable_Natural_Mortality": 1,
    "Enable_Vital_Dynamics": 1
}

Fever_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for fever.

 
{
    "Fever_Mortality_Inverse_Width": 1000
}

Fever_Mortality_Threshold

double

NA

NA

3

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the fever mortality threshold, in units of degrees Celsius above normal body temperature (defined as 37 C).

 
{
    "Fever_Mortality_Threshold": 10
}

Mortality_Blocking_Immunity_Decay_Rate

float

0

1

0.001

The rate at which mortality-blocking immunity decays after the mortality-blocking immunity offset period. Enable_Immune_Decay must be set to 1.

 
{
    "Mortality_Blocking_Immunity_Decay_Rate": 0.1
}

Mortality_Time_Course

enum

NA

NA

DAILY_MORTALITY

The method used to calculate disease deaths. Enable_Disease_Mortality must be set to 1.

Possible values are:

DAILY_MORTALITY

Calculated at every time step.

MORTALITY_AFTER_INFECTIOUS

Calculated once at the end of the disease duration.

 
{
    "Mortality_Time_Course": "MORTALITY_AFTER_INFECTIOUS"
}

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
}

Output settings

The following parameters configure whether or not output reports are created for the simulation, such as reports detailing spatial or demographic data at each time step. By default, the Inset chart output report is always created.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Custom_Coordinator_Events

array of strings

NA

NA

NA

The list of valid, user-defined events for Event Coordinators that will be included in the campaign. Any event used in the campaign must either be one of the built-in events or in this list.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Coordinator_Events": [
        "Coordinator_Event_1",
        "Coordinator_Event_2",
        "Coordinator_Event_3"
    ]
}

Custom_Individual_Events

array of strings

NA

NA

NA

The list of valid, user-defined events that will be included in the campaign. Any event used in the campaign must either be one of the built-in events or in this list.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Individual_Events": [
        "Individual_Event_1",
        "Individual_Event_2",
        "Individual_Event_3"
    ]
}

Custom_Node_Events

array of strings

NA

NA

NA

The list of valid, user-defined events for nodes that will be included in the campaign. Any event used in the campaign must either be one of the built-in events or in this list.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Node_Events": [
        "Node_Event_1",
        "Node_Event_2",
        "Node_Event_3"
    ]
}

Custom_Reports_Filename

string

NA

NA

UNINITIALIZED STRING

The name of the file containing custom report configuration parameters. Omitting this parameter or setting it to RunAllCustomReports will load all reporters found that are valid for the given simulation type. The file must be in JSON format.

 
{
    "Custom_Reports_Filename": "custom_reports.json"
}

Enable_Default_Reporting

boolean

0

1

1

Controls whether or not the default InsetChart.json report is created.

 
{
    "Enable_Default_Reporting": 1
}

Enable_Demographics_Reporting

boolean

0

1

1

Controls whether or not demographic summary data and age-binned reports are outputted to file.

 
{
    "Enable_Demographics_Reporting": 1
}

Enable_Property_Output

boolean

0

1

0

Controls whether or not to create property output reports, which detail groups as defined in IndividualProperties in the demographics file (see NodeProperties and IndividualProperties parameters). When there is more than one property type, the report will display the channel information for all combinations of the property type groups.

 
{
    "Enable_Property_Output": 1
}

Enable_Spatial_Output

boolean

0

1

0

Controls whether or not spatial output reports are created. If set to true (1), spatial output reports include all channels listed in the parameter Spatial_Output_Channels.

Note

Spatial output files require significant processing time and disk space.

 
{
    "Enable_Spatial_Output": 1,
    "Spatial_Output_Channels": [
        "Prevalence",
        "New_Infections"
    ]
}

Report_Coordinator_Event_Recorder

boolean

0

1

0

Enables or disables the ReportCoordinatorEventRecorder.csv output report for coordinator events. When enabled (set to 1) reports will be generated for the broadcasted valid coordinator events, as specified in Report_Coordinator_Event_Recorder_Events.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Coordinator_Events": [
        "Coordinator_Event_1",
        "Coordinator_Event_2",
        "Coordinator_Event_3"
    ],
    "Report_Coordinator_Event_Recorder": 1,
    "Report_Coordinator_Event_Recorder_Events": [
        "Coordinator_Event_1",
        "Coordinator_Event_2",
        "Coordinator_Event_3"
    ]
}

Report_Coordinator_Event_Recorder_Events

array of strings

NA

NA

NA

The list of events to include or exclude in the ReportCoordinatorEventRecorder.csv output report, based on how Report_Coordinator_Event_Recorder_Ignore_Events_In_List is set. This list must not be empty and is dependent upon Report_Coordinator_Event_Recorder being enabled. In addition, the events must be defined in Customer_Coordinator_Events.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Coordinator_Events": [
        "Coordinator_Event_1",
        "Coordinator_Event_2",
        "Coordinator_Event_3"
    ],
    "Report_Coordinator_Event_Recorder": 1,
    "Report_Coordinator_Event_Recorder_Events": [
        "Coordinator_Event_1",
        "Coordinator_Event_2",
        "Coordinator_Event_3"
    ]
}

Report_Coordinator_Event_Recorder_Ignore_Events_In_List

boolean

0

1

0

If set to false (0), only the events listed in the Report_Coordinator_Event_Recorder_Events array will be included in the ReportCoordinatorEventRecorder.csv output report. If set to true (1), only the events listed in the array will be excluded, and all other events will be included. If you want to return all events from the simulation, leave the events array empty.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Coordinator_Events": [
        "Coordinator_Event_1",
        "Coordinator_Event_2",
        "Coordinator_Event_3"
    ],
    "Report_Coordinator_Event_Recorder": 1,
    "Report_Coordinator_Event_Recorder_Events": [
        "Coordinator_Event_1",
        "Coordinator_Event_2",
        "Coordinator_Event_3"
    ],
    "Report_Coordinator_Event_Recorder_Ignore_Events_In_List": 0
}

Report_Event_Recorder

boolean

0

1

0

Set to true (1) to enable or to false (0) to disable the ReportEventRecorder.csv output report that lists individual events in the simulation. See Event list for a list of all possible built-in events that will be recorded in the output when enabled.

 
{
    "Report_Event_Recorder": 1,
    "Report_Event_Recorder_Events": [
        "VaccinatedA",
        "VaccineExpiredA",
        "VaccinatedB",
        "VaccineExpiredB"
    ],
    "Report_Event_Recorder_Ignore_Events_In_List": 0
}

Report_Event_Recorder_Events

array

NA

NA

The list of events to include or exclude in the ReportEventRecorder.csv output report, based on how Report_Event_Recorder_Ignore_Events_In_List is set. See Event list for a list of all possible built-in events. You can also define events in Custom_Individual_Events. The list cannot be empty.

 
{
    "Report_Event_Recorder": 1,
    "Report_Event_Recorder_Events": [
        "VaccinatedA",
        "VaccineExpiredA",
        "VaccinatedB",
        "VaccineExpiredB"
    ],
    "Report_Event_Recorder_Ignore_Events_In_List": 0
}

Report_Event_Recorder_Ignore_Events_In_List

boolean

0

1

0

If set to false (0), only the events listed in the Report_Event_Recorder_Events array will be included in the ReportEventRecorder.csv output report. If set to true (1), only the events listed in the array will be excluded, and all other events will be included. If you want to return all events from the simulation, leave the events array empty.

Value

Events array

Output file

0

No events

No events

0

One or more events

Only the listed events.

1

No events

All events occurring in the simulation.

1

One or more events

All simulation events occurring in the simulation, except for those listed.

 
{
    "Report_Event_Recorder": 1,
    "Report_Event_Recorder_Events": [
        "VaccinatedA",
        "VaccineExpiredA",
        "VaccinatedB",
        "VaccineExpiredB"
    ],
    "Report_Event_Recorder_Ignore_Events_In_List": 0
}

Report_Event_Recorder_Individual_Properties

array of strings

NA

NA

[]

Specifies an array of (optional) individual property keys, as defined in IndividualProperties in the demographics file, to be added as additional columns to the output report. Individual’s IP value will be added to the (key) column at the time of the event.

 
{
    "Report_Event_Recorder_Individual_Properties": [
        "Accessibility",
        "Risk"
    ]
}

Report_Node_Event_Recorder

boolean

0

1

0

Enables or disables the ReportNodeEventRecorder.csv output report. When enabled (set to 1) reports will be generated for the broadcasted valid node events, as specified in Report_Node_Event_Recorder_Events.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Node_Events": [
        "Node_Event_1",
        "Node_Event_2"
    ],
    "Report_Node_Event_Recorder": 1,
    "Report_Node_Event_Recorder_Events": [
        "Node_Event_1",
        "Node_Event_2"
    ]
}

Report_Node_Event_Recorder_Ignore_Events_In_List

boolean

0

1

0

If set to false (0), only the node events listed in the Report_Node_Event_Recorder_Events array will be included in the ReportNodeEventRecorder.csv output report. If set to true (1), only the node events listed in the array will be excluded, and all other node events will be included. If you want to return all node events from the simulation, leave the node events array empty.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

Value

Events array

Output file

0

No events

No events

0

One or more events

Only the listed events.

1

No events

All events occurring in the simulation.

1

One or more events

All simulation events occurring in the simulation, except for those listed.

 
{
    "Custom_Node_Events": [
        "Node_Event_1",
        "Node_Event_2"
    ],
    "Report_Node_Event_Recorder": 1,
    "Report_Node_Event_Recorder_Events": [
        "Node_Event_1",
        "Node_Event_2"
    ],
    "Report_Node_Event_Recorder_Ignore_Events_In_List": 0
}

Report_Node_Event_Recorder_Node_Properties

array of strings

NA

NA

[]

Specifies an array of (optional) node property keys, as defined in NodeProperties in the demographics file, to be added as additional columns to the ReportNodeEventRecorder.csv output report.

 
{
    "Custom_Node_Events": [
        "Node_Event_1",
        "Node_Event_2"
    ],
    "Report_Node_Event_Recorder": 1,
    "Report_Node_Event_Recorder_Events": [
        "Node_Event_1",
        "Node_Event_2"
    ],
    "Report_Node_Event_Recorder_Ignore_Events_In_List": 0,
    "Report_Node_Event_Recorder_Node_Properties": [
        "Geographic"
    ]
}

Report_Node_Event_Recorder_Stats_By_IPs

array of strings

NA

NA

[]

Specifies an array of (optional) individual property keys, as defined in IndividualProperties in the demographics file, to be added to the ReportNodeEventRecorder.csv output report. For each key:value pair there will be two additional columns (Key:Value:NumIndividuals, Key:Value:NumInfected) added to the report. For example, with a Risk property key assigned the values of LOW and HIGH there would then be four additional columns (Risk:LOW:NumIndividuals, Risk:LOW:NumInfected, Risk:HIGH:NumIndividuals, Risk:HIGH:NumInfected). An empty array equals no additional columns added.

 
{
    "Custom_Node_Events": [
        "Node_Event_1",
        "Node_Event_2"
    ],
    "Report_Node_Event_Recorder": 1,
    "Report_Node_Event_Recorder_Events": [
        "Node_Event_1",
        "Node_Event_2"
    ],
    "Report_Node_Event_Recorder_Ignore_Events_In_List": 0,
    "Report_Node_Event_Recorder_Node_Properties": [
        "Geographic"
    ],
    "Report_Node_Event_Recorder_Stats_By_IPs": [
        "Risk"
    ]
}

Report_Surveillance_Event_Recorder

boolean

0

1

0

Enables or disables the ReportSurveillanceEventRecorder.csv output report. When enabled (set to 1) reports will be generated for the broadcasted valid coordinator events, as specified in Report_Surveillance_Event_Recorder_Events.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Coordinator_Events": [
        "Start_ACF",
        "Start_SIA_2",
        "Start_SIA_4",
        "Ind_Start_SIA_2",
        "Ind_Start_SIA_4",
        "Respond_To_Surveillance"
    ],
    "Report_Surveillance_Event_Recorder": 1,
    "Report_Surveillance_Event_Recorder_Events": [
        "Respond_To_Surveillance"
    ]
}

Report_Surveillance_Event_Recorder_Events

array of strings

NA

NA

NA

The list of events to include or exclude in the ReportSurveillanceEventRecorder.csv output report, based on how Report_Surveillance_Event_Recorder_Ignore_Events_In_List is set. This list must not be empty and is dependent upon Report_Surveillance_Event_Recorder being enabled.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Coordinator_Events": [
        "Start_ACF",
        "Start_SIA_2",
        "Start_SIA_4",
        "Ind_Start_SIA_2",
        "Ind_Start_SIA_4",
        "Respond_To_Surveillance"
    ],
    "Report_Surveillance_Event_Recorder": 1,
    "Report_Surveillance_Event_Recorder_Events": [
        "Respond_To_Surveillance"
    ]
}

Report_Surveillance_Event_Recorder_Ignore_Events_In_List

boolean

0

1

0

If set to false (0), only the events listed in the Report_Surveillance_Event_Recorder_Events array will be included in the ReportSurveillanceEventRecorder.csv output report. If set to true (1), only the events listed in the array will be excluded, and all other events will be included. If you want to return all events from the simulation, leave the events array empty.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

Value

Events array

Output file

0

No events

No events

0

One or more events

Only the listed events.

1

No events

All events occurring in the simulation.

1

One or more events

All simulation events occurring in the simulation, except for those listed.

 
{
    "Custom_Coordinator_Events": [
        "Start_ACF",
        "Start_SIA_2",
        "Start_SIA_4",
        "Ind_Start_SIA_2",
        "Ind_Start_SIA_4",
        "Respond_To_Surveillance"
    ],
    "Report_Surveillance_Event_Recorder": 1,
    "Report_Surveillance_Event_Recorder_Events": [
        "Respond_To_Surveillance"
    ],
    "Report_Surveillance_Event_Recorder_Ignore_Events_In_List": 0
}

Report_Surveillance_Event_Recorder_Stats_By_IPs

array of strings

NA

NA

[]

Specifies an array of (optional) individual property keys, as defined in IndividualProperties in the demographics file, to be added to the ReportSurveillanceEventRecorder.csv output report. For each key:value pair there will be two additional columns (Key:Value:NumIndividuals, Key:Value:NumInfected) added to the report. For example, with a Risk property key assigned the values of LOW and HIGH there would then be four additional columns (Risk:LOW:NumIndividuals, Risk:LOW:NumInfected, Risk:HIGH:NumIndividuals, Risk:HIGH:NumInfected). An empty array equals no additional columns added.

 
{
    "Custom_Coordinator_Events": [
        "Start_ACF",
        "Start_SIA_2",
        "Start_SIA_4",
        "Ind_Start_SIA_2",
        "Ind_Start_SIA_4",
        "Respond_To_Surveillance"
    ],
    "Report_Surveillance_Event_Recorder": 1,
    "Report_Surveillance_Event_Recorder_Events": [
        "Respond_To_Surveillance"
    ],
    "Report_Surveillance_Event_Recorder_Stats_By_IPs": []
}

Spatial_Output_Channels

array of strings

NA

NA

[]

An array of channel names for spatial output by node and time step. The data from each channel will be written to a separate binary file. Enable_Spatial_Output must be set to true (1). Possible values are:

Air_Temperature

Data related to air temperature.

Births

Data related to the number of births.

Campaign_Cost

Data related to the costs of a campaign.

Disease_Deaths

Data related to the number of deaths due to disease.

Human_Infectious_Reservoir

Data related to the total infectiousness of the population.

Infection_Rate

Data related to infection rates.

Land_Temperature

Data related to the average land temperature over all nodes.

New_Infections

Data related to the presence of new infections.

New_Reported_Infections

Data related to the presence of reported new infections.

Population

Data related to the total population in the simulation.

Prevalence

Data related to the fraction of the population that is infected.

Rainfall

Data related to the presence of rainfall.

Relative_Humidity

Data related to the presence of relative humidity.

Fever_Prevalence

Data related to the presence of fever.

Mean_Parasitemia

Data related to the presence of mean parasitemia.

New_Clinical_Cases

Data related to the presence of new clinical cases.

New_Diagnostic_Prevalence

Data related to the presence of a new diagnostic.

New_Severe_Cases

Data related to the presence of new severe cases.

Parasite_Prevalence

Data related to the presence of parasites.

Adult_Vectors

Data related to the presence of adult vectors.

Daily_EIR

Data related to entomological inoculation rate (EIR) for mosquitoes.

 
{
    "Spatial_Output_Channels": [
        "Prevalence",
        "New_Infections"
    ]
}

Parasite dynamics

The following parameters determine the dynamics of the Plasmodium falciparum parasite life cycle, including dynamics within the host and human population. For more information, see Malaria infection and immune model.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Base_Gametocyte_Fraction_Male

double

NA

NA

0.2

Fraction of gametocytes that are male.

 
{
    "Base_Gametocyte_Fraction_Male": 0.25
}

Base_Gametocyte_Mosquito_Survival_Rate

float

0

1

0.01

Average fraction of gametocytes in a blood meal that are successful in infecting the mosquito in the absence of other modulating effects, such as fever.

 
{
    "Base_Gametocyte_Mosquito_Survival_Rate": 0.015
}

Base_Gametocyte_Production_Rate

double

NA

NA

0.02

The fraction of infected red blood cells (IRBCs) producing gametocytes.

 
{
    "Base_Gametocyte_Mosquito_Survival_Rate": 0.01
}

Base_Sporozoite_Survival_Fraction

float

0

1

0.25

The fraction of sporozoites that survive to infect a hepatocyte in the absence of anti-CSP protection.

 
{
    "Base_Sporozoite_Survival_Fraction": 0.25
}

Cytokine_Gametocyte_Inactivation

float

0

1

0.02

The strength of inflammatory response inactivation of gametocytes.

 
{
    "Cytokine_Gametocyte_Inactivation": 0.0167
}

Enable_Sexual_Combination

boolean

0

1

0

Controls whether or not male and female gametocytes undergo sexual combination. Set to true (1) to allow for sexual combination; set to false (0) for transmission of each strain only.

Note

This parameter is currently not in use.

 
{
    "Enable_Sexual_Combination": 0
}

Gametocyte_Stage_Survival_Rate

double

0

1

1

The rate of gametocyte survival from one development stage to the next in the absence of drugs or inflammatory immune response.

 
{
    "Gametocyte_Stage_Survival_Rate": 0.8
}

Mean_Sporozoites_Per_Bite

float

0

1000

11

The mean number of sporozoites per infectious mosquito bite.

 
{
    "Mean_Sporozoites_Per_Bite": 11
}

Merozoites_Per_Hepatocyte

double

NA

NA

15000

The number of IRBCs caused by a single infected hepatocyte at the start of infection.

 
{
    "Merozoites_Per_Hepatocyte": 15000
}

Merozoites_Per_Schizont

double

NA

NA

16

The number of merozoites released by a single infected schizont after each asexual cycle. The number of resulting IRBC’s depends on the RBC availability and merozoite-specific immunity.

 
{
    "Merozoites_Per_Schizont": 16
}

Number_Of_Asexual_Cycles_Without_Gametocytes

integer

0

500

1

The number of asexual reproduction cycles that do not produce gametocytes. All later cycles will produce gametocytes according to Base_Gametocyte_Production_Rate.

 
{
    "Number_Of_Asexual_Cycles_Without_Gametocytes": 1
}

Parasite_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ).

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for parasite density.

 
{
    "Parasite_Mortality_Inverse_Width": 100
}

Parasite_Mortality_Threshold

double

NA

NA

2000000

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the parasite-density mortality threshold for a simulation.

 
{
    "Parasite_Mortality_Threshold": 3000000
}

Parasite_Severe_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for parasite density.

 
{
    "Parasite_Severe_Inverse_Width": 48.66825295
}

Parasite_Severe_Threshold

float

0

3.40E+38

1000000

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures parasite density threshold level that results in severe disease.

 
{
    "Parasite_Severe_Threshold": 253871
}

Parasite_Smear_Sensitivity

float

0.0001

100

0.1

The number of microliters of blood tested to find single parasites in a traditional smear (corresponds to inverse parasites/microliters sensitivity).

 
{
    "Parasite_Smear_Sensitivity": 0.1
}

Parasite_Switch_Type

enum

NA

NA

CONSTANT_SWITCH_RATE_2VARS

The parasite switch type for erythrocyte surface antigens. Possible values are:

CONSTANT_SWITCH_RATE_2VARS

Introduction of new variants has a fixed probability which does not depend on the level of parasitemia.

RATE_PER_PARASITE_7VARS

Each IRBC has a fixed rate of switching to each of seven possible variants.

RATE_PER_PARASITE_5VARS_DECAYING

Each IRBC has a rate of switching to several possible variants, and the rate decreases with distance from the original variant.

 
{
    "Parasite_Switch_Type": "RATE_PER_PARASITE_7VARS"
}

Population dynamics

The following parameters determine characteristics related to population dynamics, such as age distribution, births, deaths, and gender. The values set here generally interact closely with values in the demographics file.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Age_Initialization_Distribution_Type

enum

NA

NA

DISTRIBUTION_OFF

The method for initializing the age distribution in the simulated population. Possible values are:

DISTRIBUTION_OFF

All individuals default to age 20 years old.

DISTRIBUTION_SIMPLE

Individual ages are drawn from a distribution whose functional form is specified in the demographics file using the IndividualAttributes simple Age distribution parameters.

DISTRIBUTION_COMPLEX

Individual ages are drawn from a piecewise linear function specified in the demographics file complex distribution parameters.

 
{
    "Age_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE"
}

Birth_Rate_Boxcar_Forcing_Amplitude

float

0

3.40E+38

0

Fractional increase in birth rate during high birth season when Birth_Rate_Time_Dependence is set to ANNUAL_BOXCAR_FUNCTION.

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION",
    "Birth_Rate_Boxcar_Forcing_Amplitude": 0.1
}

Birth_Rate_Boxcar_Forcing_End_Time

float

0

365

0

Day of the year when the high birth rate season ends when Birth_Rate_Time_Dependence is set to ANNUAL_BOXCAR_FUNCTION.

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION",
    "Birth_Rate_Boxcar_Forcing_End_Time": 220
}

Birth_Rate_Boxcar_Forcing_Start_Time

float

0

365

0

Day of the year when the high birth rate season begins when Birth_Rate_Time_Dependence is set to ANNUAL_BOXCAR_FUNCTION.

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "ANNUAL_BOXCAR_FUNCTION",
    "Birth_Rate_Boxcar_Forcing_Start_Time": 130
}

Birth_Rate_Dependence

enum

NA

NA

FIXED_BIRTH_RATE

The method used to modify the value set in BirthRate in the demographics file (see NodeAttributes parameters). Possible values are:

NONE

Births are not allowed during the simulation, even if Enable_Birth is set to true (1).

FIXED_BIRTH_RATE

The absolute rate at which new individuals are born, as set by BirthRate.

POPULATION_DEP_RATE

Scales the node population to determine the birth rate. If BirthRate is greater than 0.005, a value of 2% per year (0.02/365) is used instead.

DEMOGRAPHIC_DEP_RATE

Scales the female population within fertility age ranges to determine the birth rate. If BirthRate is greater than 0.005, a value of 1 child every 8 years of fertility [1/8/365(~0.000342)] is used instead.

INDIVIDUAL_PREGNANCIES

Scales the female population within fertility age ranges to determine the birth rate, but pregnancies are assigned on an individual basis and result in a 40-week pregnancy for a specific individual with a birth at the end.

INDIVIDUAL_PREGNANCIES_BY_URBAN_AND_AGE

Similar to INDIVIDUAL_PREGNANCIES, but determines the rate based on the FertilityDistribution (in IndividualAttributes) and Urban (in NodeAttributes), as well as the individual’s age.

INDIVIDUAL_PREGNANCIES_BY_AGE_AND_YEAR

Similar to INDIVIDUAL_PREGNANCIES, but determines the rate based on the FertilityDistribution (in IndividualAttributes), using the individual’s age and the year of the simulation.

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Dependence": "POPULATION_DEP_RATE"
}

Birth_Rate_Sinusoidal_Forcing_Amplitude

float

0

1

0

The amplitude of sinusoidal variations in birth rate when Birth_Rate_Time_Dependence is set to SINUSOIDAL_FUNCTION_OF_TIME.

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Birth_Rate_Time_Dependence": "SINUSOIDAL_FUNCTION_OF_TIME",
    "Birth_Rate_Sinusoidal_Forcing_Amplitude": 0.1
}

Birth_Rate_Sinusoidal_Forcing_Phase

float

0

365

0

The phase of sinusoidal variations in birth rate. Birth_Rate_Time_Dependence must be set to SINUSOIDAL_FUNCTION_OF_TIME.

 
{
    "Birth_Rate_Sinusoidal_Forcing_Phase": 20
}

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"
}

Death_Rate_Dependence

enum

NA

NA

NOT_INITIALIZED

Determines how likely individuals are to die from natural, non-disease causes. Enable_Natural_Mortality must be set to 1. Possible values are:

NOT_INITIALIZED

The daily mortality rate is 0, and no one dies from non-disease related causes.

NONDISEASE_MORTALITY_BY_AGE_AND_GENDER

The individual’s age and gender are taken into account to determine the daily mortality rate.

NONDISEASE_MORTALITY_BY_YEAR_AND_AGE_FOR_EACH_GENDER

Gender, age, and year, are all taken into account to determine the daily mortality rate.

Properties, rates, and bin sizes can be set for non-disease mortality for each gender in the demographics file (see Complex distributions parameters).

 
{
    "Death_Rate_Dependence": "NONDISEASE_MORTALITY_BY_AGE_AND_GENDER"
}

Default_Geography_Initial_Node_Population

integer

0

1000000

1000

When using the built-in demographics for default geography, the initial number of individuals in each node. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing. Enable_Demographics_Builtin must be set to true (1).

 
{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}

Demographics_Filenames

array of strings

NA

NA

An array of the paths to demographics files containing information on the identity and demographics of the region to simulate. The files must be in .json format. Note that this parameter is only required when Enable_Demographics_Builtin is set to 0.

 
{
    "Demographics_Filenames": [
        "Namawala_single_node_demographics.json",
        "Namawala_demographics_overlay.json"
    ]
}

Enable_Aging

boolean

0

1

1

Controls whether or not individuals in a population age during the simulation. Enable_Vital_Dynamics must be set to true (1).

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Aging": 1
}

Enable_Birth

boolean

0

1

1

Controls whether or not individuals will be added to the simulation by birth. Enable_Vital_Dynamics must be set to true (1). If you want new individuals to have the same intervention coverage as existing individuals, you must add a BirthTriggeredIV to the campaign file.

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

Enable_Demographics_Birth

boolean

0

1

0

Controls whether or not newborns have identical or heterogeneous characteristics. Set to false (0) to give all newborns identical characteristics; set to true (1) to allow for heterogeneity in traits such as sickle-cell status. Enable_Birth must be set to true (1).

 
{
    "Enable_Birth": 1,
    "Enable_Demographics_Birth": 1
}

Enable_Demographics_Builtin

boolean

0

1

0

Controls whether or not built-in demographics for default geography will be used. Note that the built-in demographics feature does not represent a real geographical location and is mostly used for testing. Set to true (1) to define the initial population and number of nodes using Default_Geography_Initial_Node_Population and Default_Geography_Torus_Size. Set to false (0) to use demographics input files defined in Demographics_Filenames.

 
{
    "Enable_Demographics_Builtin": 1,
    "Default_Geography_Initial_Node_Population": 1000,
    "Default_Geography_Torus_Size": 3
}

Enable_Demographics_Risk

boolean

0

1

0

Controls whether or not the simulation includes the impact of disease risk in demographics.

 
{
    "Enable_Demographics_Risk": 1
}

Enable_Vital_Dynamics

boolean

0

1

1

Controls whether or not births and deaths occur in the simulation. Births and deaths must be individually enabled and set.

 
{
    "Enable_Vital_Dynamics": 1,
    "Enable_Birth": 1,
    "Death_Rate_Dependence": "NOT_INITIALIZED",
    "Base_Mortality": 0.002
}

Minimum_Adult_Age_Years

float

0

3.40E+38

15

The age, in years, after which an individual is considered an adult. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP.

 
{
    "Minimum_Adult_Age_Years": 17
}

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"
}

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"
}

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
}

Sampling

The following parameters determine how a population is sampled in the simulation. While you may want every agent (individual object) to represent a single person, you can often optimize CPU time with without degrading the accuracy of the simulation but having an agent represent multiple people. The sampling rate may be adapted to have a higher or lower sampling rate for particular regions or age groups.

For vector and malaria simulations, the same concepts apply to sampling the vector population.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Base_Individual_Sample_Rate

float

0.001

1

1

The base rate of sampling for individuals, equal to the fraction of individuals in each node being sampled. Reducing the sampling rate will reduce the time needed to run simulations. Individual_Sampling_Type must be set to FIXED_SAMPLING or ADAPTED_SAMPLING_BY_IMMUNE_STATE.

 
{
    "Base_Individual_Sample_Rate": 0.01
}

Immune_Threshold_For_Downsampling

float

0

1

0

The threshold on acquisition immunity at which to apply immunity-dependent downsampling; individuals who are more immune than this this threshold are downsampled. A value of 1 is equivalent to full susceptibility and 0 is equivalent to full immunity. If the acquisition immunity modifier is larger than the threshold, no downsampling occurs. Individual_Sampling_Type must set to ADAPTED_SAMPLING_BY_IMMUNE_STATE.

 
{
    "Relative_Sample_Rate_Immune": 0.1,
    "Immune_Threshold_For_Downsampling": 0.5,
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_IMMUNE_STATE"
}

Individual_Sampling_Type

enum

NA

NA

TRACK_ALL

The type of individual human sampling to use, which can be used to down sample large populations, certain age groups, or the immune population that does not contribute to transmission. Possible values are:

TRACK_ALL

Each person in the population is tracked as a single Individual object with a sampling weight of 1.

FIXED_SAMPLING

Members of the population are added to the simulation with a probability of Base_Individual_Sample_Rate and sampling weight of 1 / Base_Individual_Sample_Rate. This allows a smaller set of Individual objects to represent the overall population.

ADAPTED_SAMPLING_BY_POPULATION_SIZE

For each node, a maximum number of Individual objects is tracked (set in Max_Node_Population_Samples). If the population is smaller than this number, each person is tracked with a sampling rate of 1; if the population is larger, members of the population are added to the simulation with a probability of Max_Node_Population_Samples / population and sampling weight of population / Max_Node_Population_Samples. This setting is useful for simulations over large geographic areas with large heterogeneities in population density.

ADAPTED_SAMPLING_BY_AGE_GROUP

The population is binned by age and each age bin is sampled at a different rate as defined by Sample_Rate parameters. The setting is useful for diseases in which only infants or children are relevant by allowing full sampling of these age groups while using fewer objects to represent the rest of the population.

ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE

Each node has a maximum number of Individual objects as described in ADAPTED_SAMPLING_BY_POPULATION_SIZE, but when the population grows beyond that threshold, sampling is not done at a fixed rate, but varies by age as described in ADAPTED_SAMPLING_BY_AGE_GROUP.

ADAPTED_SAMPLING_BY_IMMUNE_STATE

Individuals who have acquired immunity are sampled at a lower rate as defined by Relative_Sample_Rate_Immune and Immune_Threshold_For_Downsampling parameters. This converges with regular sampling when those parameters are set to 1 or 0, respectively.

The following example shows how to sampling immune individuals at a lower rate.

{
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_IMMUNE_STATE",
    "Immune_Threshold_For_Downsampling": 0.5,
    "Relative_Sample_Rate_Immune": 0.1
}

The following example shows how to sampling older individuals at a lower rate.

{
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_AGE_GROUP",
    "Sample_Rate_0_18mo": 1,
    "Sample_Rate_10_14": 0.5,
    "Sample_Rate_15_19": 0.3,
    "Sample_Rate_18mo_4yr": 1,
    "Sample_Rate_20_Plus": 0.2,
    "Sample_Rate_5_9": 1,
    "Sample_Rate_Birth": 1
}

Max_Node_Population_Samples

float

1

3.40E+38

30

The maximum number of individuals to track in a node. When the population exceeds this number, the sampling rate will drop according to the value set in Individual_Sampling_Type.

 
{
    "Individual_Sampling_Type": "ADAPTED_SAMPLING_BY_POPULATION_SIZE",
    "Max_Node_Population_Samples": 100000
}

Mosquito_Weight

integer

1

10000

1

The value indicating how many mosquitoes are represented by a sample mosquito in the simulation. Vector_Sampling_Type must be set to SAMPLE_IND_VECTORS.

 
{
    "Mosquito_Weight": 10
}

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"
}

Sample_Rate_0_18mo

float

0.001

1000

1

For age-adapted sampling, the relative sampling rate for infants age 0 to 18 months. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.

 
{
    "Sample_Rate_0_18mo": 1
}

Sample_Rate_10_14

float

0.001

1000

1

For age-adapted sampling, the relative sampling rate for children age 10 to 14 years. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.

 
{
    "Sample_Rate_10_14": 1
}

Sample_Rate_15_19

float

0.001

1000

1

For age-adapted sampling, the relative sampling rate for adolescents age 15 to 19 years. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.

 
{
    "Sample_Rate_15_19": 1
}

Sample_Rate_18mo_4yr

float

0.001

1000

1

For age-adapted sampling, the relative sampling rate for children age 18 months to 4 years. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.

 
{
    "Sample_Rate_18mo_4yr": 1
}

Sample_Rate_20_plus

float

0.001

1000

1

For age-adapted sampling, the relative sampling rate for adults age 20 and older. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.

 
{
    "Sample_Rate_20_plus": 1
}

Sample_Rate_5_9

float

0.001

1000

1

For age-adapted sampling, the relative sampling rate for children age 5 to 9 years. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.

 
{
    "Sample_Rate_5_9": 1
}

Sample_Rate_Birth

float

0.001

1000

1

For age-adapted sampling, the relative sampling rate for births. Individual_Sampling_Type must be set to ADAPTED_SAMPLING_BY_AGE_GROUP or ADAPTED_SAMPLING_BY_AGE_GROUP_AND_POP_SIZE.

 
{
    "Sample_Rate_Birth": 1
}

Vector_Sampling_Type

enum

NA

NA

TRACK_ALL_VECTORS

The type of vector sampling used. Possible values are:

TRACK_ALL_VECTORS

Each vector in a node is part of the simulation as a separate object.

SAMPLE_IND_VECTORS

Each vector object in the simulation represents multiple vectors in the node population. Mosquito_Weight sets the number of mosquitos represented by each object.

VECTOR_COMPARTMENTS_NUMBER

Does not track every vector individually, but provides a compartment for every possible entry in state space and tracks the number of vectors in each compartment. This successfully accounts for each vector, but does not distinguish between vectors that have identical states, just counts how many identical vectors of each state are present at a location.

VECTOR_COMPARTMENTS_PERCENT

Similar to VECTOR_COMPARTMENTS_NUMBER, but it only tracks the percentage of the population in each state. Less useful, but included for comparison to other models.

 
{
    "Vector_Sampling_Type": "TRACK_ALL_VECTORS"
}

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.

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
                    }
                }
            }
        }
    }
}

Susceptibility_Scaling_Rate

float

0

3.40282e+38

0

The scaling rate for the variation in time of the log-linear susceptibility scaling. Susceptibility_Scaling_Type must be set to LOG_LINEAR_FUNCTION_OF_TIME.

 
{
    "Susceptibility_Scaling_Type": "LOG_LINEAR_FUNCTION_OF_TIME",
    "Susceptibility_Scaling_Rate": 1.58
}

Susceptibility_Scaling_Type

enum

NA

NA

CONSTANT_SUSCEPTIBILITY

The effect of time on susceptibility. Possible values are:

  • CONSTANT_SUSCEPTIBILITY

  • LOG_LINEAR_FUNCTION_OF_TIME

 
{
    "Susceptibility_Scaling_Type": "CONSTANT_SUSCEPTIBILITY"
}

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_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_Temporary_Larval_Habitat

double

NA

NA

1

Scale factor for the habitat size for all mosquito populations.

 
{
    "x_Temporary_Larval_Habitat": 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
}

Simulation setup

These parameters determine the basic setup of a simulation including the type of simulation you are running, such as “GENERIC_SIM” or “MALARIA_SIM”, the simulation duration, and the time step duration.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Config_Name

string

NA

NA

UNINITIALIZED STRING

The optional, user-supplied title naming a configuration file.

 
{
    "Config_Name": "My_First_Config"
}

Custom_Coordinator_Events

array of strings

NA

NA

NA

The list of valid, user-defined events for Event Coordinators that will be included in the campaign. Any event used in the campaign must either be one of the built-in events or in this list.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Coordinator_Events": [
        "Coordinator_Event_1",
        "Coordinator_Event_2",
        "Coordinator_Event_3"
    ]
}

Custom_Individual_Events

array of strings

NA

NA

NA

The list of valid, user-defined events that will be included in the campaign. Any event used in the campaign must either be one of the built-in events or in this list.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Individual_Events": [
        "Individual_Event_1",
        "Individual_Event_2",
        "Individual_Event_3"
    ]
}

Custom_Node_Events

array of strings

NA

NA

NA

The list of valid, user-defined events for nodes that will be included in the campaign. Any event used in the campaign must either be one of the built-in events or in this list.

Note: This configuration parameter is currently in beta release and has not yet been fully tested.

 
{
    "Custom_Node_Events": [
        "Node_Event_1",
        "Node_Event_2",
        "Node_Event_3"
    ]
}

Enable_Interventions

boolean

0

1

0

Controls whether or not campaign interventions will be used in the simulation. Set Campaign_Filename to the path of the file that contains the campaign interventions.

 
{
    "Enable_Interventions": 1,
    "Campaign_Filename": "campaign.json"
}

Enable_Random_Generator_From_Serialized_Population

boolean

0

1

0

Determines if the random number generator(s) should be extracted from a serialized population file. Enabling this will start a simulation from this file with the exact same random number stream and location in that stream as when the file was serialized.

 
{
    "Run_Number": 12,
    "Random_Number_Generator_Type": "USE_AES_COUNTER",
    "Random_Number_Generator_Policy": "ONE_PER_NODE",
    "Enable_Random_Generator_From_Serialized_Population": 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 probablistically exposing individuals rather than exposing every single person. Useful in low-prevalence, high-population scenarios. Infectivity_Scale_Type must be set to CONSTANT_INFECTIVITY.

 
{
    "Exposure_Skipping": 1
}

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
}

Listed_Events

array of strings

NA

NA

[]

The list of valid, user-defined events that will be included in the campaign. Any event used in the campaign must either be one of the built-in events or in this list.

 
{
    "Listed_Events": [
        "Vaccinated",
        "VaccineExpired"
    ]
}

Malaria_Model

enum

NA

NA

MALARIA_MECHANISTIC_MODEL

The type of malaria model used in a simulation. Possible values are:

  • MALARIA_FIXED_DURATION

  • MALARIA_EXPONENTIAL_DURATION

  • MALARIA_REDUCEDSTATE_MODEL

  • MALARIA_MECHANISTIC_MODEL

Note

All malaria simulations should use MALARIA_MECHANISTIC_MODEL. The others are placeholder values.

 
{
    "Malaria_Model": "MALARIA_MECHANISTIC_MODEL"
}

Memory_Usage_Halting_Threshold_Working_Set_MB

integer

0

1.00E+06

8000

The maximum size (in MB) of working set memory before the system throws an exception and halts.

 
{
    "Memory_Usage_Halting_Threshold_Working_Set_MB": 4000
}

Memory_Usage_Warning_Threshold_Working_Set_MB

integer

0

1.00E+06

7000

The maximum size (in MB) of working set memory before memory usage statistics are written to the log regardless of log level.

 
{
    "Memory_Usage_Warning_Threshold_Working_Set_MB": 3500
}

Node_Grid_Size

float

0.00416

90

0.004167

The spatial resolution indicating the node grid size for a simulation in degrees.

 
{
    "Node_Grid_Size": 0.042
}

Random_Number_Generator_Policy

enum

NA

NA

ONE_PER_CORE

The policy that determines if random numbers are generated for objects in a simulation on a per-core or per-node basis. The following values are available:

ONE_PER_CORE

A random number generator (RNG) is created for each computing core running a simulation. When running a simulation on a single core, there will be only one RNG. If running the single simulation on multiple cores, each core will have its own RNG. The RNGs on the different cores start out such that they will not generate the same stream of random numbers. Prior to EMOD 2.19, all simulations used this policy.

ONE_PER_NODE

An RNG is created for each geographic node in the simulation. The advantages of this policy are that 1) an event that causes a random number to be drawn in one node does not cause things to change in another node and 2) changing a simulation from single core to multi-core will not change the results. The RNGs on the different nodesstart out such that they will not generate the same stream of random numbers.

 
{
    "Run_Number": 15,
    "Random_Number_Generator_Type": "USE_AES_COUNTER",
    "Random_Number_Generator_Policy": "ONE_PER_NODE"
}

Random_Number_Generator_Type

enum

NA

NA

USE_PSEUDO_DES

The type of random number generator to use for objects in a simulation. Must set the RNG seed in Run_Number. The following values are available:

USE_PSEUDO_DES

Based on Numerical Recipes in C. The Art of Scientific Computing, 2nd ed. Press, William H. et. al, 1992. Prior to EMOD 2.19, this was the only generator available.

USE_LINEAR_CONGRUENTIAL

Based on The Structure of Linear Congruential Sequences, Marsaglia, George, 1972.

USE_AES_COUNTER

Based on AES in CTR Mode encryption as implemented in Intel (R) Advanced Encryption Standard (AES) New Instruction Set.

 
{
    "Run_Number": 15,
    "Random_Number_Generator_Type": "USE_LINEAR_CONGRUENTIAL",
    "Random_Number_Generator_Policy": "ONE_PER_NODE",
    "Enable_Random_Generator_From_Serialized_Population": 1
}

Run_Number

integer

0

65535

1

Sets the random number seed used with Random_Number_Generator_Type and Random_Number_Generator_Policy to assign random numbers to objects in a simulation.

 
{
    "Run_Number": 15,
    "Random_Number_Generator_Type": "USE_PSEUDO_DES",
    "Random_Number_Generator_Policy": "ONE_PER_NODE",
    "Enable_Random_Generator_From_Serialized_Population": 1
}

Serialization_Times

array of floats

0

The list of times at which to save the serialized state to file. 0 indicates the initial state before simulation, n indicates the time to serialize in terms of start time and step size, and will be rounded up to the nearest time step. The serialized population files can then be loaded at the beginning of a simulation using Serialized_Population_Filenames and Serialized_Population_Path.

 
{
    "Serialization_Type": "TIME",
    "Serialization_Times": [
        40.5,
        81
    ]
}

Serialization_Time_Steps

array of integers

0

2.15E+09

The list of time steps after which to save the serialized state to file. 0 (zero) indicates the initial state before simulation, n indicates after the nth time step. Serialization_Type must be set to TIMESTEP. The serialized population files can then be loaded at the beginning of a simulation using Serialized_Population_Filenames and Serialized_Population_Path.

 
{
    "Serialization_Type": "TIMESTEP",
    "Serialization_Time_Steps": [
        0,
        10
    ]
}

Serialization_Type

enum

NA

NA

NONE

The type of serialization to perform. Serialization saves the population state at particular times so you can start from that state in other simulations. Accepted values are:

NONE

No serialization.

TIME

Use the definition from Serialization_Times.

TIMESTEP

Use the definition from Serialization_Timestep.

 
{
    "Serialization_Times": [
        365,
        3650
    ],
    "Serialization_Type": "TIMSTEP"
}

j

{}

Serialized_Population_Filenames

array of strings

NA

NA

NA

An array of filenames with serialized population data. The number of filenames must match the number of cores used for the simulation. The files must be in .dtk format. Serialized population files are created using Serialization_Time_Steps.

 
{
    "Serialized_Population_Filenames": [
        "state-00010.dtk"
    ]
}

Serialized_Population_Path

string

NA

NA

.

The root path for the serialized population files. Serialized population files are created using Serialization_Time_Steps.

 
{
    "Serialized_Population_Path": "../00_Generic_Version_1_save/output"
}

Simulation_Duration

float

0

1000000

1

The elapsed time (in days) from the start to the end of a simulation.

 
{
    "Simulation_Duration": 7300
}

Simulation_Timestep

float

0

1000000

1

The duration of a simulation time step, in days.

 
{
    "Simulation_Timestep": 1
}

Simulation_Type

enum

NA

NA

GENERIC_SIM

The type of disease being simulated. Possible IDM-supported values are:

  • GENERIC_SIM

  • VECTOR_SIM

  • MALARIA_SIM

  • TBHIV_SIM

  • STI_SIM

  • HIV_SIM

  • ENVIRONMENTAL_SIM

  • TYPHOID_SIM

 
{
    "Simulation_Type": "STI_SIM"
}

Start_Time

float

0

1000000

1

The time, in days, when the simulation begins. This time is used to identify the starting values of the temporal input data, such as specifying which day’s climate values should be used for the first day of the simulation.

Note

The Start_Day of campaign events is in absolute time, so time relative to the beginning of the simulation depends on this parameter.

 
{
    "Start_Time": 365
}

Symptoms and diagnosis

The following parameters determine the characteristics of malaria diagnosis and symptoms as the disease progresses, such as anemia and fever. See Malaria symptoms and diagnostics for more information on malaria diagnostics and symptoms.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Anemia_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia.

 
{
    "Anemia_Mortality_Inverse_Width": 150
}

Anemia_Mortality_Threshold

double

NA

NA

3

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for hemoglobin count in grams per deciliter (g/dL) at which 50% of individuals die per day.

 
{
    "Anemia_Mortality_Threshold": 1.5
}

Anemia_Severe_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for anemia.

 
{
    "Anemia_Severe_Inverse_Width": 20
}

Anemia_Severe_Threshold

float

0

100

5

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the severe disease threshold level for anemia. Threshold units are in grams per deciliter (g/dL).

 
{
    "Anemia_Severe_Threshold": 3.0
}

Clinical_Fever_Threshold_High

float

0

15

1

The fever threshold (in degrees Celsius above normal) to start a clinical incident.

 
{
    "Clinical_Fever_Threshold_High": 1.5
}

Clinical_Fever_Threshold_Low

float

0

5

1

The fever threshold (in degrees Celsius above normal) to end a clinical incident.

 
{
    "Clinical_Fever_Threshold_Low": 0.5
}

Erythropoiesis_Anemia_Effect

float

0

1000

3.5

The exponential rate of increased red-blood-cell production from reduced red-blood-cell availability.

 
{
    "Erythropoiesis_Anemia_Effect": 3
}

Fever_Detection_Threshold

float

0.5

5

1

The level of body temperature above normal (defined as 37 C), in degrees Celsius, corresponding to detectable fever.

 
{
    "Fever_Detection_Threshold": 1
}

Fever_IRBC_Kill_Rate

float

0

1000

0.15

The maximum kill rate for infected red blood cells due to the inflammatory innate immune response. As fever increases above 38.5 degrees Celsius, the kill rate becomes successively higher along a sigmoidal curve approaching this rate.

 
{
    "Fever_IRBC_Kill_Rate": 1.4
}

Fever_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for fever.

 
{
    "Fever_Mortality_Inverse_Width": 1000
}

Fever_Mortality_Threshold

double

NA

NA

3

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the fever mortality threshold, in units of degrees Celsius above normal body temperature (defined as 37 C).

 
{
    "Fever_Mortality_Threshold": 10
}

Fever_Severe_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for fever.

 
{
    "Fever_Severe_Inverse_Width": 18.7
}

Fever_Severe_Threshold

float

0

10

1.5

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the threshold (in degrees Celsius above normal) for fever indicating severe disease.

 
{
    "Fever_Severe_Threshold": 2.5
}

Min_Days_Between_Clinical_Incidents

float

0

1000000

3

The number of days with fever below the low-threshold before a new incident can start, when fever again exceeds the high-threshold.

 
{
    "Min_Days_Between_Clinical_Incidents": 14
}

New_Diagnostic_Sensitivity

float

0.0001

100000

0.01

The number of microliters of blood tested to find single parasites in a new diagnostic (corresponds to inverse parasites/microliters sensitivity).

 
{
    "New_Diagnostic_Sensitivity": 0.025
}

Vector control

The following parameters determine the characteristics of campaign interventions aimed at vector control, such as the homing endonuclease gene (HEG), sugar feeding, and Wolbachia infection. When, to whom, and how those interventions are distributed is determined by the campaign file.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

HEG_Fecundity_Limiting

float

0

1

0

The fractional reduction in the number of eggs laid by a female mosquito who is homozygous in the homing endonuclease gene (HEG). HEG_Model must be set to GERMLINE_HOMING, EGG_HOMING, DUAL_GERMLINE_HOMING, or DRIVING_Y.

 
{
    "HEG_Model": "EGG_HOMING",
    "HEG_Fecundity_Limiting": 0.7
}

HEG_Homing_Rate

float

0

1

0

The fractional redistribution from heterozygous offspring to the homozygous homing endonuclease gene (HEG) behavior. HEG_Model” must be set to GERMLINE_HOMING, EGG_HOMING, DUAL_GERMLINE_HOMING, or DRIVING_Y.

 
{
    "HEG_Model": "EGG_HOMING",
    "HEG_Homing_Rate": 0.4
}

HEG_Model

enum

NA

NA

OFF

This parameter determines the structure of homing endonuclease gene (HEG) dynamics. Possible values are:

OFF

No HEG dynamics occur.

GERMLINE_HOMING

Female mosquito allele applies homing and then the fraction of wild/half/full HEG progeny are generated from combining with the male allele.

EGG_HOMING

The fraction of wild/half/full HEG progeny are calculated and then homing is applied to bias half towards full.

DUAL_GERMLINE_HOMING

Both male and female alleles apply germline bias before calculating progeny.

DRIVING_Y

Homing is applied as a bias of otherwise heterozygous progeny to be Y-drive male eggs.

 
{
    "HEG_Model": "EGG_HOMING",
    "HEG_Homing_Rate": 0.4,
    "HEG_Fecundity_Limiting": 0.9
}

Vector_Sugar_Feeding_Frequency

enum

NA

NA

VECTOR_SUGAR_FEEDING_NONE

The frequency of sugar feeding by a female mosquito. Used is used in conjunction with the SugarTrap and OvipositionTrap interventions. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS. Possible values are:

VECTOR_SUGAR_FEEDING_NONE

No sugar feeding.

VECTOR_SUGAR_FEEDING_ON_EMERGENCE_ONLY

Sugar feeding once at emergence.

VECTOR_SUGAR_FEEDING_EVERY_FEED

Sugar feeding occurs once per blood meal.

VECTOR_SUGAR_FEEDING_EVERY_DAY

Sugar feeding occurs every day.

 
{
    "Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE"
}

Wolbachia_Infection_Modification

float

0

100

1

The change in vector susceptibility to infection due to a Wolbachia infection.

 
{
    "Wolbachia_Infection_Modification": 1.0
}

Wolbachia_Mortality_Modification

float

0

100

1

The change in vector mortality due to a Wolbachia infection.

 
{
    "Wolbachia_Infection_Modification": 0.0
}

Vector life cycle

The following parameters determine the characteristics of the vector life cycle. Set the vector species to include in the simulation and the feeding, egg-laying, migration, and larval development habits of each using these parameters. The parameters for larval development related to habitat and climate are described in Larval habitat.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Adult_Life_Expectancy

float

0

730

10

The number of days an adult mosquito survives. The daily adult mortality rate is 1 / (value of this parameter).

 
{
    "Vector_Species_Params": {
        "arabiensis": {
            "Adult_Life_Expectancy": 5.9
        }
    }
}

Anthropophily

float

0

1

1

Mosquito preference for humans over animals, measured as a fraction of blood meals from human hosts. This dimensionless propensity is important in differentiating between mosquito species.

 
{
    "Vector_Species_Params": {
        "aegypti": {
            "Anthropophily": 0.95
        }
    }
}

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
        }
    }
}

Days_Between_Feeds

float

0

730

2

The number of days between female mosquito feeding attempts. In the cohort model, this value is converted to a feeding rate, equal to 1/(value of this parameter), and is used to determine the probability that one of each of the various feeding modes (animal host, human host, indoor, outdoor, etc) occurs. In the individual model, this parameter determines the number of days a vector waits between feeds.

 
{
    "Vector_Species_Params": {
        "gambiae": {
            "Days_Between_Feeds": 3
        }
    }
}

Drought_Egg_Hatch_Delay

float

0

1

0.33

Proportion of regular egg hatching that still occurs when habitat dries up. Enable_Drought_Egg_Hatch_Delay must be set to 1.

 
{
    "Enable_Drought_Egg_Hatch_Delay": 1,
    "Drought_Egg_Hatch_Delay": 0.33
}

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
}

Egg_Batch_Size

float

0

10000

100

Number of eggs laid by one female mosquito that has fed successfully. The value of Egg_Batch_Size is used for both the number of female eggs and for the number of male eggs. For example, the default value of 100 means that there are 100 female eggs and 100 male eggs.

 
{
    "Vector_Species_Params": {
        "arabiensis": {
            "Egg_Batch_Size": 100
        }
    }
}

Egg_Hatch_Delay_Distribution

enum

NA

NA

NO_DELAY

The distribution of the delay from oviposition to egg hatching. Possible values are:

NO_DELAY

No delay between oviposition and egg hatching.

EXPONENTIAL_DURATION

There is a delay that follows an exponential distribution. Set the mean delay in Mean_Egg_Hatch_Delay.

 
{
    "Egg_Hatch_Delay_Distribution": "EXPONENTIAL_DURATION",
    "Mean_Egg_Hatch_Delay": 2
}

Egg_Hatch_Density_Dependence

enum

NA

NA

NO_DENSITY_DEPENDENCE

The effect of larval density on egg hatching rate. Possible values are:

DENSITY_DEPENDENCE

Egg hatching is reduced when the habitat is nearing its carrying capacity.

NO_DENSITY_DEPENDENCE

Egg hatching is not dependent upon larval density.

 
{
    "Egg_Hatch_Density_Dependence": "NO_DENSITY_DEPENDENCE"
}

Egg_Saturation_At_Oviposition

enum

NA

NA

NO_SATURATION

If laying all eggs from ovipositing females would overflow the larval habitat capacity on a given day, the means by which the viable eggs become saturated. Possible values are:

NO_SATURATION

Egg number does not saturate; all eggs are laid.

SATURATION_AT_OVIPOSITION

Eggs are saturated at oviposition; habitat is filled to capacity and excess eggs are discarded.

SIGMOIDAL_SATURATION

Eggs are saturated along a sigmoidal curve; proportionately fewer eggs are laid depending on how oversubscribed the habitat would be.

 
{
    "Egg_Saturation_At_Oviposition": "SATURATION_AT_OVIPOSITION"
}

Enable_Egg_Mortality

boolean

0

1

0

Controls whether or not to include a daily mortality rate on the egg population, which is independent of climatic factors.

 
{
    "Enable_Egg_Mortality": 1
}

Enable_Temperature_Dependent_Egg_Hatching

boolean

0

1

0

Controls whether or not temperature has an effect on egg hatching, defined by Egg_Arrhenius_1 and Egg_Arrhenius_2.

 
{
    "Enable_Temperature_Dependent_Egg_Hatching": 1,
    "Egg_Arrhenius1": 61599956.864,
    "Egg_Arrhenius2": 5754.033
}

Enable_Vector_Aging

boolean

0

1

0

Controls whether or not vectors undergo senescence as they age.

 
{
    "Enable_Vector_Aging": 1
}

Enable_Vector_Mortality

boolean

0

1

1

Controls whether or not vectors can die. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS.

 
{
    "Vector_Sampling_Type": "TRACK_ALL_VECTORS",
    "Enable_Vector_Mortality": 1
}

Human_Feeding_Mortality

float

0

1

0.1

The fraction of mosquitoes, for all species, that die while feeding on a human.

 
{
    "Human_Feeding_Mortality": 0.15
}

Immature_Duration

float

0

730

2

The number of days for larvae to develop into adult mosquitoes. The value is used to calculate mosquito development rate, which equals 1 / (value of this parameter). Development from immature to adult is not dependent on temperature.

 
{
    "Vector_Species_Params": {
        "funestus": {
            "Immature_Duration": 4
        }
    }
}

Indoor_Feeding_Fraction

float

0

1

1

The fraction (dimensionless) of feeds in which mosquitoes feed on humans indoors; the fraction of feeds on humans that occur outdoors equals 1 - (value of this parameter).

 
{
    "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
        }
    }
}

Larval_Density_Dependence

enum

NA

NA

UNIFORM_WHEN_OVERPOPULATION

The functional form of mortality and growth delay for mosquito larvae based on population density. Possible values are:

UNIFORM_WHEN_OVERPOPULATION

Mortality is uniformly applied to all larvae when the population exceeds the specified carrying capacity for that habitat.

GRADUAL_INSTAR_SPECIFIC

Mortality and delayed growth are instar-specific, where the younger larvae are more susceptible to predation and competition from older larvae.

LARVAL_AGE_DENSITY_DEPENDENT_MORTALITY_ONLY

Mortality is based only on larval age.

DENSITY_DELAYED_GROWTH_NOT_MORTALITY

There is no mortality, only delayed growth in larvae.

NO_DENSITY_DEPENDENCE

There is no additional larval density-dependent mortality factor.

 
{
    "Larval_Density_Dependence": "GRADUAL_INSTAR_SPECIFIC"
}

Larval_Density_Mortality_Offset

float

0.0001

1000

0.1

An offset 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_Offset": 0.001
}

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
}

Mean_Egg_Hatch_Delay

float

0

120

0

The mean delay in egg hatch time, in days, from the time of oviposition. Set the delay distribution with Egg_Hatch_Delay_Distribution.

 
{
    "Egg_Hatch_Delay_Distribution": "EXPONENTIAL_DURATION",
    "Mean_Egg_Hatch_Delay": 2
}

Nighttime_Feeding_Fraction

float

0

1

1

The fraction of feeds on humans (for a specific mosquito species) that occur during the nighttime. Thus the fraction of feeds on humans that occur during the day equals 1 - (value of this parameter).

 
{
    "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
        }
    }
}

Temperature_Dependent_Feeding_Cycle

enum

NA

NA

NO_TEMPERATURE_DEPENDENCE

The effect of temperature on the duration between blood feeds. Possible values are:

NO_TEMPERATURE_DEPENDENCE

No relation to temperature; days between feeds will be constant and specified by Days_Between_Feeds for each species.

ARRHENIUS_DEPENDENCE

Use the Arrhenius equation with parameters Cycle_Arrhenius_1 and Cycle_Arrhenius_2.

BOUNDED_DEPENDENCE

Use an equation bounded at 10 days at 15C and use Days_Between_Feeds to set the duration at 30C.

 
{
    "Temperature_Dependent_Feeding_Cycle": "BOUNDED_DEPENDENCE"
}

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_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
}

Vector_Species_Names

array of strings

NA

NA

[]

An array of vector species names for all species that are present in the simulation. You may provide any species names you desire, but the same names must be used in Vector_Species_Params.

 
{
    "Vector_Species_Names": [
        "arabiensis",
        "funestus",
        "gambiae"
    ]
}

Vector_Species_Params

JSON object

NA

NA

NA

A JSON object that lists each vector species, as defined in Vector_Species_Names, and the parameters that define them.

 
{
    "Vector_Species_Params": {
        "arabiensis": {
            "Acquire_Modifier": 1,
            "Adult_Life_Expectancy": 10,
            "Anthropophily": 0.95,
            "Aquatic_Arrhenius_1": 84200000000,
            "Aquatic_Arrhenius_2": 8328,
            "Aquatic_Mortality_Rate": 0.1,
            "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": 10000000000.0,
                "WATER_VEGETATION": 1000000.0
            },
            "Transmission_Rate": 0.5
        }
    }
}

Vector_Sugar_Feeding_Frequency

enum

NA

NA

VECTOR_SUGAR_FEEDING_NONE

The frequency of sugar feeding by a female mosquito. Used is used in conjunction with the SugarTrap and OvipositionTrap interventions. Vector_Sampling_Type must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS. Possible values are:

VECTOR_SUGAR_FEEDING_NONE

No sugar feeding.

VECTOR_SUGAR_FEEDING_ON_EMERGENCE_ONLY

Sugar feeding once at emergence.

VECTOR_SUGAR_FEEDING_EVERY_FEED

Sugar feeding occurs once per blood meal.

VECTOR_SUGAR_FEEDING_EVERY_DAY

Sugar feeding occurs every day.

 
{
    "Vector_Sugar_Feeding_Frequency": "VECTOR_SUGAR_FEEDING_NONE"
}